(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • T0357 NESG:GR101, Archaeoglobus fulgidus, 141 res
              10        20        30             40        50        60
              |         |         |              |         |         |
   1 MVKFACRAITRGRAEGEALVTKEYISFLGGIDKETG.....IVKEDCEIKGESVAGRILVFPGGK
   2 -IKLKGRTISRGCAKGEVLLSRDPISFLGNVDPKTGv....VIEENHALEGKSIQGKVLVFPHGK
   3 -IKLKGRTISRGCAEGEILISRDPISFLGSVDPKTGi....VVEEKHSLAGKSIKGKVLVFPHGK
   4 -IKFKGRTISRGCAEGEVLISRDPISFLGSVDPRTGi....VVEEKHSLAGKSIKGKVLVFPHGK
   5 -IVLRGRKVVGGCVEGEALVTRDRISGWGGIDPRTGt....IIETRHELRGQSFANKVLVFPGAK
   6 -IVLRGRKVVGGRIEGEALVTRDRISGWGGIDPRTGt....IIETRHELRGQSFANKVLVFPGAK
   7 --KIECRTIARGVAEGEVLLSEDALSFLGNVDPKTGv....VVDPGHAIYGECIRDKILVFPHGK
   8 --KLKGRKIVGGKAEGEVIVSRKPLSFLGGVDPETGi....VTDAESDIRGQSIAGKILVFPRGK
   9 -IVLRGRKVVGGCVEGEALVTRDRISGWGGIDPRTGt....IIETRHELRGRSFANKVLVFPGAK
  10 --KFACRAITRGRAEGEALVTKEYISFLGGIDKETG.....IVKEDCEIKGESVAGRILVFPGGK
  11 --KLKGRGIVKGVAEGELVVSRKPLSFLGGVDPNTGi....ITDPESDIQGEKITGKILAFPRGK
  12 ---IKCRIISKGKDSGNALVTKDPISFLGGVDPKTGi....VIDKKHELYNECITDKILVIPSGK
  13 ---MTASSILPGIADGPILFSDEPLSFWGGVDPATGr....IIDVHHPLQGRSIAGRVLMMPSTR
  14 --KLKGKGIGKVVVEGEVIVSRKPLSFLGGVDPETGt....ITDPESDIKGESITGKILVFPKGK
  15 ---YHGHCLVDSAATGKLLYANVGLSFWAGVDSQTGe....IIDRHHPLHGQSVNGRILAIPCSR
  16 --KLKGKGVGKNIVEGEVIVSKKPLSFLGGVDPETGi....IIDPDSDIKGESIEGKILVFPKGR
  17 ---LTGDTLVPGSACARPFVLDKPLSFWGGYDSGAGr....IVDRGHPQAGASLAGKVMVMPHAK
  18 ---LMGDTLVPGSACARPFVLDKPLSFWGGYDSGAGr....IVDRGHPQAGASLAGKVMVMPHAK
  19 -----ARSILQGSAEGPVIATGEALSFWGGVDPATGc....VIDVHHPLHGVPLTGSILMMPSSR
  20 --EIKCHRVSGGCAEGPALVTRERISFLGNVDPETGv....VVDPAHELYGRSIAGVVLIFPGGK
  21 -----GDTLVPGSACARPFVLDKPLSFWGGYDSGAGr....IVDRGHPQAGASLAGKVMVMPHAK
  22 ---WTGTAYVQGRASAKLLASNLELSFWGGVDPQTSe....VIDRHHTLSGKHLQNTILAIPGGR
  23 -RQLTGDTLVPGSACANTVVLDKPLSFWGGYDSGVGr....IVDCGHPQAGASLAGRIMVMPHAK
  24 ---IVPRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  25 ---IVPRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  26 ---IVPRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  27 ---LTGDTLVPGSACARPFVLDKPLSFWGGYDSGAGk....IVDRGHPQAGASLAGKVMVMPHAK
  28 ---IVPRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  29 ---IVSRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  30 ---IVPRTLVAGSASGELLYAPTGLSFWGGVDPRSAe....VIDRHHPLSGRHLHGRLLAIPGGR
