(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)
- R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
- K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
- A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
Sequence numbers correspond to the following labels:
-
- T0187 TM1585, T. maritima
-
- gi|15644333|ref|NP_229385.1|_301:416 (NC_000853) glycerate kinase, putative [Thermotoga maritima]
- gi|7462843|pir||A72236 hypothetical protein TM1585 - Thermotoga maritima (strain MSB8)
- gi|4982155|gb|AAD36652.1|AE001803_5 (AE001803) glycerate kinase, putative [Thermotoga maritima]
-
- gi|16119561|ref|NP_396267.1|_305:420 (NC_003064) AGR_pAT_bx66p [Agrobacterium tumefaciens] [Agrobacterium tumefaciens str. C58 (Cereon)]
- gi|17938918|ref|NP_535706.1| (NC_003306) hydroxypyruvate reductase [Agrobacterium tumefaciens str. C58 (Dupont)] [Agrobacterium tumefaciens str. C58 (U. Washington)]
- gi|15162117|gb|AAK90708.1| (AE007902) AGR_pAT_bx66p [Agrobacterium tumefaciens str. C58 (Cereon)]
- gi|17743779|gb|AAL46022.1| (AE008955) hydroxypyruvate reductase [Agrobacterium tumefaciens str. C58 (U. Washington)]
-
- gi|17549668|ref|NP_523008.1|_324:439 (NC_003296) PROBABLE HYDROXYPYRUVATE REDUCTASE OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum]
- gi|17431922|emb|CAD18600.1| (AL646084) PROBABLE HYDROXYPYRUVATE REDUCTASE OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum]
-
- gi|17936943|ref|NP_533732.1|_305:422 (NC_003305) hydroxypyruvate reductase [Agrobacterium tumefaciens str. C58 (U. Washington)]
- gi|17741611|gb|AAL44048.1| (AE009253) hydroxypyruvate reductase [Agrobacterium tumefaciens str. C58 (U. Washington)]
-
- gi|15891700|ref|NP_357372.1|_308:425 (NC_003063) AGR_L_3166p [Agrobacterium tumefaciens] [Agrobacterium tumefaciens str. C58 (Cereon)]
- gi|15160156|gb|AAK90157.1| (AE008360) AGR_L_3166p [Agrobacterium tumefaciens str. C58 (Cereon)]
-
- gi|15596696|ref|NP_250190.1|_305:419 (NC_002516) conserved hypothetical protein [Pseudomonas aeruginosa]
- gi|11347789|pir||E83459 conserved hypothetical protein PA1499 [imported] - Pseudomonas aeruginosa (strain PAO1)
- gi|9947454|gb|AAG04888.1|AE004578_10 (AE004578) conserved hypothetical protein [Pseudomonas aeruginosa]
-
- gi|13474290|ref|NP_105858.1|_305:420 (NC_002678) hypothetical protein [Mesorhizobium loti]
- gi|14025042|dbj|BAB51644.1| (AP003005) hypothetical protein [Mesorhizobium loti]
-
- gi|16265133|ref|NP_437925.1|_306:421 (NC_003078) putative hydroxypyruvate reductase protein [Sinorhizobium meliloti]
- gi|15141272|emb|CAC49785.1| (AL603646) putative hydroxypyruvate reductase protein [Sinorhizobium meliloti]
-
- gi|17987853|ref|NP_540487.1|_285:401 (NC_003317) PUTATIVE HYDROXYPYRUVATE REDUCTASE [Brucella melitensis]
- gi|17983583|gb|AAL52751.1| (AE009592) PUTATIVE HYDROXYPYRUVATE REDUCTASE [Brucella melitensis]
-
- gi|21314996|gb|AAH30732.1|_272:393 (BC030732) Unknown (protein for MGC:37913) [Mus musculus]
-
- gi|15967047|ref|NP_387400.1|_337:454 (NC_003047) PUTATIVE HYDROXYPYRUVATE REDUCTASE PROTEIN [Sinorhizobium meliloti]
- gi|15076320|emb|CAC47873.1| (AL591793) PUTATIVE HYDROXYPYRUVATE REDUCTASE PROTEIN [Sinorhizobium meliloti]
