--------------------------------------------------------------------------------
Domain name : PF01537.9_Herpes_glycop_D
Domain size : 56
Domain Description : Herpesvirus glycoprotein D
Domain gathering score : 25.0000
Domain trusted cutoff : 49.3000
Domain architecture : non-TM/SP [1 372], TM [373 410]
--------------------------------------------------------------------------------
Example 1
gi|125558650|gb|EAZ04186.1| hypothetical protein OsI_025418 [Oryza sativa (indica cultivar-group)] 682 (length) 252 324 .. (wrt seq) 326 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 47 [13%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
Pkinase         Protein kinase domain                   198.0    2.5e-56   1
DUF26           Domain of unknown function DUF26        142.8    1.7e-41   2
Pkinase_Tyr     Protein tyrosine kinase                 134.4    2.4e-39   2
Herpes_glycop_D Herpesvirus glycoprotein D               27.2    3.5e-08   1
HrpE            HrpE protein                              6.9      0.073   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
Pkinase           1/1     350   551 ..     1   210 [.   198.0  2.5e-56
DUF26             1/2      71   124 ..     1    55 []    70.7  3.4e-20
DUF26             2/2     188   242 ..     1    55 []    72.1  1.4e-20
Pkinase_Tyr       1/2     350   549 ..     1   209 [.   133.6    4e-39
Pkinase_Tyr       2/2     602   622 ..   250   270 .]     0.8      4.5
Herpes_glycop_D   1/1     252   324 ..   326   409 .]    27.2  3.5e-08
HrpE              1/1     621   631 ..     1    11 [.     6.9    0.073

Alignments of top-scoring domains:
Pkinase: domain 1 of 1, from 350 to 551: score 198.0, E = 2.5e-56
                CS    EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHH
                   *->yelleklGsGsfGtVykakhkgtgkiVAvKiikkrkekskkdktarr
                      +    klG+G+fGtVy++k  + +k VAvK+++      + + ++ +
  gi|1255586   350    FSDSNKLGEGGFGTVYRGKLGNGQK-VAVKKLSQAQYTREGLNQLHN 395  

                CS EHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-..EEBHHHHHH.
                   lsEiqilkrLsHpNIvrlidvfedkdhlylVlEycegGLrvldLfdylse
                     E+q+l++L+H+N vrl++++   d++ lV E+  +G    +L  +l +
  gi|1255586   396 --ELQLLAELQHKNFVRLLGFCSHQDEMMLVYEHIKNG----SLDIFLFD 439  

                CS .HHHHST---HHHHHHHHHHHHHHHHHHHHT   TEE-S--SGGGEEEET
                   trrkgpllfsedeakkialQilrgleYLHsn...giiHRDLKPeNILldn
                   t+r+++l   +++  +i+l i++g+ YLH+ ++ +iiHRDLK  NILld+
  gi|1255586   440 TSRGKTL--NWEQRHNIILGIAKGILYLHEDssiRIIHRDLKANNILLDE 487  

                CS TTEE--EEEE--GTT.E... E CSS C-S--S-GGGS-HHHHCCS-CTH
                   ngvvdaflKiaDFGlAkkls.t.sss.lttfvGTpwYmAPEvllggngyg
                   n+++    KiaDFGl ++l + + ++++ t+vGT++YmAPE +l   + +
  gi|1255586   488 NMNP----KIADFGLGRLLGgGhTQTkTATVVGTYGYMAPEYVL-FGKVS 532  

                CS HHHHHHHHHHHHHHHHHSS   
                   tkvDvWSlGvilyelltGk<-*
                   +k+D++S+Gv++ e +tG+   
  gi|1255586   533 PKIDIFSFGVLVLEIVTGR    551  

DUF26: domain 1 of 2, from 71 to 124: score 70.7, E = 3.4e-20
                   *->vYglaQCrgDls.psdCrsCLasavaellpkcCpgkkggrvlydsCf
                      +Ygla+CrgD++++++C +C+a+a+++  +++C+++++++v+yd C+
  gi|1255586    71    AYGLALCRGDTTnATACGACVAAAFQDG-QQLCAYAREATVFYDPCY 116  

                   lRYslypsF<-*
                   lR+s  ++F   
  gi|1255586   117 LRFS-GRNF    124  
DUF26: domain 2 of 2, from 188 to 242: score 72.1, E = 1.4e-20
                   *->vYglaQCrgDlspsdCrsCLasavae..llpkcCpgkkggrvlydsC
                      +Y+l+QC++D+sp+ CrsCLa++++  +  p +++g+  grvl+++C
  gi|1255586   188    IYALVQCTPDMSPAGCRSCLAGIISWvnD-PDYFSGSPTGRVLGVRC 233  

                   flRYslypsF<-*
                   +  Y+++p F   
  gi|1255586   234 NYWYDVHP-F    242  

Pkinase_Tyr: domain 1 of 2, from 350 to 549: score 133.6, E = 4e-39
                CS    EEEEEEEEEETTEEEEEEEEECSTTSTEEEEEEEEE SSSSHHHH..
                   *->ltlgkkLGeGaFGeVykGtlkgsgdgteikVAVKtL.kegaseeeie
                       +   kLGeG FG+Vy+G+l      +++kVAVK+L+ ++++ e   
  gi|1255586   350    FSDSNKLGEGGFGTVYRGKLG-----NGQKVAVKKLsQAQYTREG-- 389  

                CS HHHHHHHHHHHHHHTCTTTB-EEEEEECSESSSS..EEEEEEETTTEBHH
                   redFlrEAsiMkklGdHpNiVrLlGvCtlkqgePnglyiVtEymegGdLl
                   +  + +E++++ +l +H+N VrLlG C+  +++   +++V E+ ++G+L+
  gi|1255586   390 LNQLHNELQLLAEL-QHKNFVRLLGFCS--HQDE--MMLVYEHIKNGSLD 434  

                CS HHHHHTTCTTTSHHHHHHHHHHHHHHHHHHHH   HTTEECSTSSGGGEE
                   dfLrkhreggkLtlkdLlsfalQiAkGMeYLe...sknfvHRDLAARNcL
                    fL + + g+ L+ ++  ++ l iAkG  YL++++s++++HRDL A N+L
  gi|1255586   435 IFLFDTSRGKTLNWEQRHNIILGIAKGILYLHedsSIRIIHRDLKANNIL 484  

                CS EETTTEEEE-STTTHEESTTSSEETEETTSSE CCGGGSHHHHHHHCEEH
                   VsenlvVKIsDFGLaRdiysddyYvrkrgggk.lPvkWmAPEslkygkFt
                   ++en+  KI+DFGL R++   +   ++++ +       mAPE   +gk +
  gi|1255586   485 LDENMNPKIADFGLGRLL-GGGHT-QTKTATVvGTYGYMAPEYVLFGKVS 532  

                CS HHHHHHHHHHHHHHHHT   
                   skSDVWSFGVlLWEift<-*
                    k D+ SFGVl  Ei+t   
  gi|1255586   533 PKIDIFSFGVLVLEIVT    549  
Pkinase_Tyr: domain 2 of 2, from 602 to 622: score 0.8, E = 4.5
                CS    HHHTSSSGGGS-HHHHHHHHH   
                   *->lqCWaedPedRPtFselveeL<-*
                      l+C +e P dRP+ s ++ +L   
  gi|1255586   602    LLCVQESPVDRPSISSVILML    622  

Herpes_glycop_D: domain 1 of 1, from 252 to 324: score 27.2, E = 3.5e-08
                CS    .XXXXXXXXXXXX........XXXXXXXXXXXXXXXX.....XXXXX
                   *->daeqlpetgevpeadPevvPsisdeevpspppatpaNpdakvtsvii
                      da+ ++ +++ p+        + ++++ s ppa+ a  + + t vii
  gi|1255586   252    DAPAFDVAPPAPS--------PAPVAADSTPPADRAGRK-R-TAVII 288  

                CS XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX   
                   givvlalligaiivgvvyyilrRrRkeakkyvrlpps<-*
                   +++v++++   +i+ ++++i+++rRk a k +++p++   
  gi|1255586   289 SASVACSIVFVLIISGSVFICLKRRK-ASKNQKTPII    324  

HrpE: domain 1 of 1, from 621 to 631: score 6.9, E = 0.073
                   *->MLtrRrItLva<-*
                      MLtrRrI+L +   
  gi|1255586   621    MLTRRRIKLQQ    631  

