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Domain name : PF00672.17_HAMP
Domain size : 79
Domain Description : HAMP domain
Domain gathering score : 19.8000
Domain trusted cutoff : 19.8000
Domain architecture : TM/SP [1 23], non-TM/SP [24 106]
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Example 1
gi|169185846|ref|ZP_02846008.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2]gi|169007267|gb|EDS54116.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2] 755 (length) 297 360 .. (wrt seq) 1 79 [] (wrt HMM) 
No.of residues in non-TM/SP region : 40 [48%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
HTH_AraC      Bacterial regulatory helix-turn-helix p    59.0    1.8e-14   2
HAMP          HAMP domain                                37.8    4.4e-08   1
Cache_1       Cache domain                               -5.8      0.064   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
HTH_AraC        1/2     653   699 ..     1    49 []    20.0   0.0097
HTH_AraC        2/2     705   749 ..     1    49 []    38.9    2e-08
HAMP            1/1     297   360 ..     1    79 []    37.8  4.4e-08
Cache_1         1/1     157   238 ..     1    92 []    -5.8    0.064

Alignments of top-scoring domains:
HTH_AraC: domain 1 of 2, from 653 to 699: score 20.0, E = 0.0097
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      +  r+Lee++ ++++  +++A e+G+ S sy ++   + tG +  +y
  gi|1691858   653    RIIRYLEEHF-RKEIVFEEMAKEIGI-SYSYMRKIVYELTGKSLIDY 697  

                CS HH   
                   rr<-*
                   ++   
  gi|1691858   698 MN    699  

HTH_AraC: domain 2 of 2, from 705 to 749: score 38.9, E = 2e-08
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      kA++lL e   s+ ++i++iA+evGy + + f r F+ky G+ Ps y
  gi|1691858   705    KAKQLLVE---SK-MTITQIASEVGYYNVQSFNRFFRKYEGMPPSSY 747  

                CS HH   
                   rr<-*
                    +   
  gi|1691858   748 KT    749  


HAMP: domain 1 of 1, from 297 to 360: score 37.8, E = 4.4e-08
                CS    HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX
                   *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri
                      ++++++i+++++ +la+lla ++++P+rrL++++r+ +   +L    
  gi|1691858   297    IIFITGIIIIAGTILAVLLATWLSQPVRRLVRTMRERS---NL---- 336  

                CS XXXXX.........XXXXXXXXXXXXXXXXXX   
                   esgrdrvlpvsgpDEigeLarafNqMaerLre<-*
                             + ++E+  L  af +M+e+ +    
  gi|1691858   337 --------GGTNKNELVFLESAFRRMQEEEEG    360  

Cache_1: domain 1 of 1, from 157 to 238: score -5.8, E = 0.064
                   *->wTePYvdaalktgdlViTiaqPvydtseqrnktnddgdll....GVi
                      +  +   ++l++g +V+++ +P+              +l+++++G i
  gi|1691858   157    IGGVWYPRQLQSGMQVVSYVLPLN-------------RLStttrGTI 190  

                   giDvsledLlkltksiklGktGYaFivdnnGkvlaHPnlqpvtkllgdw<
                     +++ + + +++ s+ +G +G+ +++  +G+++ H+++    + ++++ 
  gi|1691858   191 VVNLKESQIASYLRSFEPGSEGF-MLLKSDGTIISHNDKSLLLTDGNKQ  238  

                   -*
                     
  gi|1691858     -    -    


Example 2
gi|118725971|ref|ZP_01574605.1| transcriptional regulator, AraC family [Clostridium cellulolyticum H10]gi|118664670|gb|EAV71298.1| transcriptional regulator, AraC family [Clostridium cellulolyticum H10] 760 (length) 300 364 .. (wrt seq) 1 79 [] (wrt HMM) 
No.of residues in non-TM/SP region : 41 [49%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
HTH_AraC        Bacterial regulatory helix-turn-helix    84.0    5.2e-22   2
HAMP            HAMP domain                              30.8    5.7e-06   1
Cache_1         Cache domain                             -5.7      0.063   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
HTH_AraC          1/2     660   706 ..     1    49 []    34.1  5.6e-07
HTH_AraC          2/2     712   756 ..     1    49 []    49.9  9.7e-12
HAMP              1/1     300   364 ..     1    79 []    30.8  5.7e-06
Cache_1           1/1     161   241 ..     1    92 []    -5.7    0.063