-
- gi|4033482sp|P70788|TUD3_AGRVI_267:384 Putative hydroxypyruvate reductase
- gi|984369|gb|AAB61624.1| (U32375) enzyme degrading primary tartrate degradation product [Rhizobium vitis]
-
- gi|21315005|gb|AAH30736.1|_239:360 (BC030736) Unknown (protein for IMAGE:5132880) [Mus musculus]
-
- gi|21687104|ref|NP_660305.1|_333:454 (NM_145262) similar to CG9886 gene product [Homo sapiens]
- gi|18256912|gb|AAH21896.1|AAH21896 (BC021896) Unknown (protein for MGC:9528) [Homo sapiens]
-
- gi|13676533|dbj|BAB41180.1|_272:393 (AB060262) hypothetical protein [Macaca fascicularis]
-
- gi|18976396|ref|NP_577753.1|_333:449 (NC_003413) putative glycerate kinase [Pyrococcus furiosus DSM 3638]
- gi|18891922|gb|AAL80148.1| (AE010128) putative glycerate kinase [Pyrococcus furiosus DSM 3638]
-
- gi|16263221|ref|NP_436014.1|_304:418 (NC_003037) putative TtuD3 hydroxypyruvate reductase [Sinorhizobium meliloti]
- gi|14523892|gb|AAK65426.1| (AE007264) putative TtuD3 hydroxypyruvate reductase [Sinorhizobium meliloti]
-
- gi|14521745|ref|NP_127221.1|_313:428 (NC_000868) hypothetical protein [Pyrococcus abyssi]
- gi|7518011|pir||E75001 hypothetical protein PAB1021 - Pyrococcus abyssi (strain Orsay)
- gi|5458965|emb|CAB50451.1| (AJ248288) hypothetical protein [Pyrococcus abyssi]
-
- gi|14590403|ref|NP_142469.1|_318:433 (NC_000961) hypothetical protein [Pyrococcus horikoshii]
- gi|7518673|pir||B71162 hypothetical protein PH0495 - Pyrococcus horikoshii
- gi|3256900|dbj|BAA29583.1| (AP000002) 440aa long hypothetical protein [Pyrococcus horikoshii]
-
- gi|4033487sp|Q44472|TUD4_AGRVI_321:437 Putative hydroxypyruvate reductase
- gi|805293|gb|AAA68699.1| (U25634) putative hydroxypyruvate reductase; inducible by tartrate; Method: conceptual translation supplied by author [Rhizobium vitis]
- gi|1585264|prf||2124372D ttuD gene [Rhizobium vitis]
-
- gi|18312544|ref|NP_559211.1|_327:441 (NC_003364) conserved hypothetical protein [Pyrobaculum aerophilum]
- gi|18160010|gb|AAL63393.1| (AE009815) conserved hypothetical protein [Pyrobaculum aerophilum]
-
- gi|17545205|ref|NP_518607.1|_314:432 (NC_003295) PUTATIVE HYDROXYPYRUVATE REDUCTASE OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum]
- gi|17427496|emb|CAD14014.1| (AL646059) PUTATIVE HYDROXYPYRUVATE REDUCTASE OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum]
-
- gi|14601127|ref|NP_147655.1|_271:389 (NC_000854) hypothetical protein [Aeropyrum pernix]
- gi|7516171|pir||D72697 hypothetical protein APE0996 - Aeropyrum pernix (strain K1)
- gi|5104665|dbj|BAA79980.1| (AP000060) 400aa long hypothetical protein [Aeropyrum pernix]
-
- gi|16082522|ref|NP_393931.1|_306:417 (NC_002578) Predicted glycerate kinase [Thermoplasma acidophilum]
-
- gi|10639623|emb|CAC11595.1|_283:394 (AL445064) glycerate kinase related protein [Thermoplasma acidophilum]
-
- gi|20894723|ref|XP_135143.1|_399:520 (XM_135143) similar to CG9886 gene product [Mus musculus]
-
- gi|19388000|gb|AAH25834.1|_399:520 (BC025834) similar to hypothetical protein [Mus musculus]
- gi|19684145|gb|AAH25935.1| (BC025935) similar to hypothetical protein [Mus musculus]
