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

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • T0193 AT-rich DNA binding protein (ATBP), T. aquaticus
    • gi|4557113|gb|AAD22519.1|AF061257_1_1:211 (AF061257) AT-rich DNA-binding protein p25 [Thermus aquaticus]
    • gi|15900958|ref|NP_345562.1|_6:211 (NC_003028) conserved hypothetical protein [Streptococcus pneumoniae TIGR4]
    • gi|14972565|gb|AAK75202.1| (AE007410) conserved hypothetical protein [Streptococcus pneumoniae TIGR4]
    • gi|15903042|ref|NP_358592.1|_6:211 (NC_003098) Conserved hypothetical protein [Streptococcus pneumoniae R6]
    • gi|15458613|gb|AAK99802.1| (AE008472) Conserved hypothetical protein [Streptococcus pneumoniae R6]
    • gi|20807044|ref|NP_622215.1|_7:217 (NC_003869) AT-rich DNA-binding protein [Thermoanaerobacter tengcongensis]
    • gi|20515531|gb|AAM23819.1| (AE013024) AT-rich DNA-binding protein [Thermoanaerobacter tengcongensis]
    • gi|15613114|ref|NP_241417.1|_6:208 (NC_002570) DNA-binding protein [Bacillus halodurans]
    • gi|4514349|dbj|BAA75386.1| (AB013375) YdiH [Bacillus halodurans]
    • gi|10173164|dbj|BAB04270.1| (AP001508) DNA-binding protein [Bacillus halodurans]
    • gi|15675100|ref|NP_269274.1|_5:210 (NC_002737) conserved hypothetical protein [Streptococcus pyogenes] [Streptococcus pyogenes M1 GAS]
    • gi|19746069|ref|NP_607205.1| (NC_003485) conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
    • gi|21910315|ref|NP_664583.1| (NC_004070) conserved hypothetical protein [Streptococcus pyogenes MGAS315]
    • gi|13622257|gb|AAK33995.1| (AE006554) conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
    • gi|19748239|gb|AAL97704.1| (AE010034) conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
    • gi|21904511|gb|AAM79386.1| (AE014152) conserved hypothetical protein [Streptococcus pyogenes MGAS315]
    • gi|16801243|ref|NP_471511.1|_6:210 (NC_003212) similar to a putative DNA binding proteins [Listeria innocua]
    • gi|16804111|ref|NP_465596.1| (NC_003210) similar to a putative DNA binding proteins [Listeria monocytogenes EGD-e]
    • gi|16411542|emb|CAD00150.1| (AL591982) similar to a putative DNA binding proteins [Listeria monocytogenes]
    • gi|16414691|emb|CAC97407.1| (AL596171) similar to a putative DNA binding proteins [Listeria innocua]
    • gi|15895970|ref|NP_349319.1|_5:207 (NC_003030) AT-rich DNA-binding protein [Clostridium acetobutylicum]
    • gi|15025747|gb|AAK80659.1|AE007769_1 (AE007769) AT-rich DNA-binding protein [Clostridium acetobutylicum]
    • gi|15925036|ref|NP_372570.1|_5:208 (NC_002758) conserved hypothetical protein [Staphylococcus aureus subsp. aureus Mu50]
    • gi|15927621|ref|NP_375154.1| (NC_002745) conserved hypothetical protein [Staphylococcus aureus subsp. aureus N315]
    • gi|21283699|ref|NP_646787.1| (NC_003923) conserved hypothetical protein [Staphylococcus aureus subsp. aureus MW2]