Alignments of top-scoring domains:
HTH_AraC: domain 1 of 2, from 660 to 706: score 34.1, E = 5.6e-07
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      k + ++++n+  +++ i+ +Ae+vG+ S s+ ++ F  +tG ++  y
  gi|1187259   660    KILDYIHKNY-KKDIAINMLAEHVGL-SYSHVRKIFNDETGENIVNY 704  

                CS HH   
                   rr<-*
                   ++   
  gi|1187259   705 IN    706  

HTH_AraC: domain 2 of 2, from 712 to 756: score 49.9, E = 9.7e-12
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      +A rlL++   +n ++i+diA+++Gy +++ f r Fkky+G++P+ey
  gi|1187259   712    EAQRLLRQ---TN-MNINDIALSLGYNNKQSFNRFFKKYVGINPGEY 754  

                CS HH   
                   rr<-*
                   r+   
  gi|1187259   755 RN    756  

HAMP: domain 1 of 1, from 300 to 364: score 30.8, E = 5.7e-06
                CS    HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX
                   *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri
                      ++++++++l+l +ll+++++rr+ +P+++L++ ++  ++G       
  gi|1187259   300    IIYISIFLLVLFVLLSYVISRRLFNPVKKLVQEIKS-RKG------- 338  

                CS XXXXX...... ...XXXXXXXXXXXXXXXXXX   
                   esgrdrvlpvs.gpDEigeLarafNqMaerLre<-*
                           ++ + ++E+  L+++f+ M+ +  +   
  gi|1187259   339 ----I---DIIgNGNEFTLLSKTFDVMIKQEDQ    364  

Cache_1: domain 1 of 1, from 161 to 241: score -5.7, E = 0.063
                   *->wTePYvdaalktgdlViTiaqPvydtseqrnktnddgdllGVigiDv
                      wT+P ++ +  +++ Vi++  P+              +l+G i i++
  gi|1187259   161    WTDPRPSDT-NGNSSVISYIFPLTY----------TTNLKGSITINI 196  

                   sledLlkltksiklGktGYaFivdnnGkvlaHPnlqpvtkllgdw<-*
                     + L +l++s +     ++ i++ nG+v+   ++++ +k+l d+   
  gi|1187259   197 YESRLSNLINSNNYDISDFISIINANGEVISSVDKTILNKNLTDV    241  


Example 4
gi|169187094|ref|ZP_02847254.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2]gi|169005926|gb|EDS52777.1| transcriptional regulator, AraC family [Paenibacillus sp. JDR-2] 788 (length) 304 371 .. (wrt seq) 1 79 [] (wrt HMM) 
No.of residues in non-TM/SP region : 44 [53%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
HTH_AraC        Bacterial regulatory helix-turn-helix    85.6    1.8e-22   2
HAMP            HAMP domain                              28.2    3.4e-05   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
HTH_AraC          1/2     679   725 ..     1    49 []    36.0  1.5e-07
HTH_AraC          2/2     731   775 ..     1    49 []    49.5  1.3e-11
HAMP              1/1     304   371 ..     1    79 []    28.2  3.4e-05

Alignments of top-scoring domains:
HTH_AraC: domain 1 of 2, from 679 to 725: score 36.0, E = 1.5e-07
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      + + ++++n+ ++++s++ iA+++ + +psy srlFk++  vt+++y
  gi|1691870   679    QILAYIQNNF-DKEISLGGIADQLQL-DPSYASRLFKQEISVTFMDY 723  

