Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1tqja_ | D-ribulose-5-phosphate 3-epimerase | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1q7za2 | Cobalamin-dependent methionine synthase MetH, N-terminal domain | Homocysteine S-methyltransferase | TIM beta/alpha-barrel | α/β |
Query <-- 2.347 --> IntermediateDALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 2.156 --> HitDALI alignment (Z-score: 14.6 Raw score:1439.90) d1tqja_ 1 ------------KNIVVAPS-ILSAD----------------FSRLGEEIKAVDEAGADW 31 :::::::: ::::: :::::::::::::::::: d1q7za2 1 mrnrrevskllsERVLLLDGaYGTEFmkygyddlpeelnikaPDVVLKVHRSYIESGSDV 60 d1tqja_ 32 IHV-DVMD-gRFVP-------nitIGPLIVDAIRPL-TKKTLDVHLMIV----------- 70 ::: :::: :::: :::::::::::: :::::::::::: d1q7za2 61 ILTnTFGAtrMKLRkhgledkldpIVRNAVRIARRAaGEKLVFGDIGPTgelpyplgstl 120 d1tqja_ 71 ------EPEKYVEDFAKAGADIISV--HVEHnasPHLHRTLCQIREL--GKKAGAVLNPS 120 ::::::::::::::::::: :::: ::::::::::::: ::::::::::: d1q7za2 121 feefyeNFRETVEIMVEEGVDGIIFetFSDI---LELKAAVLAAREVsrDVFLIAHMTFD 177 d1tqja_ 121 --------TPLDFL-EYVL-PVCDLILIMSVnpqSFIPEVLPKIRALRQMCderglDPWI 170 :::::: :::: ::::::::::: ::::::::::::::::: :::: d1q7za2 178 ekgrsltgTDPANFaITFDeLDIDALGINCS---LGPEEILPIFQELSQYT-----DKFL 229 d1tqja_ 171 EVDGG------------------lKPNNTWQVLEAGANAIVA-gSAVFNApnyAEAIAGV 211 ::::: :::::::::::::::::: :::::: ::::::: d1q7za2 230 VVEPNagkpivengktvyplkphdFAVHIDSYYELGVNIFGGccGTTPEH--vKLFRKVL 287 d1tqja_ 212 RN--------skr 216 :: d1q7za2 288 GNrkplqrkkkri 300 FAST alignment (Normalized score: 9.88 Raw score:2516.00) d1tqja_ 1 ------------KNIVV-APSILSADFS--------------------RLGEEIKAVDEA 27 ::::: :::::: :::::::::::: d1q7za2 1 MRNRREVSKLLSERVLLLDGAYGT----EFMKYGYDDLPEELNIKAPDVVLKVHRSYIES 56 d1tqja_ 28 GADWIHVDVMDGRFVPNIT-------------------IGPLIVDAIRPL-TKKTLDVHL 67 ::::::::: :::::::::::: ::::::::: d1q7za2 57 GSDVILTNT----------FGATRMKLRKHGLEDKLDPIVRNAVRIARRAAGEKLVFGDI 106 d1tqja_ 68 MIV-------------------EPEKYVEDFAKAGADIISVHVEHNAS------PHLHRT 102 : ::::::::::::::::::: :::::: d1q7za2 107 G--PTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIF-------ETFSDILELKAA 157 d1tqja_ 103 LCQIRE--LGKKAGAVLNPST------------PLDFLEYVL-PVCDLILIMSVNPQSF- 146 :::::: :::::::::: ::::::::: :::::::: d1q7za2 158 VLAAREVSRDVFLIAHMT---FDEKGRSLTGTDPANFAITFDELDIDALGI--------N 206 d1tqja_ 147 ----IPEVLPKIRALRQMCDERGLDPWIEVDGGL---------------------KPNNT 181 :::::::::::::: :::::::: ::::: d1q7za2 207 CSLGPEEILPIFQELSQY-----TDKFLVVE---PNAGKPIVENGKTVYPLKPHDFAVHI 258 d1tqja_ 182 WQVLEAGANAIVAGSAVFNAPN-YAEAIAGVRNSKR---------------- 216 :::::::::::::::: ::::::::: d1q7za2 259 DSYYELGVNIFGGCCG------TTPEHVKLFR----KVLGNRKPLQRKKKRI 300 TMalign alignment (TM-score: 0.72 Raw score:155.42) d1tqja_ 1 ----------K--NIVVAPSIL-SAD----------------FSRLGEEIKAVDEAGADW 31 : ::::::::: ::: :::::::::::::::::: d1q7za2 1 MRNRREVSKLLSERVLLLDGAYGTEFMKYGYDDLPEELNIKAPDVVLKVHRSYIESGSDV 60 d1tqja_ 32 IHV-DVMDG-RFV-PNI-T---I--GP-LIVDAIRPLT-KKTLDVHLMIV---------- 70 ::: ::::: ::: :: : : :: :::::::::: ::::::::::: d1q7za2 61 ILTNTFGATRMKLR-KHGLEDKLDPIVRNAVRIARRAAGEKLVFGDIGPTGELPYPLGST 119 d1tqja_ 71 ----E---PEKYVEDFAKAGADIISV--HVEHNASPHLHRTLCQIRELGKKAGAVLNP-- 119 : :::::::::::::::::: ::::::::::::::::::: :::::::::: d1q7za2 120 LFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSR-DVFLIAHMTFDE 178 d1tqja_ 120 --ST----PL-DFLEYVLP-VCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIE 171 :: :: :::::::: :::::::::: ::::::::::::::::: :::::: d1q7za2 179 KGRSLTGTDPANFAITFDELDIDALGINCS---LGPEEILPIFQELSQYT----DKFLVV 231 d1tqja_ 172 VDGGL--------------KPNNTWQVLEA--G-ANAIVAG-SAVFNAPNYAEAIAGVRN 213 ::::: ::::::::::: : ::::::: :::: : :::::::::: d1q7za2 232 EPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTP-E--HVKLFRKVLG 288 d1tqja_ 214 ------------SKR 216 d1q7za2 289 NRKPLQRKKKRI--- 300 HHsearch alignment (Probability: 0.84 E-value:0.00) d1tqja_ 69 IVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKA--GAVLNPS------ 120 ::::::::::::::::::::::::: ::::::::::::::::::: ::::::: d1q7za2 125 YENFRETVEIMVEEGVDGIIFETFS-DILELKAAVLAAREVSRDVFLIAHMTFDEKGRSL 183 d1tqja_ 121 --TPLDFLEYVLPV--CDLILIMS-VNPQSFIPEVLPKIRALRQMC-DE-RGLDPWIEVD 173 :::::::::::: :::::::: :::: :::::::::::::::: :: :::::::::: d1q7za2 184 TGTDPANFAITFDELDIDALGINCSLGPE-EILPIFQELSQYTDKFLVVEPNAGKPIVEN 242 d1tqja_ 174 G----GLKPN----NTWQVLEAGANAI 192 : ::::: ::::::::::::: d1q7za2 243 GKTVYPLKPHDFAVHIDSYYELGVNIF 269