Revised version of Example 1
gi|218199763|gb|EEC82190.1|hypothetical protein OsI_26328 [Oryza sativa Indica Group] 658 (length)
Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N 
--------        -----------                             -----    ------- ---
Pkinase         Protein kinase domain                   198.0    2.5e-56   1
DUF26           Domain of unknown function DUF26        142.8    1.7e-41   2
Pkinase_Tyr     Protein tyrosine kinase                 134.4    2.4e-39   2
Herpes_glycop_D Herpesvirus glycoprotein D                7.9      0.022   1
HrpE            HrpE protein                              6.9      0.073   1
ABC1            ABC1 family                               6.8       0.45   1
Lgl_C           Lethal giant larvae(Lgl) like, C-term     1.6        1.6   1
RIO1            RIO1 family                               1.4        2.8   1
Inh             Protease inhibitor Inh                    2.6        3.5   1
Nitrate_red_del Nitrate reductase delta subunit           1.9        3.7   1
GTP_EFTU_D2     Elongation factor Tu domain 2             3.7        3.8   1
Sm_multidrug_ex Putative small multi-drug export prot     2.0        4.2   1
ELL             RNA polymerase II elongation factor E     0.4        4.3   1
APH             Phosphotransferase enzyme family          1.0        5.2   1
FPL             Uncharacterised conserved protein         1.6        5.9   1
HIM             Haemagglutinin                            3.5        6.2   1
TrbI            Bacterial conjugation TrbI-like prote     0.3        6.3   1
TrbC            TrbC/VIRB2 family                         2.7        6.5   1
DUF682          Protein of unknown function (DUF682)      0.9        6.7   1
DUF1130         Protein of unknown function (DUF1130)     1.0          7   1
Gate            Nucleoside recognition                    1.8        7.3   1
DUF159          Uncharacterised ACR, COG2135             -0.9        8.1   1
DUF1796         Putative papain-like cysteine peptida     0.4        8.4   1
AF-4            AF-4 proto-oncoprotein                   -3.2        9.1   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
Gate              1/1       2    65 ..    52   108 .]     1.8      7.3
Nitrate_red_del   1/1      37    61 ..   136   160 ..     1.9      3.7
TrbC              1/1      53    71 ..     1    20 [.     2.7      6.5
ELL               1/1      67    85 ..     1    19 [.     0.4      4.3
DUF26             1/2      71   124 ..     1    55 []    70.7  3.4e-20
HIM               1/1     137   156 ..     1    24 []     3.5      6.2
DUF1130           1/1     171   188 ..   105   123 .]     1.0        7
DUF26             2/2     188   242 ..     1    55 []    72.1  1.4e-20
Herpes_glycop_D   1/1     279   300 ..   387   409 .]     7.9    0.022
Pkinase           1/1     326   527 ..     1   210 [.   198.0  2.5e-56
Pkinase_Tyr       1/2     326   525 ..     1   209 [.   133.6    4e-39
GTP_EFTU_D2       1/1     333   351 ..     1    19 [.     3.7      3.8
ABC1              1/1     338   354 ..    25    42 ..     6.8     0.45
RIO1              1/1     339   354 ..     1    18 [.     1.4      2.8
Inh               1/1     341   355 ..    89   103 .]     2.6      3.5
Lgl_C             1/1     350   364 ..     1    15 [.     1.6      1.6
AF-4              1/1     359   374 ..  1416  1431 .]    -3.2      9.1
DUF1796           1/1     373   397 ..   157   185 .]     0.4      8.4
DUF682            1/1     374   387 ..   143   156 .]     0.9      6.7
Sm_multidrug_ex   1/1     425   438 ..     1    15 [.     2.0      4.2
FPL               1/1     429   436 ..   149   156 .]     1.6      5.9
APH               1/1     448   462 ..   177   191 ..     1.0      5.2
Pkinase_Tyr       2/2     578   598 ..   250   270 .]     0.8      4.5
HrpE              1/1     597   607 ..     1    11 [.     6.9    0.073
TrbI              1/1     618   624 ..   196   202 .]     0.3      6.3
DUF159            1/1     647   655 ..   273   281 .]    -0.9      8.1

Alignments of top-scoring domains:
Gate: domain 1 of 1, from 2 to 65: score 1.8, E = 7.3
                   *->aalalllgftagesalasliillgle..........aseleviftll
                      a+++lll f+++ +++a++++  g  ++   ++++ +s l++++++l
  gi|2181997     2    AITTLLLAFLVALPGGAKAWHFCGSSgdvfapnttyQSNLALLSAGL 48   

                   sasciavfllpvivsilGik<-*
                     + +++   pv+++ +G++   
  gi|2181997    49 AKNASSS---PVLFAAGGVG    65   

Nitrate_red_del: domain 1 of 1, from 37 to 61: score 1.9, E = 3.7
                   *->yavilalLagrLeqrespYaelvda<-*
                      y ++lalL++ L++++s   +l++a   
  gi|2181997    37    YQSNLALLSAGLAKNASSSPVLFAA    61   

TrbC: domain 1 of 1, from 53 to 71: score 2.7, E = 6.5
                   *->falPalAqaaggggdpvesv<-*
                      +++P l +a gg gdp++++   
  gi|2181997    53    SSSPVLFAA-GGVGDPPDTA    71   

ELL: domain 1 of 1, from 67 to 85: score 0.4, E = 4.3
                   *->qeelsygLscgriteadrt<-*
                      +++++ygL+++r++++  t   
  gi|2181997    67    PPDTAYGLALCRGDTTNAT    85   

DUF26: domain 1 of 2, from 71 to 124: score 70.7, E = 3.4e-20
                   *->vYglaQCrgDls.psdCrsCLasavaellpkcCpgkkggrvlydsCf
                      +Ygla+CrgD++++++C +C+a+a+++  +++C+++++++v+yd C+
  gi|2181997    71    AYGLALCRGDTTnATACGACVAAAFQDG-QQLCAYAREATVFYDPCY 116  

                   lRYslypsF<-*
                   lR+s  ++F   
  gi|2181997   117 LRFS-GRNF    124  

HIM: domain 1 of 1, from 137 to 156: score 3.5, E = 6.2
                CS    EEEEEE--S...-EETT-TT--CC   
                   *->qqItNVasGeitvtktDAvnvsQL<-*
                       ++ NV +    + ++DA++v +L   
  gi|2181997   137    SKVRNVTAP---AEVFDAAVV-AL    156  

DUF1130: domain 1 of 1, from 171 to 188: score 1.0, E = 7
                   *->RrivadrallarGveVvHi<-*
                      Rr+ ++ +   rG+ V++i   
  gi|2181997   171    RRFATG-VEAFRGWGVRDI    188  

DUF26: domain 2 of 2, from 188 to 242: score 72.1, E = 1.4e-20
                   *->vYglaQCrgDlspsdCrsCLasavae..llpkcCpgkkggrvlydsC
                      +Y+l+QC++D+sp+ CrsCLa++++  +  p +++g+  grvl+++C
  gi|2181997   188    IYALVQCTPDMSPAGCRSCLAGIISWvnD-PDYFSGSPTGRVLGVRC 233  

                   flRYslypsF<-*
                   +  Y+++p F   
  gi|2181997   234 NYWYDVHP-F    242  

Herpes_glycop_D: domain 1 of 1, from 279 to 300: score 7.9, E = 0.022
                CS    XXXXXXXXXXXX.XXXXXXXXXX   
                   *->gvvyyilrRrRkeakkyvrlpps<-*
                      +++++i+++rRk a k +++p++   
  gi|2181997   279    AGSVFICLKRRK-ASKNQKTPII    300  

Pkinase: domain 1 of 1, from 326 to 527: score 198.0, E = 2.5e-56
                CS    EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHH
                   *->yelleklGsGsfGtVykakhkgtgkiVAvKiikkrkekskkdktarr
                      +    klG+G+fGtVy++k  + +k VAvK+++      + + ++ +
  gi|2181997   326    FSDSNKLGEGGFGTVYRGKLGNGQK-VAVKKLSQAQYTREGLNQLHN 371  

                CS EHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-..EEBHHHHHH.
                   lsEiqilkrLsHpNIvrlidvfedkdhlylVlEycegGLrvldLfdylse
                     E+q+l++L+H+N vrl++++   d++ lV E+  +G    +L  +l +
  gi|2181997   372 --ELQLLAELQHKNFVRLLGFCSHQDEMMLVYEHIKNG----SLDIFLFD 415  

                CS .HHHHST---HHHHHHHHHHHHHHHHHHHHT   TEE-S--SGGGEEEET
                   trrkgpllfsedeakkialQilrgleYLHsn...giiHRDLKPeNILldn
                   t+r+++l   +++  +i+l i++g+ YLH+ ++ +iiHRDLK  NILld+
  gi|2181997   416 TSRGKTL--NWEQRHNIILGIAKGILYLHEDssiRIIHRDLKANNILLDE 463  

                CS TTEE--EEEE--GTT.E... E CSS C-S--S-GGGS-HHHHCCS-CTH
                   ngvvdaflKiaDFGlAkkls.t.sss.lttfvGTpwYmAPEvllggngyg
                   n+++    KiaDFGl ++l + + ++++ t+vGT++YmAPE +l   + +
  gi|2181997   464 NMNP----KIADFGLGRLLGgGhTQTkTATVVGTYGYMAPEYVL-FGKVS 508  

                CS HHHHHHHHHHHHHHHHHSS   
                   tkvDvWSlGvilyelltGk<-*
                   +k+D++S+Gv++ e +tG+   
  gi|2181997   509 PKIDIFSFGVLVLEIVTGR    527  

Pkinase_Tyr: domain 1 of 2, from 326 to 525: score 133.6, E = 4e-39
                CS    EEEEEEEEEETTEEEEEEEEECSTTSTEEEEEEEEE SSSSHHHH..
                   *->ltlgkkLGeGaFGeVykGtlkgsgdgteikVAVKtL.kegaseeeie
                       +   kLGeG FG+Vy+G+l      +++kVAVK+L+ ++++ e   
  gi|2181997   326    FSDSNKLGEGGFGTVYRGKLG-----NGQKVAVKKLsQAQYTREG-- 365  

                CS HHHHHHHHHHHHHHTCTTTB-EEEEEECSESSSS..EEEEEEETTTEBHH
                   redFlrEAsiMkklGdHpNiVrLlGvCtlkqgePnglyiVtEymegGdLl
                   +  + +E++++ +l +H+N VrLlG C+  +++   +++V E+ ++G+L+
  gi|2181997   366 LNQLHNELQLLAEL-QHKNFVRLLGFCS--HQDE--MMLVYEHIKNGSLD 410  

                CS HHHHHTTCTTTSHHHHHHHHHHHHHHHHHHHH   HTTEECSTSSGGGEE
                   dfLrkhreggkLtlkdLlsfalQiAkGMeYLe...sknfvHRDLAARNcL
                    fL + + g+ L+ ++  ++ l iAkG  YL++++s++++HRDL A N+L
  gi|2181997   411 IFLFDTSRGKTLNWEQRHNIILGIAKGILYLHedsSIRIIHRDLKANNIL 460  

