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 | d1gc0a_ | Methionine gamma-lyase, MGL | PLP-dependent transferases | PLP-dependent transferases | 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 <-- 0.592 --> HitDALI alignment (Z-score: 3.4 Raw score:445.20) d1tqja_ 1 -----------------------------knivvapsilsadfsrlgeeikavdeAGAD- 30 :::: d1gc0a_ 1 lpgfatraihhgydpqdhggalvppvyqtatftfpsnptlnllearmasleggeaGLALa 60 d1tqja_ 31 --WIHVdvmdgrfvpnitigplivdairpltkkTLDVhlmivepekyvedfakagADIIs 88 :::: :::: :::: d1gc0a_ 61 sgMGAI---------------------------TSTL------------------WTLL- 74 d1tqja_ 89 vhvehnasphlhrtlcqirelGKKAGAVLNP------------------------sTPLD 124 :::::::::: :::: d1gc0a_ 75 --------------------rPGDEVLLGNTlygctfaflhhgigefgvklrhvdmADLQ 114 d1tqja_ 125 FLEYVLP-VCDLILIMSVNPqsfIPEVlpKIRALRQMCDerGLDPWIEVDG-GLKPNNTw 182 ::::::: :::::::::::: :::: :::::::::: :::::::::: ::::::: d1gc0a_ 115 ALEAAMTpATRVIYFESPAN-pnMHMA--DIAGVAKIAR--KHGATVVVDNtYCTPYLQ- 168 d1tqja_ 183 QVLEAGANAIVAG--SAVFN---------------------------------------A 201 ::::::::::::: ::::: : d1gc0a_ 169 RPLELGADLVVHSatXYLSGhgditagivvgsqalvdrirlqglkdmtgavlsphdaalL 228 d1tqja_ 202 PNY--------------------------------------------------------- 204 ::: d1gc0a_ 229 MRGiktlnlrmdrhcanaqvlaeflarqpqvelihypqpggmiafelkggigagrrfmna 288 d1tqja_ 205 -------------------------------------------------------aeaia 209 d1gc0a_ 289 lqlfsravslgdaeslaqhpasmthssytpeerahygiseglvrlsvglediddlladvq 348 d1tqja_ 210 gvrnskr 216 d1gc0a_ 349 qalkasa 355 FAST alignment (Normalized score: 1.99 Raw score:551.70) d1tqja_ 1 KNIVVAPSILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIGPLIVDAIRPLTK 60 d1gc0a_ 1 ------------------------------------------------------------ 1 d1tqja_ 61 KTLDVHLMIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLC---------------- 104 d1gc0a_ 1 --------------------------------------------LPGFATRAIHHGYDPQ 16 d1tqja_ 105 ------------------------------------------------------------ 105 d1gc0a_ 17 DHGGALVPPVYQTATFTFPSNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRP 76 d1tqja_ 105 --------------------QIRELGKKAGAVLNPS--TPLDFLEYV-LPVCDLILIMSV 141 ::::: ::::::: ::::::::: :::::::::::: d1gc0a_ 77 GDEVLLGNTLYGCTFAFLHHGIGEF-GVKLRHV---DMADLQALEAAMTPATRVIYFESP 132 d1tqja_ 142 NPQSFIPEVLP--------KIRALRQMCDERGLDPWIEVD-GGLKPNNTWQVLEAGANAI 192 ::::::::::: :::::::: :::::::: :::::::::: d1gc0a_ 133 -----------ANPNMHMADIAGVAKIARK--HGATVVVDNTYCTPYLQ-RPLELGADLV 178 d1tqja_ 193 VAGSAVFNAPNYAEAIAGVRNSKR------------------------------------ 216 :: d1gc0a_ 179 VH----------------------SATAYLSGHGDITAGIVVGSQALVDRIRLQGLKDMT 216 d1tqja_ 217 ------------------------------------------------------------ 217 d1gc0a_ 217 GAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPQPGGMIAFELK 276 d1tqja_ 217 ------------------------------------------------------------ 217 d1gc0a_ 277 GGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVG 336 d1tqja_ 217 ------------------- 217 d1gc0a_ 337 LEDIDDLLADVQQALKASA 355 TMalign alignment (TM-score: 0.40 Raw score:86.47) d1tqja_ 1 ------------------------------------------------------KNI-V- 4 ::: : d1gc0a_ 1 LPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPSNPTLNLLEARMASLEGGEAGLALA 60 d1tqja_ 5 ---VAPSI--LSADFSRLGEEIKAVDEAGADWIH----VDVMDGRFVPN-IT-IG--PLI 51 ::::: ::::: :::::: :::: :: :: : d1gc0a_ 61 SGMGAITSTL-------------------WTLLRPGDEVLLGNT-LYGCTFAFLHHG--I 98 d1tqja_ 52 VDAIRPLTKKTLDVHLMIVEPE-KYVEDFAKAGADIISVHVE----HNASPHLHRTLCQI 106 ::::: : ::::::::: ::::: ::::::::::::: :::: ::::::::: d1gc0a_ 99 GEFGV------K-LRHVDMADLQALEAA-MTPATRVIYFESPANPNMHMA-DIAGVAKIA 149 d1tqja_ 107 RELGKKAGAVLNPSTPL-DFLEYVLPVCDLILIMSVNPQSFIPEVLP-----KIRALRQM 160 ::::::::::: ::::: :::: :::::::::::: :: :::: ::: :: d1gc0a_ 150 RKHGATVVVDN-TYCTPYLQRP-LELGADLVVHSA-----TA-YLSGHGDITAGI-VV-- 198 d1tqja_ 161 CDERGLDPWIE-VDGGLKPNNTWQVLEAGANAIVA-GSAVFNAPNYAEAIAGVRNSKR-- 216 : :::::: :::::: : ::: :: ::: d1gc0a_ 199 G----SQALVDR-----------------IRLQGLK----------D-MTG-AV-LSPHD 224 d1tqja_ 217 ------------------------------------------------------------ 217 d1gc0a_ 225 AALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPQPGGMIAFELKGGIGAGRR 284 d1tqja_ 217 ------------------------------------------------------------ 217 d1gc0a_ 285 FMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLL 344 d1tqja_ 217 ----------- 217 d1gc0a_ 345 ADVQQALKASA 355 HHsearch alignment (Probability: 0.84 E-value:0.00) d1tqja_ 76 VEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVLPV-CD 134 ::::::::::::::::::::: :::::::::::::::: :::::::::::::::: :: d1gc0a_ 70 LWTLLRPGDEVLLGNTLYGCT--FAFLHHGIGEFGVKLR--HVDMADLQALEAAMTPATR 125 d1tqja_ 135 LILIMSV-NPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVLEAGANAIV 193 ::::::: ::::::: ::::::::::: :::::::::::::::::::::::::::: d1gc0a_ 126 VIYFESPANPNMHMA----DIAGVAKIARK--HGATVVVDNTYCTPYLQRPLELGADLVV 179 d1tqja_ 194 -------------AGSAVFNAPNYAEA--IAGVRN 213 :::::::::::::: :::::: d1gc0a_ 180 HSATXYLSGHGDITAGIVVGSQALVDRIRLQGLKD 214