  31 ---VDCRVISRGKGRGPVLVSTEPLSFLGGVDPGTGr....VIDQKHPLHGRSIRGKVLLIPGGK
  32 -----ARSILAGAAEGKVIATTEALSFWGGVDPATGk....VIDVHHPLHGICLTGGVLFMPTSR
  33 --EFRGQCLIKGAASAELQFCPVEISFWGGVNPETGq....VVDRHHPLCGQSIAGRVLAIPCGR
  34 --TFHCKTWVTGQTQGKAVIARERISFWGGFDPQTGr....IVDPYSSLRGRDISDCVLILLSSK
  35 -------CIVAAAASGPVLVCDEGLSFWGGVDPETGr....VIDAHHPQHGAALAGAVVMMPTSR
  36 -----PVVDVEEPVEAEVLVSSQRLSFLGGVDPKTGe....VVDPSHELCGEKLTGRVLVLPGGR
  37 --IIQGRGISRGIGKGPLLIGPDPISFLSGVDPETGi....VLEPGHPLEGKDITGSVLAFEYGK
  38 --------IVAAEVQGPILLCDEGLSVWGGVDPLSGr....IIDAHHPQQGQSLAGHVVMMPTSR
  39 --IFRGIPYVTGAASATLLAADLELSFWGGVDPRTGe....IIDRFHPLSGRFMKDTILAIPGGR
  40 --KIYGKAIVHGAATGEILYSKVPLSFWGGVEQTTGd....IIDHHHPLFGENIKDRVLVLPSTR
  41 ------DTLVAGRVCADTIVLDQPLSFWGGYDSAAGr....IVDRGHPQAGASLAGRILVMPHAK
  42 --ELKGRSISKGIIEGIAIVSKKPFSFLGGVDEEGN.....IIDKDSDLYGQSLKGKIFVFPYGR
  43 -----GTFQLAGEADGLALVFSQPLSFWGGIDAETGd....IIDHSHPGLGQNVAGRILVMPSGR
  44 -----------GQTQGKAVIARERISFWGGFDPQTGr....IVDPYSSLRGRDISDCVLILLSSK
  45 --ELNGRIISKGVVEGEAIISKSPISFLGGVNEEGI.....VTDKENELFGKSIANKIFVFPSGK
  46 ---LRALRSLPDKVVGEALVSNDAISMRYDVDASTGk....VVRPSHDLYGQSISGKVLIFKNTK
  47 ---RKGTIVVAGRADGTALVLGEPLSFWGGIDVETGt....IIDHSHPSLGARVTGRILVMPGGR
  48 ---------AAGHARGAILAL-EPLSFWGGYDAALGk....IIEKSHPAHGQSLAGKIMVMPRAK
  49 -IILKGITKVEGYAEGEALVTSSFLSHLVNAVNSDGv....IRIFGHPLVGQSYAGKIVVYDTDK
  50 ---YRSRPIVGGEAEGPAVVI-DSLSFYGEVDPETG.....VTS-----GGKPLAGRVAAIRRSR
  51 -----VDRAWGPVVEGQALVMREGFSPRYDLDRWSGv....ISRIGHSAEGESIKDRILVIPTAK
  52 ------LVKGRGRVRAEVVKITSPVSLLGDLDPEAG.....------KLAGVDVVGKIAALPYVK
  53 -KTFKGRVIVPGTVSAEALVSSQGFNTLASFQKALMfg8hcSDQNNLDLYKKEIAGKALCLPQTI


              70         80        90       100       110       120    
              |          |         |         |         |         |    
   1 GSTVGSYVLLN.LRKNGVAPKAIINKKTETIIAVGAAMAEIPLVEVRDEKFFEAVKTGDRVVVNA
   2 GSTVGSYVMYQ.LKKNGTAPAAIINLETEPIVAVGAIISEIPLVDMLEKNPYEVLNNGDLVLVNG
   3 GSTVGSYVMYQ.LKKNGAAPVAIINLETEPIVAVGAIISEIPLVDMLEKSPYESLKDGDVVQVNG
   4 GSTVGSYVMYQ.LKKNEAAPAAIINLETEPIVAVGAIISEIPLVDMLEKDPYEFLKDGDTVLVNG
   5 GSSGWSSQFHI.ARIAGTAPAAMLFNEMTTKIALGAVVSHAPSLTDFDVDPLDVIETGDWVRVDA
   6 GSSGWSSQFHI.ARIAGTAPAAMLFNEMTTKIALGAVVSHAPSLTDFDIDPLDVIETGDWVRVDA