- gi|21620001|gb|AAH33063.1| (BC033063) Unknown (protein for MGC:37851) [Mus musculus]
-
- gi|1907334|gb|AAB66496.1|_319:436 (U87316) putative glycerate kinase [Methylobacterium extorquens]
-
- gi|21542484sp|Q09235|YQ42_CAEEL_275:394 Hypothetical protein C13B9.2 in chromosome III
- gi|20198777|gb|AAA62515.2| (U21309) Hypothetical protein C13B9.2 [Caenorhabditis elegans]
-
- gi|17552152|ref|NP_498462.1|_241:360 (NM_066061) C13B9.2.p [Caenorhabditis elegans]
-
- gi|15897575|ref|NP_342180.1|_287:397 (NC_002754) Glycerate kinase, putative [Sulfolobus solfataricus]
- gi|6015809|emb|CAB57636.1| (Y18930) hypothetical protein [Sulfolobus solfataricus]
- gi|13813834|gb|AAK40970.1| (AE006694) Glycerate kinase, putative [Sulfolobus solfataricus]
-
- gi|19920578|ref|NP_608684.1|_364:486 (NM_134840) CG9886 gene product [Drosophila melanogaster]
- gi|7295954|gb|AAF51252.1| (AE003583) CG9886 gene product [Drosophila melanogaster]
- gi|16769768|gb|AAL29103.1| (AY061555) LP09309p [Drosophila melanogaster]
-
- gi|22405563|gb|ZP_00000441.1|_309:413 (NZ_AAAA01000043) hypothetical protein [Ferroplasma acidarmanus]
-
- gi|15922355|ref|NP_378024.1|_286:397 (NC_003106) 399aa long conserved hypothetical protein [Sulfolobus tokodaii]
- gi|15623144|dbj|BAB67133.1| (AP000988) 399aa long conserved hypothetical protein [Sulfolobus tokodaii]
-
- gi|13541614|ref|NP_111302.1|_306:416 (NC_002689) Predicted glycerate kinase [Thermoplasma volcanium]
- gi|14325013|dbj|BAB59939.1| (AP000993) glycerate kinase [Thermoplasma volcanium]
-
- gi|21300335|gb|EAA12480.1|_421:542 (AAAB01008964) agCP11255 [Anopheles gambiae str. PEST]
10 20 30 40 50
| | | | |
1 LKKPAALIFGGETVVHVKGN...GIGGRNQELALSAAIALEGIE....GVILCSAGTDGTDGP..
2 LKKPAALIFGGETVVHVKGN...GIGGRNQELALSAAIALEGIE....GVILCSAGTDGTDGP..
3 FRKPVVILSGGETTVTLRGK...GKGGRNTEFLLSLAIEIAEHG....DITALAADTDGIDGS..
4 FAAPCVLLSGGETTVTLRGN...GRGGRNVEFLLSLAVALDGLP....GVHAIAGDTDGVDGV..
5 VKGPAVLLSGGETTVTIGKGpa.GKGGRNTEFLLSLALTLKGAD....GIWAIAGDSDGIDGV..
6 VKGPAVLLSGGETTVTIGKGpa.GKGGRNTEFLLSLALTLKGAD....GIWAIAGDSDGIDGV..
7 --APCVILSGGETTVTVRGN...GRGGRNAEFLLSLTAELKGEP....NIWALAGDTDGIDGS..
8 FSKPVLILSGGETTVTLRAK...GKGGRNSEFLLAFAIGISGVQ....GIHALAADTDGIDGS..
9 FPKPALLLSGGETTVTVRGE...GRGGRNSEFLLSLALGIDGIG....GISALAADTDGIDGS..
10 FKKPVVILSGGETTVTIGSPg..GKGGRNSEFLLSFALDIDGYA....NIHALAADTDGIDGS..
11 -KGPVCLLAGGEPTVQLQGS...GKGGRNQELALHVGVELGRQPlgpiDVLFLSGGTDGQDGP..
12 FSKPVVLLSGGETTVTISGEry.GKGGRNSEFLLSLALDIDGIG....GIDALAADTDGIDGS..
13 VRGPAVLLSGGETSVSLPADtk.GRGGRNSEFLLSLAIGLDGAK....GIWALSGDTDGIDGI..
14 -KGPVCLLAGGEPTVQLQGS...GKGGRNQELALHVGVELGRQPlgpiDVLFLSGGTDGQDGP..
15 -RGPVCLLAGGEPTVQLQGS...GRGGRNQELALRVGAELRRWPlgpiDVLFLSGGTDGQDGP..
16 -RGPVCLLAGGEPTVQLQGS...GRGGRNQELALRVGAELRRWPlgqiDVLFLSGGTDGQDGP..
17 FKRPCVLIAGGETTVTIQGEa..GLGGPNQELALSIARKIAGLR....GVAVLVIDTDGTDGP..
18 FERPVVLLSGGETTVTLRGH...GRGGRNTEFLLSLAIAAEGLS....-FASLAADTDGIDGS..
19 FEPPVVLVFGGETTVTIEGEg..GKGGPNQELALSATRKIKGLN....-AILVAFDTDGTDGP..
20 FEPPVVLVFGGETTVTIEGKg..GKGGPNQEIALSATRKISDLE....-ALIVAFDTDGTDGP..
21 -AAPAVILSGGESTVSLGAMte.GRGGRNTEFLLSLAVALKGAS....GIWAIAGDTDGIDGV..