    • gi|13701840|dbj|BAB43133.1| (AP003135) conserved hypothetical protein [Staphylococcus aureus subsp. aureus N315]
    • gi|14247819|dbj|BAB58208.1| (AP003364) conserved hypothetical protein [Staphylococcus aureus subsp. aureus Mu50]
    • gi|21205141|dbj|BAB95835.1| (AP004829) conserved hypothetical protein [Staphylococcus aureus subsp. aureus MW2]
    • gi|21398209|ref|NP_654194.1|_4:206 (NC_003995) Octopine_DH_N, NAD/NADP octopine/nopaline dehydrogenase, NAD binding domain [Bacillus anthracis A2012] [Bacillus anthracis str. A2012]
    • gi|18311284|ref|NP_563218.1|_5:209 (NC_003366) conserved hypothetical protein [Clostridium perfringens]
    • gi|18145967|dbj|BAB82008.1| (AP003193) conserved hypothetical protein [Clostridium perfringens str. 13]
    • gi|16077664|ref|NP_388478.1|_6:212 (NC_000964) ydiH [Bacillus subtilis]
    • gi|7474965|pir||A69787 hypothetical protein ydiH - Bacillus subtilis
    • gi|1945113|dbj|BAA19721.1| (D88802) ydiH [Bacillus subtilis]
    • gi|2632910|emb|CAB12416.1| (Z99107) ydiH [Bacillus subtilis]
    • gi|21221751|ref|NP_627530.1|_14:213 (NC_003888) conserved hypothetical protein [Streptomyces coelicolor A3(2)]
    • gi|7480641|pir||T36268 probable DNA-binding protein - Streptomyces coelicolor
    • gi|5123665|emb|CAB45354.1| (AL079345) conserved hypothetical protein [Streptomyces coelicolor A3(2)]
    • gi|15805963|ref|NP_294663.1|_5:227 (NC_001263) conserved hypothetical protein [Deinococcus radiodurans]
    • gi|7471300|pir||A75458 conserved hypothetical protein - Deinococcus radiodurans (strain R1)
    • gi|6458662|gb|AAF10515.1|AE001946_7 (AE001946) conserved hypothetical protein [Deinococcus radiodurans]
    • gi|15642943|ref|NP_227984.1|_3:202 (NC_000853) conserved hypothetical protein [Thermotoga maritima]
    • gi|7462325|pir||G72408 conserved hypothetical protein - Thermotoga maritima (strain MSB8)
    • gi|4980664|gb|AAD35262.1|AE001702_2 (AE001702) conserved hypothetical protein [Thermotoga maritima]
    • gi|15217135|gb|AAK92526.1|AF401045_2_6:204 (AF401045) LaaK [Lactobacillus sakei]
    • gi|15644178|ref|NP_229227.1|_5:202 (NC_000853) conserved hypothetical protein [Thermotoga maritima]
    • gi|7462335|pir||H72256 conserved hypothetical protein - Thermotoga maritima (strain MSB8)
    • gi|4981991|gb|AAD36497.1|AE001794_13 (AE001794) conserved hypothetical protein [Thermotoga maritima]
    • gi|15673042|ref|NP_267216.1|_8:176 (NC_002662) HYPOTHETICAL PROTEIN [Lactococcus lactis subsp. lactis]
    • gi|12724014|gb|AAK05158.1|AE006339_1 (AE006339) HYPOTHETICAL PROTEIN [Lactococcus lactis subsp. lactis]
    • gi|18253153|dbj|BAB83964.1|_2:137 (AB066353) conserved hypothetical protein [Streptococcus suis] 
              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVP
   2 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVP
   3 FAIPKATAKRLSLYYRIFKRFHAEKIERANSKQIAEAIGIDSATVRRDFSYFGELGRRGFGYDVK
   4 FAIPKATAKRLSLYYRIFKRFHAEKIERANSKQIAEAIGIDSATVRRDFSYFGELGRRGFGYDVK
   5 --VSMAVIRRLPRYHRCLEELLKNDIKRISSKELSERMGVTASQIRQDLNNFGGFGQQGYGYNVE
   6 TKIPQATAKRLPLYYRFLENLHASGKQRVSSSELSEAVKVDSATIRRDFSYFGALGKKGYGYNVN
   7 KSIPKATAKRLSLYYRIFKRFHADQVEKASSKQIADAMGIDSATVRRDFSYFGELGRRGFGYDVT
   8 TKIPQATAKRLPLYHRYLKYLDESGKERVSSAELSEAVKVDSATIRRDFSYFGALGKKGYGYNVS
   9 KNISMAVIRRLPKYHRYLEELLKSDVDRISSKELSEKIGFTASQIRQDLNCFGDFGQQGYGYNVK
  10 VKIPRATLKRLPLYYRFVSSLKSKGIDRVNSKAISDALQIDSATIRRDFSYFGELGKKGYGYNID
  11 QKIPQATAKRLPLYYRFIQNLSLSGKQRVSSAELSEAVKVDSATIRRDFSYFGALGKKGYGYNVN
  12 KGISMAVIKRLPKYHRYLQELMENDVDRISSKELSEKIGFTASQIRQDLNCFGDFGQQGYGYNVK
  13 SKIPQATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGALGKKGYGYNVD
  14 RGIPEATVARLPLYLRALTALSERSVPTVSSEELAAAAGVNSAKLRKDFSYLGSYGTRGVGYDVE
  15 ADIPTATVGRVVTYIRVLEELEAQNVLRASSGELARRAGVTPFQVRKDLTYFGRFGTRGIGYTVA
  16 EKIPKPVSKRLVSYYMCLERLLDEGVEVVSSEELARRLDLKASQIRKDLSYFGEFGKRGVGYNVE
  17 HDLPEAVAKRIPIYYRYFKLLETDGIERIKSEQLAKLVAIPSATIRRDFSYIGDLGRSGYGYEVS
  18 IHLPRSTFERLKMYRKVLE---ATKKPYISSDEIARFLEINPDLVRKDFSYLNCQGKPRVGYDVE
  19 KSLPKATAKRLPQYYRLFKSLVEENVTRTNSQLISEKIGVDAATIRRDFSLFGELGRRGYGYETK
  20 -----------------------------------------------------------------


         70        80        90       100        110           120     
         |         |         |         |          |             |     
   1 VLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGF.GESFELRGFFDVD..PE..KVGRP.VRG
   2 VLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGF.GESFELRGFFDVD..PE..KVGRP.VRG
   3 KLMTFFADLLNDNSITNVMLVGIGNMGHALLHYRFHeRNKMKIIMAFDLDdhPE..VGTQT.PDG
   4 KLMTFFADLLNDNSITNVMLVGIGNMGHALLHYRFHeRNKMKIIMAFDLDdhPE..VGTQT.PDG
   5 ELYNNLTKILGLDKTYNTIIIGAGNLGQAIANYTRFeKSGFNLKGIFDIN..PR..LFGLK.IRD
   6 YLLTFFRKTLHQDELTKVMLIGVGNLGTALLNYNFSkNNHTQIVMAFDVD..RE..KIGNT.VSG
   7 KLMNFFADLLNDHSTTNVILVGCGNIGRALLHYRFHdRNKMQIAMGFDTD..DNalVGTKT.ADN
   8 YILDFFSKTLSQDKQTNVALIGVGNLGTALLHYNFMkNNNIKIVAAFDVD..PA..KVGSV.QQD
   9 DLSREVDNILGLTKMYNTIIIGAGNIGQAIANYINFqKMGFDLKAIFDIN..PK..LIGLK.IQD
  10 SLLDFFKSELSESDMIKIAIVGVGNLGKALLTYNFSiHDDMTITEAFDVK..ED..VIGQK.IGN
  11 YLLSFFRETLDQDDITRVALIGVGNLGTAFLHYNFTkNNNTKIEMAFDVS..EE..KVGTE.IGG
  12 ELYNNIGSILGLTRDYNTVIIGAGNIGQAIANYNSFnRLGFKLKGIFDAN..PR..MFGIK.IRD
  13 YLLSFFRKTLDQDEMTDVILIGVGNLGTAFLHYNFTkNNNTKISMAFDIN..ES..KIGTE.VGG
  14 YLVYQISRELGLTQDWPVVIVGIGNLGAALANYGGFaSRGFRVAALIDAD..PG..MAGKP.VAG
  15 VLRRELLRALGLDQTWNVVIVGMGRLGHAIANYPGAsDYQFQNVGLFDVA..PD..VVGRE.VRG
  16 HLYDAIGEILGVKKEWKLVVVGAGNIGRAVANYTVMkEKGFRIIGIFDSD..PS..KIGKEaAPG
  17 HLIQIFSAVLKADILTKMAVIGVGNLGRALIENNFRrNDNLQITCAFDTN..PA..LVGQT.LNG
  18 ELRKELDDLFGVNNTTNMIIVGANDLARALLSLDFS.KAGVKVVAVFDTE..RE..NVGKF.IGE
  19 VLRDFFGELLGQDQETHIALIGVGNLGRALLHYQFQdRNKMRITQAYDIS..GNplVGTQT.DDG
  20 ---DFFADILNDTSITNVMLVGVGNMGRALLHYRFHeRNKMKIVMAFEAD..DNp.AVGTT.DEN


