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 | d1d3ga_ | Dihydroorotate dehydrogenase | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
| Hit | d1oyba_ | Old yellow enzyme (OYE) | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
Query <-- 1.647 --> IntermediateDALI alignment (Z-score: 7.2 Raw score:865.90) query 1 mietpyyLIDKAK-----------------------------------ltrnmeriahvr 25 :::::: d1d3ga_ 1 -------MATGDErfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlg 53 query 26 eksgaKALLALKcfatwsvfDLMRD-YMDGTTSSSL------------------------ 60 ::::::: ::::: :::::::::: d1d3ga_ 54 hkfrnPVGIAAGfdkhgeavDGLYKmGFGFVEIGSVtpkpqegnprprvfrlpedqavin 113 query 61 ----------------fevrlgRERFG---KETHAYSVA---------YGDNEIDEVVSH 92 ::::: ::::::::: :::::::::::: d1d3ga_ 114 rygfnshglsvvehrlrarqqkQAKLTedgLPLGVNLGKnktsvdaaeDYAEGVRVLGPL 173 query 93 ADKIIFNS-------------ISQLERFADKAA------GIARGLRLNPQrlgewDVPKV 133 :::::::: :::::::::::: ::::::::::: ::::: d1d3ga_ 174 ADYLVVNVsspntaglgkaelRRLLTKVLQERDglrrvhRPAVLVKIAPD-ltsqDKEDI 232 query 134 ERVM--DRINGFMIHNN-------------------CENKdfglFDRMLGEIEErFGALI 172 :::: ::::::::::: :::: :::::::::: ::::: d1d3ga_ 233 ASVVkeLGIDGLIVTNTtvsrpaglqgalrsetgglSGKP---lRDLSTQTIREmYALTQ 289 query 173 ARVdWVSLGGGIHFtgddypvdAFSARLRAFSdrygvqIYLEPGEASITKSttlevtvld 232 ::: :::::::::: :::::::::: ::::::::::::: d1d3ga_ 290 GRV-PIIGVGGVSS-------gQDALEKIRAG-----aSLVQLYTALTFWG--------- 327 query 233 tlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaee 292 d1d3ga_ 328 ------------------------------------------------------------ 328 query 293 lkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1d3ga_ 328 -----------------------ppvvgkvkreleallkeqgfggvtdaigadhrr 360 FAST alignment (Normalized score: 4.17 Raw score:1474.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA------------------------------ 30 d1d3ga_ 1 ------------------------------MATGDERFYAEHLMPTLQGLLDPESAHRLA 30 query 31 ----------------------------KALLALKCFA--TWSVFDLMR-DYMDGTTSS- 58 :::::::: ::::::::: ::::::: d1d3ga_ 31 VRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGF--DKHGEAVDGLYKMGFGFVE--I 86 query 59 -----------------------------------SLFEVRLGRERFG------------ 71 :::::::::: d1d3ga_ 87 GSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRA---RQQKQAKLTEDG 143 query 72 KETHAYSVAY------------GDNEIDEVVSHADKIIFN--------------SISQLE 105 ::::::: ::::::::::::::::: :::::: d1d3ga_ 144 LPLGVNL---GKNKTSVDAAEDYAEGVRVLGPLADYLVV-NVSSPNTAGLGKAELRRLLT 199 query 106 RFADKAA------GIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNC 149 ::::::: :::::::::: ::::::: :::::: d1d3ga_ 200 KVLQERDGLRRVHRPAVLVKIAP------DLTSQDKEDIASVVKE---LGIDGLI----- 245 query 150 ENK---------------------------DFGLFDRMLGEIEERFGALIARV----DWV 178 ::::::::::::::: ::: d1d3ga_ 246 ---VTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYAL--------TQGRVPI 294 query 179 SLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLY 235 :::::: ::::::::::: ::::::::: d1d3ga_ 295 IGVGGV-----------SSGQDALEKIRA----GASLVQLYTAL---------------- 323 query 236 NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKV 295 d1d3ga_ 324 ------------------------------------------------------------ 324 query 296 GDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------- 348 d1d3ga_ 324 -----------------------------------------------------TFWGPPV 330 query 349 ------------------------------ 349 d1d3ga_ 331 VGKVKRELEALLKEQGFGGVTDAIGADHRR 360 TMalign alignment (TM-score: 0.36 Raw score:123.76) query 1 ---------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWS-------- 43 :: d1d3ga_ 1 