Table I.
Amino acid sequences encoded by 42 random alpaca VHH cDNA clones separated into predicted protein domain regions
| CLONE | LEADER | FR1 | CDR1 | FR2 | CDR2 | FR3 |
|---|---|---|---|---|---|---|
| A02
A52 |
VVLAALL
VVLAALL |
QGIKARSQFVESGGGLVQPGGSLRLSCTAS
QGVQAQLQLVESGGGLVQPGGSLQLACEAS |
G--FSLKYWA
G--VTLEEVS |
VGWFRQAPGK---EREGVLC
VAWFRQAPGK---EREGVSC |
VSQ-SGE--IT
INS-NGNGGST |
NVANSVKGRFTISRDNDK
TYARSVKGRFTISRDSAK |
| A53 | VVLAALL | QSVDAYLRIVESGGGLVQSGGSLRLSCSAS | G--DKLARYA | VGWFRQAPGK---QREAVAC | IDN-SVG--NT | TYADAVKGRFTISRDKAE |
| A07 | VVLAALL | QGVQAEVQLVESGGGSVQAGGYLRLSCAVS | G--SLASMNS | MGWYRQSPEK---EREFVAS | INR-SN---YT | IYSTSVKDRFILSRDHDK |
| A31 | VVLAALL | RGVQAEVRLEESGGGLVQAGGSLRLVCVAY | G--TIFSYNA | MGWYRQPPGK---ERELVAG | ITA-QG---TI | EYAEAVKGRATISRDNAK |
| A54 | VVLAALL | QGVQAQVFLEESGGALVQPGDSLRLTCKVS | G--NIADVYA | MAWYRQAPGQ---QRKMVAG | ISD-AG---TT | NYGTSMRGRVTISRNSAK |
| A55 | VVLAALL | QGVQAQIQLVESGGGLVQSGGSLRLSCEVS | G--TIFSIYA | MAWYRQAPGK---QRDLVAA | ITT-TG---TT | DYADSVTGRFTISRDNAK |
| A56 | VVLAALL | QGVQAQEQFVETGGGLVQPGGSLTLSCSVY | G-GAVYHRSG | LGWYRQAPGK---ERAWVGR | IHS-G-G--GT | GYADFVKGRFTLSRPFGN |
| A57 | VVLAALL | QGVQAQEQLVESGGGLVQPGGSLRLSCAAS | G-FTIENYH- | VRYYRQAPGK---ECELVAG | IAV-GNA--WT | SYADSVKGRFTISRDSDN |
| A58 | VVLAALL | QGVRAQVQFVESGGGEVRTGESLRLSCLAS | G--GVTSLYS | LAWYRQTPGN---QRETVAV | IKS-G-G--ST | NYADSVKGRFTVSRDNTK |
| A59 | VVLXALX | QGVQGQVQFVESGGDLVQPGGSXRLSCEAS | G--IRIKLYP | MGWYRQAPGR---QRELVAR | VT--IRE--ST | NYTDSVKGRFTISRDDAK |
| A60 | VVLAALL | QGVQAQVQLVESGGGFVQAGGSLNLSCTAS | G--SNLRLYG | MGWFRQAPGS---ERELVAQ | ISW-IGG--AA | YYSTSVKGRFTLTRDYDQ |
| A61 | VVLAALL | QGVQAQVQLKESGGGYVQPGGSLRLSCAAS | G--STIKNYD | MGWFRQAPGK---EREFVAV | ISG-G-G--GD | YYSDSVKGRFWISRDDGQ |
| A08 | VVLAALL | QGVQTQLQLVESGGGLVQPGSSLLLSCSAS | G--STFRVYK | VGWFRTAPGK---EREKVSC | LS---AVE-TT | DYAAAVKGRFTTFRNKAE |
| A23 | VVLAALL | QGVQAQLHFVESGGGSVQPGGSLRLTCAAS | T--FTLNYYS | IAWFRRAPGK---EREGVSC | MS---GGG-VT | VYAESVKGRFTISRDSAK |
| A38 | VVLAALL | QGVQAQFQLVESGGGFVQPGGSLTLSCVGS | G--ISLDHRG | IGWFRQAPGK---EREGVSC | IN---SDDRTT | SYADSVNGRFTISKDRAK |
| A06
A51 |
VVLAALQ
VVLAALL |
QGVQAQLQLAESGGGLVQPGGSLRLSCVAS
QGVQAQMHLVESGGGLVQPGDSLNLSCTAS |
G--LTLDHHN
G--IPLRSHV |
ILWFRQAPGK---DREGVSC
IGWFRQVPGK---EREAVAC |
IK---MRGGSA
ID---GSGGTI |
KYADSVKGRFTVSRDNAE
NYAGSVLDRFSISRDDAK |
| A11 | VVLAALL | QGVRPQVRPVESGGGSVQPGEALRLSCTQP | K--VNLNNFA | IGWFRQAPGK---EREGVSC | I----GNRGTP | YYADFLEGRFTISRDNAK |
| A62 | VVLAALL | QGVQAQFQLVESGGGLVQPGGSLRLSCTAS | D--AAFEFYA | IGWFRQAPGK---EREGVSC | IS---PSRAFT | NYTDAVKGRFTISRDNSK |