   7 GSTVGSYVIYQ.LKKNNVSPAAMINIDSEPIVAVGAIISDIPLVDRLDKDPFTIFKNGDRVKVDS
   8 GSTVGSYVIYA.LKKNNKAPKAIIVGEAETIVATGAIISDIPMVDGVD---VSKLKTGMKVRVDA
   9 GSSGWSSQFHI.ARIAGTAPAAMLFNEMTTKIALGAVVSHAPSLTDFDIDPLDVIETGDWVRVDA
  10 GSTVGSYVLLN.LRKNGVAPKAIINKKTETIIAVGAAMAEIPLVEVRDEKFFEAVKTGDRVVVNA
  11 GSTVGSYVIYA.LAKKGTGPKAIIVEEAEAIVAVGAIIAGIPLVTGID---ISKLKSGMKVRVDG
  12 GSTVGSYVIYQ.MAKNNTAPRAIICQKAEPIIAIGAIISKIPMVDNPDVDIINTINTNDEITVDA
  13 GSCTGSGVLLD.LVLSGRGPAALVFSEPEDVVTLGALIAAEMFGKALPVLRLSPSAFDVLSGQAS
  14 GSTVGSYILYA.LSKNGKGPKAIIVEEAEPIVTAGAIISGIPLITNVD---ISKLKTGMRVRINP
  15 GSCTGSIVLIE.LLLNQCAPAGLIFQQPEQIITLGVVVAKTLLGLSIPVLVLKPAEFHSLKDYRY
  16 GSTVGSYVIYA.LSRNGKAPKAIIVEEAEPIVTVGAIISGIPLIAGVD---ISKLRTGMKVRINP
  17 GSSSSSSVLAE.AVRNGTGPVGIVLKERDLIISIGAIVAAELYAIAVPVVCVSDEVYDAIVAATG
  18 GSSSSSSVLAE.AVRNGTGPVGIVLKERDLIISIGAIVAAELYAIAVPVVCVSDEVYDAIVAATG
  19 GSCTGSGVLLD.LVLTGRGPAALVFSEPEDVLTLGALIASEMFGKPLPVLRLAPEAFAALARAKT
  20 GSTVGSYVIYQ.LRKRGMAPAAMINLKSEPIVAVGAIISDIPLVDRVPEWILDV-KDGTRVV---
  21 GSSSSSSVLAE.AVRNGTGPVGIVLKERDLIISIGAIVAAELYAIAVPVVCVSDVVYDAIVAATG
  22 GSCTGSGIMLE.LLLNGKAPEAIIFERREDILTLGVMIAEEVFQQSIPVLVLKKEDFRQLLKLDG
  23 GSSSSSSVLAE.AVRNGTGPVGIVLKERDLIISIGAIVAAELYAIAVPVVRVTDDVYDAIVAATG
  24 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  25 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  26 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  27 GSSSSSSVLAE.AVRNGTGPVAIVLKERDLIISIGAIVAAELYAIAVPVVCVTDDVYDAIVAATG
  28 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  29 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  30 GSCTGSSVLLE.LILGGRAPAAILLREPDEILALGAIVAEELFGRSLPIACLGE-----------
  31 GSTVGSYVIFQ.MAKNETAPAAIICLNAEPIIATGAIMAGIPMVDRPSEDLLGLLEDSMEVEVDA
  32 GSCTGSGVLLD.LILTGRAPSALVFCEAEDVLTLGALVAAEMFDKALPVIRLDAETFSRFSRAAH
  33 GSCSGSTVMLK.LLLNGCAPAALIFEKPEQILTLGVLVGKVLLDCPIPVVVLSSSDFSKICN---
  34 GSSGTSGMLSL.ATRAGHAPAAMIQVEMDPVTVMGCLVNNIPLLQATGFDPFEQIQDGDLVRIDG
  35 GSCSGSGVLLA.LALNGHAPAALVFREGEDVLTLGALVAAWMYDRPVAVLRLSAAEYAALAMEPS
  36 GSTVGSYVLME.MADRGTAPAGIVVREAEPILVVGCVLGDIPLFHRPERDLVEELSTGDVVK---
  37 GSTVGSYILYA.LSRNGHAPAAIINQEAETIIVVGAIMGKIPMIDRIK-TPLTSLPSGTIVEVDG
  38 GSCTGSGVLLG.LAFAGTAPKALVFREGEDILTLGALVATRLFERPIAVLRLSAAEYDRLAQQSH
  39 GSCGGSVIMME.LILNGLGPKALIFERREEIITLGVMVAEELFDKTAAVVTLNPEDFCEALGWDG