22 -RPPLALLAGGETVVTVRGG...GRGGRNQELCLSFSIAVRGLR....NISAACLGTDGVDGN..
23 -AAPVALVSGGECTVTLPPGltgGRGGRCAEFLLSLGIALEDMG....DVYALAADTDGIDGS..
24 VKPPAALLAGGETTVTVRGG...GRGGRNMELALAWSLAMAYWSpea.PAAILAMDTDGIDGR..
25 -GRSFWIVMGGETTVNVRGN...GIGGRNLELSLLFMKKC-NFS....DFLFISMGTDGIDGV..
26 -GRSFWIVMGGETTVNVRGN...GIGGRNLELSLLFMKKC-NFS....DFLFISMGTDGIDGV..
27 -KGPVCLLAGGEPTVQLQGS...GKGGRNQELALHVGVELGRQPlgpiDVLFLSGGTDGQDGP..
28 -KGPVCLLAGGEPTVQLQGS...GKGGRNQELALHVGVELGRQPlgpiDVLFLSGGTDGQDGP..
29 --RRVALISGGELTVTIRGE...GDGGPNQEYALALAIALDGAE....GIAGIAADTDGTDGGrg
30 -NYPIALLFGGETTVHLSENp..GKGGRNQEMVLSCLDALKTRVpah.NFTFLSAGTDGQDGP..
31 -NYPIALLFGGETTVHLSENp..GKGGRNQEMVLSCLDALKTRVpah.NFTFLSAGTDGQDGP..
32 FRRPYYLLVGGEPEVTIQGKa..GKGGRNGEVCLSFLKYAKKRN....RFELLGFATDGIDGN..
33 -KKPLFLICGGEPVIKVSGH...GLGGRSQHLALLMSQALHRDEamr.DCTFLSAGTDGIDGP..
34 -GEPFWFVCGGETTVTVTGN...GSGGRNQELAVRIMEDISN-N....DFLFISMGTDGIDGK..
35 LKPPYTLLAGGEPDVKIEGKa..GKGGRNGEVCLGFLKWVKRNSnh..RFKLYAIATDGIDGN..
36 -GKSFWFVAGGETTVNVKGN...GIGGRNLELALRFM-KLANFS....DFLFLSIGTDGIDGV..
37 KEKPLLIVGAGEPTVCVSGG...GKGGRNQELALRFTVGVRELErvpdSVYFLSAGTDGIDGP..
60 70 80 90 100 110
| | | | | |
1 ..TDAAGGIVDGSTAKTL..K..AMGEDPYQYLKNNDSYNALKKSG...ALLITGPTGTNVNDLI
2 ..TDAAGGIVDGSTAKTL..K..AMGEDPYQYLKNNDSYNALKKSG...ALLITGPTGTNVNDLI
3 ..EDNAGSFVDGGSVARL..C..AAGLDPYDLLVSNDAWTGFNSTK...DLFVTGPTGTNVNDFR
4 ..EEIAGACIAPDTIARA..R..ALGLHPRACLDNNDGHGFFQALG...DAVITGPTLTNVNDFR
5 ..EDAAGAVVTPDTLDRI..R..AAGVDPRQSLVSHDSYTAFKAAG...DLVVTGPTLTNVNDIR
6 ..EDAAGAVVTPDTLDRI..R..AAGVDPRQSLVSHDSYTAFKAAG...DLVVTGPTLTNVNDIR
7 ..EDNAGALMTPCSHARG..E..KAGLKIRDELYDNNGYGYFQALG...DLLVTGPTRTNVNDFR
8 ..ENNAGAFADASTVSRM..R..AAGVDAKAMLAGNNAWTAFNAVG...DLFVPGPTGTNVNDLR
9 ..EDNAGAFADHTTIARL..L..ARRLDAAALLHKNDSWAAFDALG...DLFKPGPTGTNVNDFR
10 ..EDNAGAFADGGTVSRL..Q..KLGEDGMARLNANDAWTAFDALG...DLFVPGPTGTNVNDLR
11 ..TKVAGAWVMSDLISQA..S..AESLDIATSLTNNDSYTFFCRFRggtHLLHTGLTGTNVMDVH
12 ..EDNAGAFADGASIGRM..R..AAGADPRSHLAGHDAWTAFAASG...DLFVPGPTGTNVNDLR
13 ..EDAAGAMIGPDSLARM..R..GSGIDPRSALSRHDSYTAFKAID...DLVITGPTLTNVNDIR