| A43 | VVLAALL | QGVQAQLQLVESGGGQVQPGGSLRLSCATS | G--GTLDVYA | IGWFRQVPGK---DREGIAC | IS---GSGRSS | DYVDFVKGRFTISRDNAK |
| A47 | VVLAALL | QGVQAQLQFVESGGDSVQPGGSLRLSCVAS | G--LNFDVLA | MGWFRQAPGK---EREAVSC | IS---NRGGHT | EYVDSVKGRFTISRDNAK |
| A39 | VVLAALL | QGVQTQLQLVESGGGLVQPGGSLRLSCVVS | G--IKLDHYA | FGWFRQAPGK---EREAVGC | IG---SGGRTT | NYRDSVRGRATVSIDTGR |
| A45 | VVLAALL | QGVQAQLQLVESGGGLVQPGGSLRLSCTVS | G--FALDYYV | IGWFRQAPGR---EREILSC | IS---SGGSST | NYADSVKGRFTISRDNDQ |
| A03 | VVLAALL | QGVQPQVQLVESGGGLVQPGGSLRLSCVTS | G--RTLSYYV | IGWFRQAPGK---EREGVSS | IS---STDGST | YYSESVKGRFTISRDNAE |
| A12 | VVLAALL | QGVRAQVKLVESGGGFVDAGGSLTLSCASS | G--FVLEIFV | IGWFRQVPGK---EREGISC | IS---IRDGSA | YYEDSVKGRFTVSRDNAE |
| A63 | VVLAALL | QGVQPQ-QLKESGGGLVRPGGSLRLSCALS | --ERRLEDYA | IAWIRQAPGK---DHEAISC | IS---VGSRST | EYSNSVKGRFTVSRDDAR |
| A64 | VVLAALL | QGVQAQPQVAESGGGLVQPGGSLTLSCVVT | GTTSSLDYIP | VAWFRQVPGK---EREGISC | IGGVPHGEDHI | FYSTPVKGRFTSSRDDAK |
| A30 | VVLAALL | QGVQSQLQLVETGGGVVSPGGSLKLSCTHS | G--FPLERRM | ISWFRHRPGKNGDEREGLSC | IS-TIH--GGT | EYADSVEGRFTISRDIAK |
| A41 | VVLAALL | QVVQARVQLVESGGGLVQPGGSLRLSCATS | G--FTFANYA | LNWVRQPPGK---GLEWVSR | ----IHSDGDT | KYADSVKGRFTISRDIAN |
| A44 | VVLAALL | QGVQAEVQVAESGGGLVQPGGSLRLSCRAS | G--FTFSSYS | MGWARQIPGK---GLEWVSS | ----IYSDGST | YYTDSVKDRFIISRDNAK |
| A65 | VVLAALL | LGVQAEVQLRESGGGSVQAGGSLRLSCEAS | G--TTSRIDV | LAWYRQTPGN---QRVFVAS | IT---RDNGYT | KYADFVNGRFDISRDNAA |
| A10
A32 |
VVLAALL
VVLAALL |
QGVQAQVQLVESGGGLVQPGGSLRLSCVYS
QGVQAQLHVVESGGGLVQPGGSLRLSCAAS |
G--ILATGWP
G--FTLDSHH |
MSWVRQAPLK---GPEWLSD
IGWFRQAPGK---ERELVSC |
IN---DG--AT
TG---TTGDFP |
YYADSVKGRFTISRDDAK
HYADSVKGRFTISRDNAK |
| A66 | VVLAALL | QGVPAQLHVVESGGGLVQPGGSLRLSCKVS | G--LDLDYLT | LGWFRQAPGK---EREWVSC | VD---HSGDLE | VYGDSVRGRFAISRDNAK |
| A36 | VVLAALL | QGVQAQLQLVESGGGLVQPGGSLRLSCAAS | G--SSLDSYA | IGWFRQAPGK---EREGVSC | IN---SSGGTT | NYADSVKGRFTISRDNAK |
| A67 | VVLAALL | QGVQAQLQLVESGGGLVQPGGSLRLSCAAS | G--SSLDSYA | IGWFRQAPGK---EREGVSC | IN---SSGGTT | NYADSVKGRFTISRDNAK |
| A48 | VVLAALL | QGVQAQLQLVESGGGLVQPGGSLRLSCAGS | G--FTLDSYA | IGWFRQAPGK---EREGVSC | IS---SSGGST | NYADSVKGRFTISRDNAK |
| A68 | VVLAALL | QGVQARLHLVESGGGSVQPGGSLRLSCVAS | G--EPLENNA | VGWFRQSPGN---SREGISC | ISTLGSRGITD | DYAGSVKGRFTVSRNDAK |
| A69 | VVLAALL | QGVQAQVEPVESGGGLVQPGGSLRLSCTSH | I--EALYHYA | VGWFRQVPGR---KREWVAC | IS---SSGENV | DYHESVKGRFTISKDSTR |
| A14 | VVLAALL | QGVQAQLQPARAGGNLVQPGGSLRLFCGVS | E--RTLNGYD | IGWFRQAYGT---EREGISC | TS----RSGNT | VYADSVKGRFTVARDNAK |