                CS EETTTEEEE-STTTHEESTTSSEETEETTSSE CCGGGSHHHHHHHCEEH
                   VsenlvVKIsDFGLaRdiysddyYvrkrgggk.lPvkWmAPEslkygkFt
                   ++en+  KI+DFGL R++   +   ++++ +       mAPE   +gk +
  gi|2181997   461 LDENMNPKIADFGLGRLL-GGGHT-QTKTATVvGTYGYMAPEYVLFGKVS 508  

                CS HHHHHHHHHHHHHHHHT   
                   skSDVWSFGVlLWEift<-*
                    k D+ SFGVl  Ei+t   
  gi|2181997   509 PKIDIFSFGVLVLEIVT    525  

GTP_EFTU_D2: domain 1 of 1, from 333 to 351: score 3.7, E = 3.8
                CS    EEEEEEEEEESEEETTEEE   
                   *->GtVatgRvesGtlkkGdev<-*
                      G   +g+v++G+l  G++v   
  gi|2181997   333    GEGGFGTVYRGKLGNGQKV    351  

ABC1: domain 1 of 1, from 338 to 354: score 6.8, E = 0.45
                   *->AQVHrAvLkdsGeeVAVK<-*
                      + V+r++L + G++VAVK   
  gi|2181997   338    GTVYRGKLGN-GQKVAVK    354  

RIO1: domain 1 of 1, from 339 to 354: score 1.4, E = 2.8
                CS    EEEEEEEECTTEEEEEEE   
                   *->nVYhAysaedgkdevAvK<-*
                       VY +    +g+ +vAvK   
  gi|2181997   339    TVYRGKL-GNGQ-KVAVK    354  

Inh: domain 1 of 1, from 341 to 355: score 2.6, E = 3.5
                CS    EEEE-SSS-EEEEEE   
                   *->YrgrlgdGavltLkr<-*
                      Yrg+lg+G  +  k+   
  gi|2181997   341    YRGKLGNGQKVAVKK    355  

Lgl_C: domain 1 of 1, from 350 to 364: score 1.6, E = 1.6
                   *->nVavtsvSfAaetlE<-*
                      +Vav++ S A++t+E   
  gi|2181997   350    KVAVKKLSQAQYTRE    364  

AF-4: domain 1 of 1, from 359 to 374: score -3.2, E = 9.1
                   *->VrYtRQGLhwLRqdAk<-*
                      ++YtR GL +L +      
  gi|2181997   359    AQYTREGLNQLHNELQ    374  

DUF1796: domain 1 of 1, from 373 to 397: score 0.4, E = 8.4
                   *->pellsalvkknfsrLdFlllivspdqrse<-*
                      ++ll++l++knf     +ll+ + +q +    
  gi|2181997   373    LQLLAELQHKNFV----RLLGFCSHQDEM    397  

DUF682: domain 1 of 1, from 374 to 387: score 0.9, E = 6.7
                   *->aLLkhLlqlslIei<-*
                      +LL++L++++++ +   
  gi|2181997   374    QLLAELQHKNFVRL    387  

Sm_multidrug_ex: domain 1 of 1, from 425 to 438: score 2.0, E = 4.2
                   *->ElRGAIpvGiailGl<-*
                      E+R  I++Gia +G+   
  gi|2181997   425    EQRHNIILGIA-KGI    438  

FPL: domain 1 of 1, from 429 to 436: score 1.6, E = 5.9
                   *->nIvLnIlk<-*
                      nI+L+I+k   
  gi|2181997   429    NIILGIAK    436  

APH: domain 1 of 1, from 448 to 462: score 1.0, E = 5.2
                CS    EEE-SS-STTSEEEE   
                   *->vlvHGDlhpgNllvd<-*
                      +++H+Dl+++N+l+d   
  gi|2181997   448    RIIHRDLKANNILLD    462  

Pkinase_Tyr: domain 2 of 2, from 578 to 598: score 0.8, E = 4.5
                CS    HHHTSSSGGGS-HHHHHHHHH   
                   *->lqCWaedPedRPtFselveeL<-*
                      l+C +e P dRP+ s ++ +L   
  gi|2181997   578    LLCVQESPVDRPSISSVILML    598  

HrpE: domain 1 of 1, from 597 to 607: score 6.9, E = 0.073
                   *->MLtrRrItLva<-*
                      MLtrRrI+L +   
  gi|2181997   597    MLTRRRIKLQQ    607  

TrbI: domain 1 of 1, from 618 to 624: score 0.3, E = 6.3
                   *->dFSkvYe<-*
                      dFS+vY+   
  gi|2181997   618    DFSSVYQ    624  

DUF159: domain 1 of 1, from 647 to 655: score -0.9, E = 8.1
                CS    ........E   
                   *->VNnprNdgp<-*
                      VN + N++p   
  gi|2181997   647    VNDVTNTDP    655  


Example 2
gi|40886673|gb|AAR96255.1| MHC class Ib antigen [Rattus norvegicus] 364 (length) 298 351 .. (wrt seq) 355 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 18 [5%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
MHC_I           Class I Histocompatibility antigen, d   447.4   2.2e-131   1
C1-set          Immunoglobulin C1-set domain             99.4    1.9e-29   1
Herpes_glycop_D Herpesvirus glycoprotein D               25.5    1.1e-07   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
MHC_I             1/1      24   202 ..     1   180 []   447.4 2.2e-131
C1-set            1/1     215   294 ..     1    92 []    99.4  1.9e-29
Herpes_glycop_D   1/1     298   351 ..   354   409 .]    25.5  1.1e-07

Alignments of top-scoring domains:
MHC_I: domain 1 of 1, from 24 to 202: score 447.4, E = 2.2e-131
                CS    TEEEEEEEEEEEEETTSSSEEEEEEEEETTEEEEEEETTSSS-SEEE
                   *->gsHSLrYFyTaVSrPGlGePrFiaVGYVDDtqFVrFDSdaenprmeP
                      gsHSLrYF+Ta+SrPGlGePrFi+VGYVDD qFVr+D+daenprmeP
  gi|4088667    24    GSHSLRYFETAMSRPGLGEPRFISVGYVDDRQFVRYDNDAENPRMEP 70   

                CS SSGGGGTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TTTS-EEEEE
                   rapWieqegpeYWereTqiaKaneqifrvnLrtLlgYYNqSegGSHTlQw
                   ra+W+e+egpeYW reTq+aK++eq+ rvnL t+l+YYNqSegGSHT+Q+
  gi|4088667    71 RARWMEREGPEYWQRETQRAKGQEQWSRVNLGTALRYYNQSEGGSHTIQR 120  

                CS EEEEEEETTSSEEEEEEEEEETTEEEEEEETTSSEEEESSHHHHHHHHHH
                   myGCdvgpDgrllrGYeqfAYDGkDYiaLNedLrsWTAadtaAqITkrKW
                   myGCd+g+Dg+llrGYeq+AY G+DYiaLNedL++WTAad+ AqIT++KW
  gi|4088667   121 MYGCDLGSDGSLLRGYEQYAYAGRDYIALNEDLKTWTAADMVAQITQNKW 170  

                CS HHHTHHHHHHHHHHHTHHHHHHHHHHHHTHHHH   
                   eaageaerkeraYLEgeCvEwLrRYLenGKetL<-*
                    +ag aer +r YLEg+CvE+L+R+Le+GKetL   
  gi|4088667   171 DQAGTAER-HRDYLEGTCVESLLRHLELGKETL    202  

C1-set: domain 1 of 1, from 215 to 294: score 99.4, E = 1.9e-29
                CS    ESTSHHTHHTSEEEEEEEEEEEBSS-EEEEEEETTEEESTTEEEEEE
                   *->ppgspepelgkpntLvClVtgFyPpdItVtWlkNGqevtegvestep
                       p +pe    + +tL C++ gFyP+dIt tW+ NG+++t++ e  e+
  gi|4088667   215    HP-RPE----GDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVET 256  

                CS EEEETTSEEEEEEEEEEEHHHHHTSSEEEEEEEETTSTE.TSEEE   
                   lpkngDgtYqlsSyLtftasepesgdtYtCrVeHesLkvenePlt<-*
                   +p  gDgt+q++ ++ ++      +  YtC VeHe+L+   ePlt   
  gi|4088667   257 RP-AGDGTFQKWASVVVP---LGKEQNYTCLVEHEGLP---EPLT    294  

Herpes_glycop_D: domain 1 of 1, from 298 to 351: score 25.5, E = 1.1e-07
                CS    XXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X
                   *->spppatpaNpdakvtsviigivvlalligaiivgvvyyilrRrRkea
                      +p+p t++N    v++v++g+vv+++ ++aiiv++v+ ++rRrR+  
  gi|4088667   298    EPSPSTDSNMETNVIYVVVGAVVIIG-AVAIIVALVVVVRRRRRS-R 342  

                CS XXXXXXXXX   
                   kkyvrlpps<-*
                   ++++r++ +   
  gi|4088667   343 TRRRRRRNI    351  


Example 3
gi|210101265|gb|EEA49333.1| hypothetical protein BRAFLDRAFT_93828 [Branchiostoma floridae] 1324 (length) 620 664 .. (wrt seq) 364 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 9 [2%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
Y_phosphatase   Protein-tyrosine phosphatase            625.9   3.9e-185   3
fn3             Fibronectin type III domain              36.3    1.3e-09   1
Herpes_glycop_D Herpesvirus glycoprotein D               24.7      2e-07   1
ig              Immunoglobulin domain                    18.1    0.00017   1
EGF             EGF-like domain                          18.0    0.00056   2
DSPc            Dual specificity phosphatase, catalyt    13.3      0.002   1
DSL             Delta serrate ligand                     12.3     0.0043   2
Laminin_EGF     Laminin EGF-like (Domains III and V)     12.9     0.0061   1
DUF916          Bacterial protein of unknown function     9.2      0.017   1
I-set           Immunoglobulin I-set domain              10.6      0.024   1
EGF_2           EGF-like domain                          12.1      0.028   2