  40 GSCSGSLVLIE.LLVNRVAPTALVFWDSEAIVTTGVIVARTLLGLSLPVYRVSQGQFEDIE----
  41 GSSSSSSVLAE.AVRNGTGPAGIVMKERDLIISIGAIVAAELYAIAVPVVCVTERDYRAIVAAS-
  42 GSTVGSYVIYG.LAKRGIL-KGIVNKECEPIVATGAILGGIPLVDKID---IEEIKTGDRIVVDG
  43 GSSSSSSVLAE.AIRRGTAPAGILLERPDPILAVGAIVAEFLYDIHMPLVVCD------------
  44 GSSGTSGMLSL.ATRAGHAPAAMIQVEMDPVTVMGCLVNNIPLLQASGFDPFEQIQDGDLVRIDG
  45 GSTVGSYVIYG.LAKRGLL-KGMVNFESEPIVATGAILGKIPLVDKVN---IDEIKDGDIVVVDG
  46 GGVATGWALLN.LKSRGTAPIALVCDTTNPVFVQGAALAGLPIMDGFRESPRSAVRTGDVVELDG
  47 GSSSSASVFAE.SIRRGTGPLGVLLARADPILTVGAMVAASLYGRDCPIVVCDIAGIG-------
  48 GSSSSSSVLAE.AIRNGTGPSGIVLRERDLIISIGVIVANELYGVSVPLVVVDDDVFDTLYRCTQ
  49 FSTGGAWGLYFkAKVTNSAPKALICRTVHPISIGGAIDAGIPAVDSFDVDPWTVIQTGDYVKITA
  50 GSTVGSYVIYA.LKENGVAPLAILMERAEPIVIAGCVLAGIPLYDGLPPEFFERVRDGYRVRVHS
  51 GGVAGGWAFYD.LLHKGIAPKALVFGKLNPVMVQGAVLAGMPIMEGFDARLLQAIASGAALRLDP
  52 GSTVGPYVLWG.AARRGKAPLAIVAQKPDLMLISACVLAGIPLFQG-------------------
  53 GSTTGGMVIFC.AASMGRQPACMLFSEPIDSLAAAGVILAANFTD--------------------


         130       140 
          |         | 
   1 DEGYVELIELEHHHHHH
   2 SKGYIELFKQET-----
   3 SEGYIELIKPKG-----
   4 SEGYIELLKQGEG----
   5 ERGVVEVLK--------
   6 ERGVVEVLK--------
   7 TSGFVEL----------
   8 DSGEVEILE--------
   9 DRGVVEVLK--------
  10 DEGYVEL----------
  11 ERGEVEIIA--------
  12 DN---------------
  13 ARIGLDR----------
  14 QEGEVEIL---------
  15 AAITGPTLQTGEDP---
  16 RTGEVE-----------
  17 D----------------
  18 D----------------
  19 ARIGDRAIE--------
  20 -----------------
  21 D----------------
  22 QIIYV------------
  23 E----------------
  24 -----------------
  25 -----------------
  26 -----------------
  27 -----------------
  28 -----------------
  29 -----------------
  30 -----------------
  31 DEG--------------
  32 VSIDQNT----------
  33 -----------------
  34 ENGTIT-----------
  35 AEVTPE-----------
  36 -----------------
  37 TAGTLTI----------
  38 ATITATHLRAG------
  39 KTVH-------------
  40 -----------------
  41 -----------------
  42 NTGVVKI----------
  43 -----------------
  44 ENGTIT-----------
  45 NTGTVK-----------
  46 ISGELKVLRR-------
  47 -----------------
  48 -----------------
  49 PKAGDEGIIKIYPKD--
  50 -----------------
  51 A----------------
  52 -----------------
  53 -----------------