| A17 | VVLAALL | QGVQAQLQLVESGGGLVQPGGSLRLSCVAS | G--SSLSYYH | IGWFRQAPGK---GREAVAC | IS---DSGGSI | TYADSVKGRFTISRDDAE |
| CLONE | FR3 | CDR3 | FR4 | HINGE | ||
| A02 | NTVYLQMNSLKPEDTSVYYC | G-DAPTC------------SDSVGDFGS | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A52 | NAVYLQMNSLKSEDTAVYYC | SVVEPNC------------SSGRKAFGS | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A53 | NAVYLQMNNLKPEDTAIYYC | AADAIYC------------RSP--DFGA | WNQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A07 | NILSLQMNGLKPEDTAMYYC | AAEGR-------------GWG-----PV | LGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A31 | -KLSLQLNNLKDEDTAMYYC | AAWDRSDY---------RGHGH----DF | LGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A54 | NTVWLDMNNLKPEDTAVYYC | NALERTYS---------GGDDYGR--DY | WGKGALVN-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A55 | NTVYLQMNSLKPEDTGVYYC | AADGLRLD---------ACVFPRRTYSY | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A56 | NTVFLQMNNLEPEDTAVYYC | NT-------------------WPMKAST | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A57 | KTVYLQMKSLQPEDTAVYHC | NV-------------------RVFSAPC | AGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A58 | NTMYLQMNNLTPEDTAVYFC | NFPAY------------GYGGQVVAQVP | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A59 | NMVYLQMTMMQPEDTAVYYC | NADLG--------------LPSMRPFAP | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A60 | KTTLLQMNKLSPEDTAVYFC | AAST---------------TPPIFTFNS | YGPGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A61
A08 |
NTVYLQMNNLKPEDTAVYYC
TTIYLQMNNLTSEDTGVYSC |
SIESDPFDA-------IGEMIRGKHRGS
AAYYGG------Y-HCLA----EEHYDH |
WGQGTQVT-VSS
WGQGTQVT-VSA |
-------------AHHSEDPS--SKCPKCPGPELLGGP
G------------AHHSEDPS--SKCPKCPGPELLGGP |
||
| A23 | NTMYLEMNSLEPEDTAEYYC | AADEEA------V-CSVATLKRRAKYDW | WGQGIQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A38 | NTVYLRMNNPKPEDTGVYRC | AAFTWI-----CS-SAYAWANYDMDH-- | WGRGTPVN-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A06 | KTVYLQMDSLQPDDTAVYTC | AAVEWR-----GS-ACPLWGN--MDS-- | WGKGTLVN-VST | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A51 | NTVLLQMNSLKIEDTAVYYC | AAELWN----LSD-GELYPCSPRMEY-- | WGKGILVA-VSS | -------------AHHSEDPS--SECPKCPGPELLGGP | ||