         130             140       150       160       170       180   
          |               |         |         |         |         |   
   1 GVIEHVDLLPQRV.....PG.RIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPK...
   2 GVIEHVDLLPQRV.....PG.RIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPK...
   3 IPIYGISQIKDKI.....KDaDVKTAILTVPSVKSQEVANLLVDAGVKGILSFSPVHLHLPK...
   4 IPIYGISQIKDKI.....KDtDVKTAILTVPSVKSQEVANLLVDAGVKGILSFSPVHLHLPK...
   5 VEVMDVEKVEEFI.....ANnHIDIAILCIPKDNAQYTADRLVKAGIKAIWNFSPIDLKVPD...
   6 VKIENLDNLENKI.....TS.DVSVAILTVPAAVAQKTADRLVNAGVKGILNFTPARIAVPE...
   7 IPVHGISSVKERI.....ANtDIETAILTVPSIHAQEVTDQLIEAGIKGILSFAPVHLQVPK...
   8 IPIYHLNDMEEIV.....REnGVEVVILTVPADEAQVTVDRLIEADVKGILNFTPARISVPK...
   9 VEVRDVDNIDGFL.....QKnKIDIGIICVPSKNAQKVCDIIVKNNVNGIWNFAPVDLMTPE...
  10 VIVKDNDELITTL.....KKeEIDVVILTTPERVAQKVADELVQAGVKGILNFTPGRINTPS...
  11 IPVYHLDELEERL.....SS.DIQVAILTVPATVAQSVADRLAETNVHGILNFTPARLNVSD...
  12 VEIQDVEKLKDFV.....KEnDIEIGIICVPRTNAQKVCNDLVEGGIKGIWNFAPIDLEVPK...
  13 VPVYNLDDLEQHV.....KDe--SVAILTVPAVAAQSITDRLVALGIKGILNFTPARLNVPE...
  14 IPVQHTDELEKII.....QDdGVSIGVIATPAGAAQQVCDRLVAAGVTSILNFAPTVLNVPE...
  15 LTIQHMSQLGPFVas6gtPR.QVDMGLLTVPAEHAQAAAQALVAAGVGGILNFAPVVLQTQDl13
  16 LTVSDVSELEKFV.....EEhGVEIGVIAVPAEHAQEIAERLEKAGIKGILNFAPVKIKV--...
  17 VPIYAIDQLATVI.....PAaGITTAISTVPSEASQRSAEQLIDAGITSILNFAPTRLQVPR...
  18 FAVRELDVLERVI.....RRfDAEIAALCVSKDRAQATAEFLIEKGIKAVWNFTGVHLDLPE...
  19 IPIYNISDLEKNV.....KKsDIKTAILSVRKENAQEVVDTLVKAGI---------------...
  20 IPIHAISEIKERI.....SEaNSQTAILTVPSVKAQEVTDILVEAGVKGILSFSPVNLSVPK...


               190       200       210 
                |         |         | 
   1 ..EVAVENVDFLAGLTRLSFAILNPKWREEMMG
   2 ..EVAVENVDFLAGLTRLSFAILNPKWREEMMG
   3 ..DVVVQYVDLTSELQTLLYFMRK---------
   4 ..DVVVQYVDLTSELQTLLYFMRK---------
   5 ..DVILENVHLSDSLFTISYRLNEEELFKKLKG
   6 ..HVRVHHIDLSVELQALIYFLKH---------
   7 ..GVIVQSVDLTSELQTLLYFMNQ---------
   8 ..QVRVHHIDLTTELQTLIYFLENY--------
   9 ..NVIVENVHLSESLLTLSCLLQ----------
  10 ..DVQVHQIDLGIELQSLLFFMKN---------
  11 ..NIRIHHIDLAVELQTLVYFLKN---------
  12 ..DIRVENVHLSESMMTLVYLLNHN--------
  13 ..HIRIHHIDLAVELQSLVYFLKHYSVLE----
  14 ..GVDVRKVDLSIELQILAF-------------
  15 rrEVTVENVDFLAGMKRLAFYMLGP--------
  16 ..SVPVENIDITASLRVLTFE------------
  17 ..HINVRYLDLTAELQTLL--------------
  18 ..GVIVVEEDLTQSLLTIKHLL-----------
  19 ..-------------------------------
  20 ..DVVVQYVDLTSELQTLLYFMR----------