                CS HH   
                   rr<-*
                        
  gi|1691870   724 VI    725  

HTH_AraC: domain 2 of 2, from 731 to 775: score 49.5, E = 1.3e-11
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      k+++lL++   s+ l+++di ++vGy +++ f r Fkky G+tP+ey
  gi|1691870   731    KTKELLKT---SE-LTVKDIGASVGYANQRSFNRIFKKYEGMTPGEY 773  

                CS HH   
                   rr<-*
                   r    
  gi|1691870   774 RD    775  

HAMP: domain 1 of 1, from 304 to 371: score 28.2, E = 3.4e-05
                CS    HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX
                   *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri
                      +l+++++++l+a+l+a++l+ ri  P++ L++ +++     d +   
  gi|1691870   304    MLILMAFSILAAVLAAFYLTLRIYSPIHSLVQMVNNKK---DWR--- 344  

                CS XXXXX.........XXXXXXXXXXXXXXXXXX   
                   esgrdrvlpvsgpDEigeLarafNqMaerLre<-*
                       + v p + + E+++L  af  M e+  e   
  gi|1691870   345 ----SAV-PLHEQSEMAMLFSAFITMKEQGAE    371  


Example 5
gi|192810581|ref|ZP_03039254.1| helix-turn-helix- domain containing protein AraC type [Geobacillus sp. Y412MC10]gi|192800873|gb|EDV77380.1| helix-turn-helix- domain containing protein AraC type [Geobacillus sp. Y412MC10] 756 (length) 297 360 .. (wrt seq) 1 79 [] (wrt HMM) 
No.of residues in non-TM/SP region : 40 [48%(over non-TM/SP length)]

Scores for sequence family classification:
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
HTH_AraC        Bacterial regulatory helix-turn-helix    60.5    6.3e-15   2
HAMP            HAMP domain                              26.7    9.7e-05   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
HTH_AraC          1/2     654   700 ..     1    49 []    19.6    0.013
HTH_AraC          2/2     706   750 ..     1    49 []    40.9    5e-09
HAMP              1/1     297   360 ..     1    79 []    26.7  9.7e-05

Alignments of top-scoring domains:
HTH_AraC: domain 1 of 2, from 654 to 700: score 19.6, E = 0.013
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      +  ++L e + ++++  +++A  +G+ S sy ++   ++tG ++s+y
  gi|1928105   654    RIIHYLNERY-REEIVFEEMAKDIGI-SYSYMRKIVYEQTGKSISDY 698  

                CS HH   
                   rr<-*
                   ++   
  gi|1928105   699 LN    700  

HTH_AraC: domain 2 of 2, from 706 to 750: score 40.9, E = 5e-09
                CS    HHHHHHHC...SSS-SHHHHHHHHTS.-HHHHHHHHHHHTSS-HHHH
                   *->kArrlLeenlasnklsiadiAeevGysSpsyfsrlFkkytGvtPsey
                      kA++lL++   sn lsi++iA+evG+ + + f rlF+k  G+ Ps y
  gi|1928105   706    KAKELLLN---SN-LSIGQIASEVGCMNVRSFNRLFRKFEGMPPSSY 748  

                CS HH   
                   rr<-*
                        
  gi|1928105   749 KM    750  

HAMP: domain 1 of 1, from 297 to 360: score 26.7, E = 9.7e-05
                CS    HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX
                   *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri
                      +++++++++ ++ +l +++a ++++P r+L++++r    G +     
  gi|1928105   297    IIFLTIVIIFAGSILTVFMATWLSKPARELVRTIR----G-RV---- 334  

                CS XXXXX...... ...XXXXXXXXXXXXXXXXXX   
                   esgrdrvlpvs.gpDEigeLarafNqMaerLre<-*
                       +   p ++ ++E+  L +af +M+e+ +    
  gi|1928105   335 ----N---PGVqDKNELVFLEAAFRRMQEEEEG    360  