| A11 | NTVYLQMNDLKPEDTGVYSC | AADLGAGGCVLSP-AGTLSIARFLEV-- | MGPGTLVN-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A62 | NTVYLQMTSLTPEDTAVYYC | AADRGG----------PSWCNNGMDY-- | WGKGTLVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A43 | NTVFLQMNSLDSEDTATYYC | AATLSG------Y-SGLFWCVRPNSY-- | WGQGTQVAVVSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A47 | NTVYLQMDNLQVEDTAVYYC | AAP-----------TALRWQCNPAYFGS | WGQGTEVS-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A39 | NTVHLQMSSLELEDTGLYYC | AA-------VLSY-GSACVISRSDVYQH | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A45 | NMAYLEMTGLKPEDTAVYYC | AADQR----LTSI-ISTCVLDHA--YEF | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A03 | NTVYLQMNDLKSEDTAAYYC | AAADPWK-------ISXSTMTSQEPYEY | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A12 | NTVYLQMNNLKPEDTGVYTC | AAESFWV-------GPVQAMCNNP--HI | WGQGTQVT-VSA | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A63 | NMVYLDMNALKPEDTAVYRC | AADSGVR-------RHQLCQIDTKRYDY | WGLGTQVT-VPS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A64 | NTVYLHMNRLTPGDTAVYYC | SPAN-----------KGFCTLDANDYKY | WGQGTQVT-VSS | -------------AHHSEDPS--SKCPKCPGPELLGGP | ||
| A30
A41 |
RTVYLQMNDLETEDSGVYYC
STLYLQMNDLKTEDTGVYYC |
AVGGEP-------------CLYVNAMKY
VKPGS---------------------GE |
WGKGAEVI-VRS
RGEGTQVT-VSS |
-------------AHHSEDPS--SKCPKCPGPELLGGP
-------------AHHSEDPS--SKCPKCPGPELLGGP |
||
| A44 | SMVYLQMNSLKPEDTAVYYC | TTDLS-IHPFSDS-----PPLGSSQHHY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A65 | NTVSLQMNSLKPEDTGTYVC | NAHLGRIFPSRDH-----VPWDRAEDY- | WGVGIPVT-VSA | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A10 | NTLYLQMNSLKPEDTAVYYC | AQPRD---TQVDR-----NSWGR--YVN | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A32 | NTVYLQMNSLKPEDTAVYYC | A-ADSGSRSSWSL-----CPRGSVGYDY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A66 | NTVYLQMNRLEPKDQAVYYC | A-ADP---ARFTT-----CSPD--EYDY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A36 | NTVYLQMNSLKPEDTAVYYC | A-AAPGLTTFQTL-----CLMIGG--DY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A67 | NTVYLQMDSLKLEDTGIYVC | A-AGSGSTYYDCS-----GYETGWRIDK | WDQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPXCPAPELLGGP | ||
| A48 | NTVYLQMNSLKSEDTAVYYC | A-AALGMTTVQNM-----CLMWGSG-NY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A68 | NTVYLQMNNLKPEDTAVYFC | AAVYTGAGQLLPS-----LCLDENGYDY | WGQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELXXXX | ||
| A69 | NTAYLDIMNIEPEDTATYYC | G--AASDLWYSGL-----YCGP--DYDY | WGQGTRVA-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A14 | TATFLEMSDLKPEDTGTYFC | AALGGDVCVRFGRPGAYYCIANRCYDDY | WDQGTQVT-VSS | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||
| A17 | NTVHLQMTSLKAEDTAIYYC | APVTPG--YYGGS-------YSCIPDGV | WGQGTQVT-VSV | -EPKTPKPQPQPQPQPQPNPTTESKCPKCPAPELLGGP | ||