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
Y_phosphatase     1/3     760   770 ..     1    11 [.     6.9     0.15
Y_phosphatase     2/3     798  1015 ..    14   271 .]   360.4 3.3e-105
Y_phosphatase     3/3    1075  1312 ..     1   271 []   258.6  1.5e-74
fn3               1/1     521   607 ..     1    84 []    36.3  1.3e-09
Herpes_glycop_D   1/1     620   664 ..   363   409 .]    24.7    2e-07
ig                1/1     437   501 ..     1    67 []    18.1  0.00017
EGF               1/2     243   272 ..     1    38 []    13.1    0.013
EGF               2/2     290   323 ..     1    38 []     4.9      2.5
DSPc              1/1     951   969 ..   108   126 ..    13.3    0.002
DSL               1/2     255   272 ..    50    67 .]     8.9    0.045
DSL               2/2     314   323 ..    58    67 .]     3.3      2.3
Laminin_EGF       1/1     247   273 ..     1    41 [.    12.9   0.0061
DUF916            1/1     635   656 ..   347   368 .]     9.2    0.017
I-set             1/1     423   452 ..     1    30 [.    10.6    0.024
EGF_2             1/2     247   272 ..     1    37 []     8.8     0.24
EGF_2             2/2     308   323 ..    11    37 .]     3.3      7.5

Alignments of top-scoring domains:
Y_phosphatase: domain 1 of 3, from 760 to 770: score 6.9, E = 0.15
                CS    GGGG-SSTTS-   
                   *->NkeKNRykdil<-*
                      Nk+KNRy +i+   
  gi|2101012   760    NKKKNRYGNIV    770  
Y_phosphatase: domain 2 of 3, from 798 to 1015: score 360.4, E = 3.3e-105
                CS    GGGEEEBTSTTTTTTTTEEEEEEEEEEG...ECTEEEEEEEEE---G
                   *->DhtRVkLkpipgdedsDYINAsyidgpfllvvykkpkayIaTQgPlp
                      Dh+RV++     d+ sDYINAsyi+g      ykk k yIa+QgP +
  gi|2101012   798    DHSRVVMG---CDPTSDYINASYIKG------YKKDKMYIAAQGPNK 835  

                CS GGHHHHHHHHHHTT-TEEEEESHSEETTE..EC.S---S-S..STTSEEE
                   nTieDFWrMvweqkvtvIVMLtelvEkgrdseKtCaqYWPegskeggslt
                    Ti+D WrM w++k+++IVM+t+l+E+++  +K C++YWP+     +++ 
  gi|2101012   836 ATIGDLWRMTWQEKSPCIVMVTNLMENNK--VK-CERYWPD---NTQTQL 879  

                CS ETTEEEEEEEEEEESSEEEEEEEEEE TT...........TEEEEEEEEE
                   yGditVtlvseekeadytvRtleltn.gtgskinakqekkgetrtVthfh
                   yGd+ Vt+++e+ +ad+t+R+++l  ++++             +++++++
  gi|2101012   880 YGDFGVTCMREDIYADFTIRKFHLFQgDNP----------KIFHELYQYQ 919  

                CS EESS-SSSSGSC HHHHHHHHHHHHHSC.......TTTTSS.......-E
                   ytgWPDhgvPes.kslldllrkvrksqpsnvelgerspdsgprSystaPi
                   +t WPDhgvP    +l+ l+++v+++ +         p sg       Pi
  gi|2101012   920 FTVWPDHGVPTYaSPLMALRNRVKEHVT---------PESG-------PI 953  

                CS EEECSSSSHHHHHHHHHHHHHHHHHHHSEE.-HHHHHHHHHCCSTTSS-S
                   vVHCSAGvGRTGtfiaidillqqleaegevidvfdiVkelRsqRpgmVQt
                   +VHCSAGvGRTGtfi++d+++++ ++e+ v d+f+ V +lR+qR +mVQt
  gi|2101012   954 IVHCSAGVGRTGTFIMLDMMMEMFKDEEQV-DIFNNVNQLREQRINMVQT 1002 

                CS HHHHHHHHHHHHH   
                   eeQYiFlydaile<-*
                    +QYiF+yda+le   
  gi|2101012  1003 SDQYIFIYDALLE    1015 
Y_phosphatase: domain 3 of 3, from 1075 to 1312: score 258.6, E = 1.5e-74
                CS    GGGG-SSTTS-B-GGGEEEBTSTTTTTTTTEEEEEEEEEEG...ECT
                   *->NkeKNRykdilpyDhtRVkLkpipgdedsDYINAsyidgpfllvvyk
                      N++KNR +d lp D+ R  L +++++ +++YINA +i+g      yk
  gi|2101012  1075    NRNKNRRSDDLPSDRARPFLMSPGDETGTNYINAAFING------YK 1115 

                CS EEEEEEEEE---GGGHHHHHHHHHHTT-TEEEEESHSEETTE..EC.S--
                   kpkayIaTQgPlpnTieDFWrMvweqkvtvIVMLtelvEkgrdseKtCaq
                   +   yIaTQ+PlpnT+ D Wr v++++++++VML++ ++++     t+++
  gi|2101012  1116 QRDVYIATQAPLPNTVLDMWRLVYDYRISSVVMLNDMDDNDP----TYPK 1161 

                CS -S-S..STTSEEEETTEEEEEEEEEEESSEEEEEEEEEE TT........
                   YWPegskeggsltyGditVtlvseekeadytvRtleltn.gtgskinakq
                   YWP+     +s+++G + +  v e+++ + ++Rtl+l+n+  ++      
  gi|2101012  1162 YWPD---PKQSVQHGVFLIQHVGETVDGHLITRTLRLQNtLKDN------ 1202 

                CS ...TEEEEEEEEEEESS-SS SSGSC   HHHHHHHHHHHHHSC......
                   ekkgetrtVthfhytgWPDh.gvPes...kslldllrkvrksqpsnvelg
                      +  r+V+ f+ tgWP ++++P+s+ + +++ ll +v+ +q++     
  gi|2101012  1203 ---EAARMVKIFQLTGWPRDeKTPPSpcqAAMITLLSEVERWQQQ----- 1244 

                CS .TTTTSS.......-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEE.-HH
                   erspdsgprSystaPivVHCSAGvGRTGtfiaidillqqleaegevidvf
                      +++        PivVHC +Gv R+G+f+++ +++++++ e++v dvf
  gi|2101012  1245 ---TGNE-------PIVVHCIDGVERSGVFCTMGVACERVKVEQVV-DVF 1283 

                CS HHHHHHHCCSTTSS-SHHHHHHHHHHHHH   
                   diVkelRsqRpgmVQteeQYiFlydaile<-*
                   ++Vk++R++Rp mV +   Y  +++ ++e   
  gi|2101012  1284 QAVKTVRACRPSMVNNVVAYDCCHELVIE    1312 

fn3: domain 1 of 1, from 521 to 607: score 36.3, E = 1.3e-09
                CS    ----CEEEEEEECTTEEEEEEE--S    -SS--SEEEEEEEEETTT
                   *->PsaPtnltvtdvtstsltlsWspPt....gngpitgYevtyRqpkng
                      P +  ++t +dv+s+ ++++   ++++ +g+gpi+g +v+yR +  +
  gi|2101012   521    PVPLNQPTMSDVGSDFIQVNVITSSepfsGDGPIEGITVRYR-ELPD 566  

                CS CCCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTE -EBE   
                   gewkeltvpgtttsytltgLkPgteYtvrVqAvnggG.GpeS<-*
                   g+w +++ p+ ++++ ltgL+ +teY+v+V+ +++ G+G+     
  gi|2101012   567 GQWEQVDAPSGQSRVDLTGLTQDTEYNVTVV-LTRPGpGGTG    607  

Herpes_glycop_D: domain 1 of 1, from 620 to 664: score 24.7, E = 2e-07
                CS    .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX
                   *->pdakvtsviigivvlalligaiivgvvyyilrRrRkeakkyvrlpps
                      p++   ++i+g+++++ + ++++v+v+++i+ RrR  +k + r pp+
  gi|2101012   620    PGPS-LGLIAGAAGGSAALILVLVAVAIFIFWRRRR-GKESSRAPPP 664  

                CS    
                   <-*
                      
  gi|2101012     -     -    

ig: domain 1 of 1, from 437 to 501: score 18.1, E = 0.00017
                CS    TSEEEEEEEEE  ESSSSSSEEEEEETTC-SS-CEEEEEEETSSCCC
                   *->GesvtLtCsvs..sgppqvdvtWfkegkgleessetgtdenrvssqt
                      G+svt tC + +++ p   d+t++k + +++ ++    + ++++++ 
  gi|2101012   437    GQSVTVTCGANgdPEPIKDDFTLTKPDNSVIHQA----SSTNTNATA 479  

                CS EEEEEEESSE-GGG-EEEEEEE   
                   stslLtisnvteedsGtYtCvv<-*
                    +s++++s vt   +G Y+C+v   
  gi|2101012   480 VFSTFQLSEVTHAVDGQYVCRV    501  
  
EGF: domain 1 of 2, from 243 to 272: score 13.1, E = 0.013
                CS    TTSSCTTSSSTEEEEEETTEEEEEETTT.CECEESTTC   
                   *->CnpnngpCsngGtCvdtpggytCeCpeGyvllytGkrC<-*
                      C+     C +gG C  ++   tC+Cp+G    +tG++C   
  gi|2101012   243    CSTPC-LCYHGGWCDVSG---TCICPPG----FTGENC    272  
EGF: domain 2 of 2, from 290 to 323: score 4.9, E = 2.5
                CS    TTSSC  TTSSSTEEEEEETTEEEEEETTT.CECEESTTC   
                   *->Cnpnn..gpCsngGtCvdtpggytCeCpeGyvllytGkrC<-*
                      Cn+ n+  pC    +C++ p  y CeC+ G    y+G +C   
  gi|2101012   290    CNDGNpvRPCRKSLICLPDP--YGCECANG----YKGFDC    323  
  