14 ..TKVAGAWVMSDLISQA..S..AESLDIATSLTNNDSYTFFCRFRggtHLLHTGLTGTNVMDVH
15 ..TEAAGAWVTPELASQA..A..AEGLDIATFLAHNDSHTFFCCLQggaHLLHTGMTGTNVMDTH
16 ..TEAAGAWVTPELASQA..A..AEGLDMATFLAHNDSHTFFCRLQggaHLLHTGMTGTNVMDTH
17 ..TDAAGGLVDSYTLEVL..K..KENIDVEEYLKRHNAYEALKRAK...ALVITGPTRTNVNSMM
18 ..ESNAGAFADGSSATRL..R..ALGRDPVALLSGNDAWTAFNCLE...DLFVPGPTGTNVNDFR
19 ..TDAAGGIVDGETYEKL..R..RKGIDIEKVLKEHNSYEALKKVG...SLLFTGPTGTNVNSMI
20 ..TDAAGGIVDGTTYKKL..R..EKGIDVEKVLKEHNSYEALKKVG...GLLFTGPTGTNVNSIV
21 ..EDAAGALVAPDSLIRM..R..DAGIDPRATLSAHDSYTAFKAIG...DLVVTGPTLTNVNDIR
22 ..SPAAGAVVDGGVAEEA..E..AMGLDPFEYLNNNDSYTFFEKLG...RAVITGYTGTNVNDVF
23 ..EGNAGAVLDPQSIGRA..A..ARGVAARAALDAHDAYGFFAAAG...DLIVTGPTRTNVNDYR
24 ..SDAAGAVAWPWLPVAL..R..DAGLDPYQLLADNDSERAFAYAG...SLVSTGLTGTNLNSVV
25 ..SPAAGGIVDAST--KA..R..ISSEEIDQALKNNDSYTLLSKYG...SAIMTGRTGNNVSDIV
26 ..SPAAGGIVDAST--KA..R..ISSEEIDQALKNNDSYTLLSKYG...SAIMTGRTGNNVSDIV
27 ..TKVAGAWVMSDLISQA..S..AESLDIATSLANNDSYTFFCRFRggtHLLHTGLTGTNVMDVH
28 ..TKVAGAWVMSDLISQA..S..AESLDIATSLTNNDSYTFFCRFRggtHLLHTGLTGTNVMDVH
29 aaTDPAGGLVDATTLSRA..Q..AAGLDPKAMLLDNDSTRFFATIG...DLVQPGPTRTNVNDCR
30 ..TDAAGAIISNEDLPL-..-..NSLLNSSEFLQNSDSYNFWRQFKggaNHILTGPSGTNVMDIQ
31 ..TDAAGAIISNEDLPL-..-..NSLLNSSEFLQNSDSYNFWRQFKggaNHILTGPSGTNVMDIQ
32 ..SEYAGCKVSSDM----..E..IREDEINNALETHNSYGLLESHK...AVIKTGYTHTNVNNIY
33 ..TDAAGAFGDSSVVESYlgD..HTLDELAETLRNCDSYNFYKNLAqgeHHVLTGHTGTNVMDLH
34 ..SIAAGGIVDNSTRID-..-..----NLEEYLANNDTYTALSKAH...GAIITGRTGNNVSDIM
35 ..SEYAGCIVDENTIVD-..-..----NIEYYIYSHSSYEALEKVG...RVIKTGYTFTNVNNVY
36 ..SPAAGGIVSSDM--KL..K..ISSQELEETLDRNDAFTLLSAYH...GAIMTGRTGNNVSDIM
37 ..TEVAGAIGGAFVARAF..EetFHLAEAKTFLERNDSYRFYEAVSggqYFVKTGHTGTNVMDVH
1 IGLIV
2 IGLI-
3 AILI-
4 AIVI-
5 AILI-
6 AILI-
7 AILIL
8 AILI-
9 AVLI-
10 AILI-
11 LLIL-
12 AILI-
13 AILI-
14 LLIL-
15 LLFL-
16 LLFL-
17 IAVI-
18 AILV-
19 IAII-
20 IAIV-
21 AILI-
22 IALV-
23 VILIL
24 VVLL-
25 VAYV-
26 VAYV-
27 LLIL-
28 LLIL-
29 VILV-
30 ILLL-
31 ILLL-
32 VL---
33 FLVV-
34 L----
35 VLE--
36 VGY--
37 L----