Laminin_EGF: domain 1 of 1, from 247 to 273: score 12.9, E = 0.0061
                CS    --STTTCBCCC--B-T.......TT-SB-SB-TTEESTTS-   
                   *->CdCnphGslsddtCdsddelfgeetGqClkCkpnvtGrrCd<-*
                      C C + G      Cd         +G C  C p++tG++C+   
  gi|2101012   247    CLCYHGG-----WCDV--------SGTCI-CPPGFTGENCE    273  
  
DSPc: domain 1 of 1, from 951 to 969: score 13.3, E = 0.002
                CS    -EEEEE-SSSSSHHHHHHH   
                   *->gkVLVHCqAGiSRSAtlii<-*
                      g++ VHC AG+ R++t+i+   
  gi|2101012   951    GPIIVHCSAGVGRTGTFIM    969  

DSL: domain 1 of 2, from 255 to 272: score 8.9, E = 0.045
                   *->CdenGnklClnGWkGeyC<-*
                      Cd  G  +C +G +Ge+C   
  gi|2101012   255    CDVSGTCICPPGFTGENC    272  
DSL: domain 2 of 2, from 314 to 323: score 3.3, E = 2.3
                   *->ClnGWkGeyC<-*
                      C+nG kG +C   
  gi|2101012   314    CANGYKGFDC    323  

DUF916: domain 1 of 1, from 635 to 656: score 9.2, E = 0.017
                   *->glllllllllivyliwkrkkkk<-*
                      ++l+l+l+ +++++ w+r++ k   
  gi|2101012   635    AALILVLVAVAIFIFWRRRRGK    656  

I-set: domain 1 of 1, from 423 to 452: score 10.6, E = 0.024
                CS    -EEEE--EEEEEETTCEEEEEEEEE-SSS-   
                   *->PkFtqkpkdveVqeGesarFeCkvtGdPpP<-*
                      P++   p+dv ++ G+s++ +C + GdP+P   
  gi|2101012   423    PSIAFNPRDVDANLGQSVTVTCGANGDPEP    452  

EGF_2: domain 1 of 2, from 247 to 272: score 8.8, E = 0.24
                   *->C.CngshGtCvspngtstpcGkCvCdsgyedkyqGadC<-*
                      C C   +G C+ +       G C C++g    ++G  C   
  gi|2101012   247    ClCYH-GGWCDVS-------GTCICPPG----FTGENC    272  
EGF_2: domain 2 of 2, from 308 to 323: score 3.3, E = 7.5
                   *->spngtstpcGkCvCdsgyedkyqGadC<-*
                      +p+g       C+C +g    y G dC   
  gi|2101012   308    DPYG-------CECANG----YKGFDC    323  


Example 4
gi|149587184|ref|XP_001519017.1| PREDICTED: similar to poliovirus receptor related 2 [Ornithorhynchus anatinus] 849 (length) 720 776 .. (wrt seq) 348 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 25 [7%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
V-set           Immunoglobulin V-set domain              72.8    8.3e-20   3
C2-set_2        CD80-like C2-set immunoglobulin domai    43.4    1.5e-11   1
ig              Immunoglobulin domain                    25.0    1.7e-06   3
Herpes_glycop_D Herpesvirus glycoprotein D               19.6    6.5e-06   1
C1-set          Immunoglobulin C1-set domain             19.8    1.7e-05   1
I-set           Immunoglobulin I-set domain              13.9     0.0027   3

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
V-set             1/3      24   144 ..     1   142 []    34.4  4.4e-09
V-set             2/3     525   602 ..    54   142 .]    15.2   0.0011
V-set             3/3     644   721 ..    54   142 .]    23.2    6e-06
C2-set_2          1/1     145   232 ..     1   101 []    43.4  1.5e-11
ig                1/3      36   127 ..     1    67 []    15.0   0.0013
ig                2/3     181   223 ..    18    67 .]     2.0      7.3
ig                3/3     259   314 ..     1    67 []     8.0     0.14
Herpes_glycop_D   1/1     720   776 ..   347   409 .]    19.6  6.5e-06
C1-set            1/1     186   233 ..    39    92 .]    19.8  1.7e-05
I-set             1/3     461   476 ..    66    81 ..     4.2      1.7
I-set             2/3     563   601 ..    58    96 .]     5.1     0.96
I-set             3/3     685   720 ..    61    96 .]     4.6      1.3

Alignments of top-scoring domains:
V-set: domain 1 of 3, from 24 to 144: score 34.4, E = 4.4e-09
                CS    XEEEEEECSS.............EEEEETTSEEEEEEEEECHHSSSG
                   *->qsvvtqepprWGLLLTASLsWptsvtvaeGgsvtLpCtysGtfddss
                       ++v +                 +v++ +Gg+v LpC +  ++++  
  gi|1495871    24    RVEVIP-----------------VVRGRLGGTVDLPCRLL-PTGPDV 52   

                CS SSTTCEEEEEEECEETTSEEEEEE.EESSCTEEEEETTTCEEEEETTEEE
                   sssgtfsiyWyrqqppgkgpeliiisyysyystsegngtvgerfkgrvtl
                    +s++++++W r             sy +  s+ e +  ++++  + ++ 
  gi|1495871    53 KVSQVTWVRWDR-VGR---------SYSVAVSHPEHGASFPDPEADGRR- 91   

                CS EEETC        TTEEEEEESSCSGGGCEEEEEEEEETSEEEEECEEEE
                   sgnps........kgdfsLtIsnlqlsDsGtYyCavsnsnelvfgggtrL
                       s ++ ++    d++L+ + l++ D G Y+C   +++ ++  g t+L
  gi|1495871    92 LKFLSagsvgeaaLRDATLQVRELRAQDQGNYTCEFATFPRGNSKGATWL 141  

                CS EEE   
                   tVl<-*
                   +V+   
  gi|1495871   142 RVE    144  
V-set: domain 2 of 3, from 525 to 602: score 15.2, E = 0.0011
                CS    EEEEEECEETTSEEEEEE.EESSCTEEEEETTTCEEEEETTEEEEEE
                   *->siyWyrqqppgkgpeliiisyysyystsegngtvgerfkgrvtlsgn
                      +++Wyr   ++++p+li  +y+++   s  n   g+ ++gr      
  gi|1495871   525    TYTWYR--GAAGKPHLIL-RYNTGVGVS--NWLLGPAHSGREA---- 562  

                CS TCTTEEEEEESSCSGGGCEEEEEEEEETSEEEEECEEEEEEE   
                   pskgdfsLtIsnlqlsDsGtYyCavsnsnelvfgggtrLtVl<-*
                    + ++ sL ++++++ DsG Y  +v +   +  ++ ++  V+   
  gi|1495871   563 -GTKNGSLLLRDVSPQDSGRYIVHVVTL-QGKEEASITIDVS    602  
V-set: domain 3 of 3, from 644 to 721: score 23.2, E = 6e-06
                CS    EEEEEECEETTSEEEEEE.EESSCTEEEEETTTCEEEEETTEEEEEE
                   *->siyWyrqqppgkgpeliiisyysyystsegngtvgerfkgrvtlsgn
                      +++Wyr   +++gp+ i  ++++++s+ +    +g+ ++gr t + n
  gi|1495871   644    TYTWYR--GAAGGPHRIL-RCNTGGSAPNC--LPGPAHSGRETCTKN 685  

                CS TCTTEEEEEESSCSGGGCEEEEEEEEETSEEEEECEEEEEEE   
                   pskgdfsLtIsnlqlsDsGtYyCavsnsnelvfgggtrLtVl<-*
                   +s     L ++++++ DsG Y  +v +   +  ++ ++  V+   
  gi|1495871   686 GS-----LLLRDVSPQDSGRYIVHVVTL-WGKEEASITIDVS    721  

C2-set_2: domain 1 of 1, from 145 to 232: score 43.4, E = 1.5e-11
                   *->peIeppa.sllegeksenlevvatCvlpysagGkPapritWyldgke
                        ++++a +++ ++ s  +  va C    ++ G Pa+r++W ++++ 
  gi|1495871   145    AAPQNQAwTQEVTQ-SSAPAPVAFC----VSTGLPAARLSWSTSLNH 186  

                   lvpeekteaittsseqdpesglytvtStLklvpsredhgqsltCqvsyga
                            ++ ++e+ p +g+ tvtS+L+l p+r  hgqs+tC v++++
  gi|1495871   187 E--------ANITQEELP-NGTITVTSQLSLLPTRNVHGQSVTCKVEHET 227  

                   lrgsk<-*
                   l++++   
  gi|1495871   228 LQEPQ    232  

ig: domain 1 of 3, from 36 to 127: score 15.0, E = 0.0013
                CS    TSEEEEEEEEE   ESSSSSSEEEEEETTC-SS-CEEEEEEETSSCC
                   *->GesvtLtCsvs...sgppqvdvtWfkegkgleessetgtdenrvssq
                      G++v L+C+  +++++ +  +vtW +++ +  + s  +++  ++   
  gi|1495871    36    GGTVDLPCRLLptgPDVKVSQVTWVRWDRVGRSYSVAVSHPEHGA-- 80   

                CS CEE                         EEEEESSE-GGG-EEEEEEE  
                   tst.........................slLtisnvteedsGtYtCvv<-
                    s+++++ ++++ +  + ++ ++   ++ +L+++ ++ +d G+YtC+   
  gi|1495871    81 -SFpdpeadgrrlkflsagsvgeaalrdATLQVRELRAQDQGNYTCEF   127  

                CS  
                   *
                    
  gi|1495871     -   -    
ig: domain 2 of 3, from 181 to 223: score 2.0, E = 7.3
                CS    SEEEEEETTC-SS-CEEEEEEETSSCCCEEEEEEESSE-GGG-EEEE
                   *->dvtWfkegkgleessetgtdenrvssqtstslLtisnvteedsGtYt
                      ++++ +e  +++e+ + gt +  ++       L + +++  ++ + t
  gi|1495871   181    STSLNHEANITQEELPNGTITVTSQ-------LSLLPTRNVHGQSVT 220  

                CS EEE   
                   Cvv<-*
                   C v   
  gi|1495871   221 CKV    223  
ig: domain 3 of 3, from 259 to 314: score 8.0, E = 0.14
                CS    TSEEEEEEEEEESSSSSSEEEEEETTC-SS-CEEEEEEETSSCCCEE
                   *->GesvtLtCsvssgppqvdvtWfkegkgleessetgtdenrvssqtst
                       +++ L C ++s p+++++ W+   + l+++ + + ++         
  gi|1495871   259    RSDAILNCDAQSYPEPTSYEWSTLSGFLPSTVKAQGSR--------- 296  

                CS EEEEESSE-GGG-EEEEEEE   
                   slLtisnvteedsGtYtCvv<-*
                     L + nv+   ++t++C v   
  gi|1495871   297 --LMVYNVDNLVNTTFVCKV    314  

Herpes_glycop_D: domain 1 of 1, from 720 to 776: score 19.6, E = 6.5e-06
                CS    XXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXX
                   *->isdeevpspppatpaNpdakvtsviigivvlalligaiivgvvyyil
                      +s+e++++p+++ pa       ++i+ +vv++l  ++++++++y+ +
  gi|1495871   720    VSPEPTTTPAEKAPAS-----GGIIAALVVGILVGTSLLGALGYWLF 761  

                CS XXXXX.XXXXXXXXXX   
                   rRrRkeakkyvrlpps<-*
                     rR  + +++rl+++   
  gi|1495871   762 HFRRR-SRGSPRLTET    776  

C1-set: domain 1 of 1, from 186 to 233: score 19.8, E = 1.7e-05
                CS    STTEEEEEEEEEETTSEEEEEEEEEEEHHHHHTSSEEEEEEEETTST
                   *->tegvesteplpkngDgtYqlsSyLtftasepesgdtYtCrVeHesLk
                      +e++ + e+lp   +gt +++S+L +  ++  +g + tC+VeHe+L+
  gi|1495871   186    HEANITQEELP---NGTITVTSQLSLLPTRNVHGQSVTCKVEHETLQ 229  

                CS E.TSEEE   
                   venePlt<-*
                      eP+    
  gi|1495871   230 ---EPQM    233  

I-set: domain 1 of 3, from 461 to 476: score 4.2, E = 1.7
                CS    ECCE-CGGGCEEEEEE   
                   *->IsnvqpdDeGkYtCvA<-*
                      I++v  dD+G+Yt ++   
  gi|1495871   461    IQEVREDDAGQYTLQV    476  
I-set: domain 2 of 3, from 563 to 601: score 5.1, E = 0.96
                CS    ..TEEEEEECCE-CGGGCEEEEEEEETTEEEEEEEEEEE   
                   *->GsgtytLtIsnvqpdDeGkYtCvAtNsaGeaeasaeLtV<-*
                      G  + +L  ++v p D+G Y + ++   G+ eas++  V   
  gi|1495871   563    GTKNGSLLLRDVSPQDSGRYIVHVVTLQGKEEASITIDV    601  
I-set: domain 3 of 3, from 685 to 720: score 4.6, E = 1.3
                CS    EEEEEECCE-CGGGCEEEEEEEETTEEEEEEEEEEE   
                   *->tytLtIsnvqpdDeGkYtCvAtNsaGeaeasaeLtV<-*
                      + +L  ++v p D+G Y + ++   G+ eas++  V   
  gi|1495871   685    NGSLLLRDVSPQDSGRYIVHVVTLWGKEEASITIDV    720  


Example 5
gi|198424579|ref|XP_002124481.1| PREDICTED: similar to Notch [Ciona intestinalis] 693 (length) 136 246 .. (wrt seq) 287 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 86 [23%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
EGF             EGF-like domain                         114.8    2.9e-31   3
EGF_2           EGF-like domain                          44.6    2.6e-11   3
Herpes_glycop_D Herpesvirus glycoprotein D               19.9    5.4e-06   1
DUF2077         Uncharacterized protein conserved in     13.5     0.0012   1
CUB             CUB domain                                7.7      0.064   1
DUF916          Bacterial protein of unknown function     6.5        0.1   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
EGF               1/3      28    59 ..     1    38 []    36.7  3.4e-09
EGF               2/3      66    97 ..     1    38 []    44.0  3.1e-11
EGF               3/3     104   135 ..     1    38 []    34.1  1.8e-08
EGF_2             1/3      28    59 ..     1    37 []     9.7     0.13
EGF_2             2/3      66    97 ..     1    37 []    16.3   0.0018
EGF_2             3/3     104   135 ..     1    37 []    18.5  0.00046
Herpes_glycop_D   1/1     136   246 ..   287   409 .]    19.9  5.4e-06
DUF2077           1/1     190   234 ..   165   211 .]    13.5   0.0012
CUB               1/1       1    18 [.    99   116 .]     7.7    0.064
DUF916            1/1     214   238 ..   344   368 .]     6.5      0.1

Alignments of top-scoring domains:
EGF: domain 1 of 3, from 28 to 59: score 36.7, E = 3.4e-09
                CS    TTSSCTTSSSTEEEEEETTEEEEEETTT.CECEESTTC   
                   *->CnpnngpCsngGtCvdtpggytCeCpeGyvllytGkrC<-*
                      C +n  pC+++G+C + p+ ytC+C  G    ++G++C   
  gi|1984245    28    CESN--PCQHDGECESHPDYYTCKCSDG----FAGINC    59   
EGF: domain 2 of 3, from 66 to 97: score 44.0, E = 3.1e-11
                CS    TTSSCTTSSSTEEEEEETTEEEEEETTT.CECEESTTC   
                   *->CnpnngpCsngGtCvdtpggytCeCpeGyvllytGkrC<-*
                      C++   pC++gGtCvd+  +ytC+C eG    +tGk+C   
  gi|1984245    66    CASY--PCKHGGTCVDGVRDYTCDCLEG----FTGKDC    97   
EGF: domain 3 of 3, from 104 to 135: score 34.1, E = 1.8e-08
                CS    TTSSCTTSSSTEEEEEETTEEEEEETTT.CECEESTTC   
                   *->CnpnngpCsngGtCvdtpggytCeCpeGyvllytGkrC<-*
                      C++n  pC ngG Cv+   ++ C Cp      + G++C   
  gi|1984245   104    CASN--PCENGGLCVNRNVDFVCSCPRD----FMGEKC    135  

EGF_2: domain 1 of 3, from 28 to 59: score 9.7, E = 0.13
                   *->C....CngshGtCvspngtstpcGkCvCdsgyedkyqGadC<-*
                      C++++C+  +G C+s          C+C++g    + G  C   
  gi|1984245    28    CesnpCQH-DGECESHPD----YYTCKCSDG----FAGINC    59   
EGF_2: domain 2 of 3, from 66 to 97: score 16.3, E = 0.0018
                   *->C....CngshGtCvspngtstpcGkCvCdsgyedkyqGadC<-*
                      C + +C   +GtCv +++       C+C  g    ++G+dC   
  gi|1984245    66    CasypCKH-GGTCV-DGVR---DYTCDCLEG----FTGKDC    97   
EGF_2: domain 3 of 3, from 104 to 135: score 18.5, E = 0.00046
                   *->C....CngshGtCvspngtstpcGkCvCdsgyedkyqGadC<-*
                      C +++C + +G Cv+ n+      +C+C++     + G +C   
  gi|1984245   104    CasnpCEN-GGLCVNRNV----DFVCSCPRD----FMGEKC    135  

Herpes_glycop_D: domain 1 of 1, from 136 to 246: score 19.9, E = 5.4e-06
                CS    ....HHHH------------------.---------X...XX XXXX
                   *->draRPdsveyeipakpsdaeddrpdsesdgesalperiedae.qlpe
                      +++ P +++ + pa++++a+  +++ e+   +++pe+ + +++++p+
  gi|1984245   136    EEPVPTPSPPPTPAPTTPAPTQPEPTEPAKNKPAPEVTTQPPsPAPK 182  

                CS XXXXXX........XXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXX
                   tgevpeadPevvPsisdeevpspppatpaNpdakvtsviigivvlallig
                    +e  e        + +++++++pp + +N   + tsvii +v+l+ll +
  gi|1984245   183 EDEKGE--------AAPADHEPHPPGDANN--HR-TSVII-AVILVLLVL 220  

                CS XXXXXXXXXXXXXXXX.XXXXXXXXXX   
                   aiivgvvyyilrRrRkeakkyvrlpps<-*
                   ++++g+ ++  ++ Rk +++ +r  +    
  gi|1984245   221 FLLLGIFLWYWFKLRK-GNPQKREKEV    246  

DUF2077: domain 1 of 1, from 190 to 234: score 13.5, E = 0.0012
                   *->aLSphwqgvaaarrrlrrlrrvPlWtvvaalalllllglylglsylL
                      a ++h ++++  +++ r   +v + ++ ++l l+lllg++l++++ L
  gi|1984245   190    APADHEPHPPGDANNHRT--SVIIAVILVLLVLFLLLGIFLWYWFKL 234  

                   <-*
                      
  gi|1984245     -     -    

CUB: domain 1 of 1, from 1 to 18: score 7.7, E = 0.064
                CS    EEEEESSTTS----EEEE   
                   *->ikFvsDssiqkrGFkaty<-*
                      + FvsD+s + +GFk ++   
  gi|1984245     1    MVFVSDDSAAESGFKFSF    18   

DUF916: domain 1 of 1, from 214 to 238: score 6.5, E = 0.1
                   *->iiiglllllllllivyliwkrkkkk<-*
                      i++ l+l+lll+++++++ k +k     
  gi|1984245   214    ILVLLVLFLLLGIFLWYWFKLRKGN    238  


Example 6
gi|159109774|ref|XP_001705150.1| High cysteine membrane protein Group 2 [Giardia lamblia ATCC 50803]gi|157433230|gb|EDO77476.1| High cysteine membrane protein Group 2 [Giardia lamblia ATCC 50803] 801 (length) 755 795 .. (wrt seq) 369 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 4 [1%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
VSP             Giardia variant-specific surface prot    58.6    3.7e-16   4
Herpes_glycop_D Herpesvirus glycoprotein D               18.3    1.7e-05   1
EB              EB module                                19.0    0.00017   5
TIL             Trypsin Inhibitor like cysteine rich      8.6      0.033   3
Laminin_EGF     Laminin EGF-like (Domains III and V)     10.2      0.035   3
TNFR_c6         TNFR/NGFR cysteine-rich region           10.4      0.036   3

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
VSP               1/4     126   194 ..   172   241 ..    18.0  5.6e-05
VSP               2/4     202   222 ..     1    17 [.     0.3      4.3
VSP               3/4     430   490 ..   270   327 ..    28.2  8.9e-08
VSP               4/4     754   785 ..   380   412 .]    12.1   0.0025
Herpes_glycop_D   1/1     755   795 ..   368   409 .]    18.3  1.7e-05
EB                1/5      31    58 ..     1    27 [.     9.2    0.098
EB                2/5     168   180 ..     1    13 [.     3.1      5.3
EB                3/5     442   455 ..     1    14 [.     1.5       16
EB                4/5     478   490 ..    46    58 .]     0.7       27
EB                5/5     725   742 ..    41    58 .]     4.5      2.2
TIL               1/3     267   293 ..    45    68 .]     6.8     0.13
TIL               2/3     354   360 ..    62    68 .]     1.9      4.9
TIL               3/3     660   682 ..    46    68 .]     0.0       19
Laminin_EGF       1/3     205   222 ..    43    59 .]     7.2     0.26
Laminin_EGF       2/3     269   287 ..    40    59 .]     1.7       10
Laminin_EGF       3/3     439   460 ..    40    59 .]     1.3       13
TNFR_c6           1/3     479   502 ..     1    24 [.     5.1      1.4
TNFR_c6           2/3     531   548 ..     1    20 [.     4.7      1.8
TNFR_c6           3/3     561   575 ..    19    33 ..     0.6       29

Alignments of top-scoring domains:
VSP: domain 1 of 4, from 126 to 194: score 18.0, E = 5.6e-05
                   *->DGtsYCSeCateteyPqNGVCtStaaRatatCkdstvanGvCssCan
                      +G +YCS C ++ ey   G C S +      C+     +G C  C n
  gi|1591097   126    GGNKYCSRCSVKSEYLVDGKCLSSTDN--NACTSQDYPDGTCKLCGN 170  

                   GylrmnGGCYeTtK.fPGKSVCee<-*
                   Gy+   GGCY  t + PG  +C e   
  gi|1591097   171 GYFLYKGGCYSITHgAPGNLICKE    194  
VSP: domain 2 of 4, from 202 to 222: score 0.3, E = 4.3
                   *->CaeCklGy....elsadktkc<-*
                      C++C++G+ + +e++a ++ c   
  gi|1591097   202    CKLCQDGFfrlpEPAANRQSC    222  
VSP: domain 3 of 4, from 430 to 490: score 28.2, E = 8.9e-08
                   *->CktCtssTvCttCadGyvkdggsdvCtk....CD.ssCeTCTaGatt
                      C++C+s TvC  Ca Gy+ +  s++C  ++++C  ++C+TC  G  +
  gi|1591097   430    CEECSSDTVCSRCAAGYIIS--SSACVAdpdpCSvAGCKTCVSGNRQ 474  

                   tCktCaTGYYKsgtgc<-*
                    C +C  G+YK gt+c   
  gi|1591097   475 LCLVCHDGFYKDGTTC    490  
VSP: domain 4 of 4, from 754 to 785: score 12.1, E = 0.0025
                   *->STGAIAGIsVAvviVVGGLVGFLCWWFiCRGKA<-*
                      STG IAGIsVA v +V+  +G L  WF+ R K    
  gi|1591097   754    STGMIAGISVASVAIVAVIIGCLV-WFLLRRKN    785  

Herpes_glycop_D: domain 1 of 1, from 755 to 795: score 18.3, E = 1.7e-05
                CS    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX   
                   *->tsviigivvlalligaiivgvvyyilrRrRkeakkyvrlpps<-*
                      t+ i+gi+v++++i+a+i+g  ++ l+Rr++ ++ + r p     
  gi|1591097   755    TGMIAGISVASVAIVAVIIGCLVWFLLRRKN-SGSLNREPSL    795  

EB: domain 1 of 5, from 31 to 58: score 9.2, E = 0.098
                   *->CpsgqvlvngeClpk.lvlpGesGCesd<-*
                      C +g  l++g C+ +++ ++G++GCe+d   
  gi|1591097    31    CTPGLLLIDGACVEQdSHEVGSAGCEVD    58   
EB: domain 2 of 5, from 168 to 180: score 3.1, E = 5.3
                   *->CpsgqvlvngeCl<-*
                      C +g++l+ g C+   
  gi|1591097   168    CGNGYFLYKGGCY    180  
EB: domain 3 of 5, from 442 to 455: score 1.5, E = 16
                   *->CpsgqvlvngeClp<-*
                      C  g++ +++ C++   
  gi|1591097   442    CAAGYIISSSACVA    455  
EB: domain 4 of 5, from 478 to 490: score 0.7, E = 27
                   *->qCpeGftavggrC<-*
                      +C +Gf  +g++C   
  gi|1591097   478    VCHDGFYKDGTTC    490  
EB: domain 5 of 5, from 725 to 742: score 4.5, E = 2.2
                   *->ingtCqCpeGftavggrC<-*
                      ++g+C C  G++++g++C   
  gi|1591097   725    RRGKCHCMGGQVPSGNTC    742  

TIL: domain 1 of 3, from 267 to 293: score 6.8, E = 0.13
                CS    SEEE --CCCTEEEETT  EEEECCCS   
                   *->gvCv.CqpGyVrnndgd..kCVprseC<-*
                      +vC+ C p+y++ ++gd+  C    eC   
  gi|1591097   267    PVCEaCHPDYYLLSRGDsaMCLSSQEC    293  
TIL: domain 2 of 3, from 354 to 360: score 1.9, E = 4.9
                CS    EEECCCS   
                   *->CVprseC<-*
                      CVp  eC   
  gi|1591097   354    CVPLDEC    360  
TIL: domain 3 of 3, from 660 to 682: score 0.0, E = 19
                CS    EEE--CCCTEEEETTEEEECCCS   
                   *->vCvCqpGyVrnndgdkCVprseC<-*
                      +C C++ y  +ndg+ C p   C   
  gi|1591097   660    ACMCEDSYAPSNDGTLCEPTKPC    682  

Laminin_EGF: domain 1 of 3, from 205 to 222: score 7.2, E = 0.26
                CS    E-TTEEEGTT- CGCCSE   
                   *->CkpGyyglpsg.dpgqgC<-*
                      C++G+++lp+   ++q+C   
  gi|1591097   205    CQDGFFRLPEPaANRQSC    222  
Laminin_EGF: domain 2 of 3, from 269 to 287: score 1.7, E = 10
                CS    S-EE-TTEEEGTT-CGCCSE   
                   *->CdrCkpGyyglpsgdpgqgC<-*
                      C+ C p yy l++gd++  C   
  gi|1591097   269    CEACHPDYYLLSRGDSA-MC    287  
Laminin_EGF: domain 3 of 3, from 439 to 460: score 1.3, E = 13
                CS    S-EE-TTEEEGTT-   CGCCSE   
                   *->CdrCkpGyyglpsg...dpgqgC<-*
                      C rC+ Gy   +s+   dp   C   
  gi|1591097   439    CSRCAAGYIISSSAcvaDPD-PC    460  

TNFR_c6: domain 1 of 3, from 479 to 502: score 5.1, E = 1.4
                CS    CCTTTEEEE TSSSSSEEE EESBTT   
                   *->CeegvtYtd.enhvpqCls.CskCep<-*
                      C++g +Y d++ + ++C ++C++C++   
  gi|1591097   479    CHDG-FYKDgTTC-RKCAAgCTVCSG    502  
TNFR_c6: domain 2 of 3, from 531 to 548: score 4.7, E = 1.8
                CS    CCTTTEEEETSSSSSEEEEE   
                   *->CeegvtYtdenhvpqClsCs<-*
                      C +g ++ d+   + C++Cs   
  gi|1591097   531    CGDG-HFEDTTL-KVCTRCS    548  
TNFR_c6: domain 3 of 3, from 561 to 575: score 0.6, E = 29
                CS    EESBTTGGTEEEEE-   
                   *->CskCepemGqvlvsp<-*
                      C++C+ +m+++l+s+   
  gi|1591097   561    CTRCQDDMYLKLTSS    575  


Example 7
gi|124512776|ref|XP_001349744.1| rifin [Plasmodium falciparum 3D7]gi|23615161|emb|CAD52149.1| rifin [Plasmodium falciparum 3D7] 369 (length) 311 364 .. (wrt seq) 351 410 .] (wrt HMM) 
No.of residues in non-TM/SP region : 22 [6%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
Rifin_STEVOR    Rifin/stevor family                     554.8   5.9e-171   1
Herpes_glycop_D Herpesvirus glycoprotein D               17.3    3.3e-05   1
7TM-7TMR_HD     7TM receptor with intracellular HD hy     8.4      0.068   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
Rifin_STEVOR      1/1      20   369 .]     1   380 []   554.8 5.9e-171
Herpes_glycop_D   1/1     311   364 ..   350   409 .]    17.3  3.3e-05
7TM-7TMR_HD       1/1     327   360 ..     1    34 [.     8.4    0.068

Alignments of top-scoring domains:
Rifin_STEVOR: domain 1 of 1, from 20 to 369: score 554.8, E = 5.9e-171
                   *->hNkKYNkpyITnrthtptitSRlLcEcelysPsnYDNDpEMKeVmen
                      +N+  +++yIT+   tp++t+R+LcEcely+P+nYDNDpEMKeVm+n
  gi|1245127    20    YNQ--RNHYITR---TPKATTRTLCECELYEPANYDNDPEMKEVMDN 61   

                   FnrQTsQRFeEYdERmkdkRqKCKeqcDKeIQkIIlKDKlEKELmdKfaT
                   FnrQT+QRF+EYdE m +kR++CKeqcDKeIQkIIlKDK+EKELmdKfaT
  gi|1245127    62 FNRQTQQRFHEYDECMVEKRMQCKEQCDKEIQKIILKDKMEKELMDKFAT 111  

                   LqTDIqtDAIPTCVCEKSlAdKVEKgCLrCGfgLGgGVapksGllGGiga
                   LqTDIq+DAIPTC+CEKSlAdK+EK+CL+CG+  GgG++++sG+lGGig 
  gi|1245127   112 LQTDIQNDAIPTCICEKSLADKTEKFCLNCGVNVGGGITLSSGVLGGIGS 161  

                   iavnewYkksAmaAlvaAiqkGieAGiLadelasvcKviaaglkklGvST
                   +avn+w k      ++ A++  ++A+            i++gl+ + +  
  gi|1245127   162 VAVNAW-KT-----TEIAAA--TKAA------------IDKGLALGKIAG 191  

                   LikglgkyvvildlsklrinkfcpkiisaiinasnYsapktligaIaakk
                    i+g++k v++++ + ++i ++  + +++ii a++Y++ +++ g+I ++ 
  gi|1245127   192 DIEGAAKVVELVKST-FKIEELGVRTLESIIDANTYTKSSLISGFIETEY 240  

                   aatiCa..avsanegskmcfsskigl.....silssstatriGpPakdaI
                   +++ C++ +++ +++ +++ ++++++++++++++ + t+          I
  gi|1245127   241 SRLGCGniFTGMKKP-FCNSVYERIFdtsggKGVYPITF----------I 279  

                   pkvlnglVtsaasdAaaaAkaaeeavtgtiitkataliestfassitaIi
                    k +   V+ a+s Aaa  ++++ a+ ++i + +  +ie+t+++ +t I+
  gi|1245127   280 EKKVETMVSEAESVAAAKSAKVAAAEKAAILETSKKAIETTSYNWYTTIG 329  

                   aSviAILiIvLvMlIIYLILRYRRKKKMkKKlQYiKLLne<-*
                   +S+ AILiIvL+M+IIYLILRYRRKKKMkKKlQYiKLL+e   
  gi|1245127   330 YSITAILIIVLIMVIIYLILRYRRKKKMKKKLQYIKLLKE    369  

Herpes_glycop_D: domain 1 of 1, from 311 to 364: score 17.3, E = 3.3e-05
                CS    XXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                   *->eevpspppatpaNpdakvtsviigivvlalligaiivgvvyyilrRr
                      e+  +++++t+ N      +++ig +++a+li+ +i +++y ilr r
  gi|1245127   311    ETSKKAIETTSYN-----WYTTIGYSITAILIIVLIMVIIYLILRYR 352  

                CS XX.XXXXXXXXXX   
                   Rkeakkyvrlpps<-*
                   Rk  k+ ++l  +   
  gi|1245127   353 RK-KKMKKKLQYI    364  

7TM-7TMR_HD: domain 1 of 1, from 327 to 360: score 8.4, E = 0.068
                   *->wlillglallvlllllifllylkrykkellkkrs<-*
                      +  ++++a+l+++l++++++ + ry++ + +k++   
  gi|1245127   327    TIGYSITAILIIVLIMVIIYLILRYRRKKKMKKK    360  


Example 8
gi|156334547|ref|XP_001619472.1| hypothetical protein NEMVEDRAFT_v1g224148 [Nematostella vectensis]gi|156202733|gb|EDO27372.1| predicted protein [Nematostella vectensis] 610 (length) 423 463 .. (wrt seq) 357 397 .. (wrt HMM) 
No.of residues in non-TM/SP region : 16 [4%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
ANF_receptor    Receptor family ligand binding region   143.4    1.4e-41   1
Pkinase_Tyr     Protein tyrosine kinase                  30.1    1.1e-08   1
Herpes_glycop_D Herpesvirus glycoprotein D               15.7      1e-04   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
ANF_receptor      1/1      34   378 ..     1   416 []   143.4  1.4e-41
Pkinase_Tyr       1/1     499   559 ..    58   125 ..    30.1  1.1e-08
Herpes_glycop_D   1/1     423   463 ..   356   396 ..    15.7    1e-04

Alignments of top-scoring domains:
ANF_receptor: domain 1 of 1, from 34 to 378: score 143.4, E = 1.4e-41
                   *->qvlpAmrlAvediNadggillpgitlgyedddtcsdsalcsslsFdd
                      + ++A++l ++diN+d + llp ++l+y ++d+             +
  gi|1563345    34    RIAAAAPLSIQDINNDIT-LLPAFNLTYSIHDS------------AC 67   

                   .aavaaaacllkkgVvAiiGPscssvaiavarlanewgiPlisygataps
                    a  ++  +   +g ++iiGP+cs +a +va la  w++P+i+y+a++ +
  gi|1563345    68 vAEKGLRGMVAFEGLDFIIGPGCSLTAQPVATLAKIWNKPIITYAASSAA 117  

                   lsdklknryptffRtvPsdtkqga....AiadilkhtfgWkrvaviyddd
                   + d  k+ + tf+ ++++ +   + ++ ++a+++   f+W+  +++ + +
  gi|1563345   118 FID--KTVFSTFATVTAYGRRNQQytpaFVARLMSA-FNWTVCGILTSTE 164  

                   dydkgeggcYFtlealedalkeaglkvvavAavvseviasdddftallke
                       +  +    ++ ++++        v+v    + ++  d   t ++ +
  gi|1563345   165 VE--WKAM----AQKIRALISPL----VNV----TVYEEHDPQTTRFDEI 200  

                   lkdlikskarvivvcgssddlgllkrqilqqarelGlmsggYvwiltdlw
                   l++  + +arv+++ ++ + +      i+++a++lG+++g+++++ +dl 
  gi|1563345   201 LRR-GRENARVFLLLCYVNQV----TDIMRAAKNLGMTNGDHAFVTIDLN 245  

                   sssldsdgdgstlpwariagadeGlltartfpfqpdndkareaakgvlgf
                   ++ ++s g      w +   +d                 + + ++g++ +
  gi|1563345   246 TDVFYSNG-----RWTG---ND------------GPGSQFSQDLNGIVDL 275  

                   tlk.p.spefqeflerlkk............sdtevnsyallaYDAVyll
                    + +p  +  ++f  r+++ ++   ++ ++ ++  ++ ya+++YDA++l 
  gi|1563345   276 SVDrPlLS--EDFKARYRAmgsalvpevrqyLNAKPSWYAAFLYDAIWLA 323  

                   AhAlnealsddpngtaggcnacrdrvddasnalgglnlglskwdGsqlle
                   A Aln++  d+ ++t+ +                            + ++
  gi|1563345   324 ALALNDTIADGYDVTNTS----------------------------ATVQ 345  

                   ylrnkmvkvnfeGltGdvqfddnggrrpdysleilnwd<-*
                   ++ n    ++f+G +G v++   g r+p + +  +      
  gi|1563345   346 RMFN----RQFQGESGKVRMIN-GTRVPLFAVGNIVNG    378  

Pkinase_Tyr: domain 1 of 1, from 499 to 559: score 30.1, E = 1.1e-08
                CS    HHHTCTTTB-EEEEEECSESSSS.. EEEEEEETTTEBHHHHHHHTT
                   *->kklGdHpNiVrLlGvCtlkqgePng.lyiVtEymegGdLldfLrkhr
                      ++l +H N+  ++GvC+    eP  +++iV E++++G+L d L +  
  gi|1563345   499    CEL-RHVNVNPCVGVCV----EP-LtVCIVNEFCAKGSLQDILLDD- 538  

                CS CTTTSHHHHHHHHHHHHHHHHH   
                   eggkLtlkdLlsfalQiAkGMe<-*
                    + kL+   + sfa++iA+GMe   
  gi|1563345   539 -NLKLDWTFKMSFAMDIARGME    559  

Herpes_glycop_D: domain 1 of 1, from 423 to 463: score 15.7, E = 1e-04
                CS    XXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX   
                   *->ppatpaNpdakvtsviigivvlalligaiivgvvyyilrRr<-*
                      +++tp  + ++ t++ii++v +a++++ ++vgv+++ +rR+   
  gi|1563345   423    INKTPDGKSSDETQLIIFAVLGACICLVVLVGVAVFLRRRQ    463  