MATGDERFY-----------------------------------------AEHLMPTLQG 19 query 44 -------VFDLMRDYMDGTTSSSLFE--VR----L-GRE---------------RFGKET 74 ::::: : : :: :::: d1d3ga_ 20 LLDPESA--------------HRLAVRF-TSLGLLP-FQDSDMLEVRVLGHKFR--NPVG 61 query 75 HAY--SVAYGDNEIDEVVSH-A-DKIIF-N------------------------------ 99 ::: ::::: :::::::: : ::::: : d1d3ga_ 62 IAAGFDKHGE--AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNS 119 query 100 --SISQLERFA-D--KAA-G----IARGLRLNPQR-L--G-EWDVPKVERVMDRINGFMI 145 ::::::::: : ::: : ::::::::::: : : ::::::::::::::::::: d1d3ga_ 120 HGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVV 179 query 146 HNNCEN---KDFGLFDRMLGEIEERFGALIA------RVDWVSLGGGIHFTGDDYPVDAF 196 :::::: :::::::::::::::::: ::::::::: ::: ::: :: d1d3ga_ 180 NVSSPNTAG----LGKAELRRLLTKVLQERDGLRRVHRPAVLVKIA-PDL----TSQ-DK 229 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 :::::::::::::::::::::: ::::::: :::::: : d1d3ga_ 230 EDIASVVKELGIDGLIVTNTTV-SRPAGLQ---------------------GALRSE--T 265 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV------ 310 : :::::: d1d3ga_ 266 -G----------------------------------------------GLSGKPLRDLST 278 query 311 ------------------------------------------------------------ 311 d1d3ga_ 279 QTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKREL 338 query 311 ----------------------KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1d3ga_ 339 EALLKEQGFGGVTDAIGADHRR-------------------------------------- 360 HHsearch alignment (Probability: 0.13 E-value:0.02) query 98 FNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR-INGFMI----------- 145 :::::::::::::::::::::::::::::::::::::::::: :::::: d1d3ga_ 198 LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGL 257 query 146 -----HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGG 182 ::::::::::::::::::::::::::::::::::::: d1d3ga_ 258 QGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGG 299
Intermediate <-- 2.650 --> HitDALI alignment (Z-score: 15.9 Raw score:1878.30) d1d3ga_ 1 matgderFYAEhlmptlqglldpesahrlavrftslgllpfqdsdMLEVRVLGHKFRNPV 60 :::: ::::::::::::::: d1oyba_ 1 -------SFVK----------------------dfkpqalgdtnlFKPIKIGNNELLHRA 31 d1d3ga_ 61 GIAAGFD-------------khgeAVDGLYKMgfGFVEIGSVTPKP--QEGNprprvfrl 105 ::::::: :::::::: :::::::::::: :::: d1oyba_ 32 VIPPLTRmralhpgnipnrdwaveYYTQRAQRpgTMIITEGAFISPqaGGYD-------- 83 d1d3ga_ 106 pedqavinrygfNSHGLSV--VEHRLRARQQKQAKLTedgLPLGVNLGKNKT-------- 155 ::::::: :::::::::::::::: :::::::::::: d1oyba_ 84 ------------NAPGVWSeeQMVEWTKIFNAIHEKK---SFVWVQLWVLGWaafpdnla 128 d1d3ga_ 156 -------------------------------------sVDAAEDYAEGVRVLGP-LADYL 177 :::::::::::::::: ::::: d1oyba_ 129 rdglrydsasdnvfmdaeqeakakkannpqhsltkdeiKQYIKEYVQAAKNSIAaGADGV 188 d1d3ga_ 178 VVNVSSPnTAGL--------------------GKAELRRLLTKVLQERDglrrvhrpAVL 217 ::::::: :::: ::::::::::::::::: ::: d1oyba_ 189 EIHSANG-YLLNqfldphsntrtdeyggsienRARFTLEVVDALVEAIG------heKVG 241 d1d3ga_ 218 VKIAPD------------lTSQDKEDIASVVKEL-----GIDGLIVTnttvsrpaglqga 260 :::::: ::::::::::::::: :::::::: d1oyba_ 242 LRLSPYgvfnsmsggaetgIVAQYAYVAGELEKRakagkRLAFVHLV------------- 288 d1d3ga_ 261 lrsetgGLSGKPL--rdlstqTIREMYALTqgRVPIIGVGGVS-SGQDALEKIRAGASLV 317 ::::::: ::::::::: ::::::::::: :::::::::::::::: d1oyba_ 289 --eprvTNPFLTEgegeyeggSNDFVYSIW--KGPVIRAGNFAlHPEVVREEVKDKRTLI 344 d1d3ga_ 318 QLYTALTFwGPPVVGKVKRE-------------leallkeqgfggvtdaigadhrr 360 :::::::: ::::::::::: d1oyba_ 345 GYGRFFIS-NPDLVDRLEKGlplnkydrdtfyqmsahgyidyptyeealklgwdkk 399 FAST alignment (Normalized score: 8.46 Raw score:3208.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDM-------------- 46 d1oyba_ 1 ----------------------------------------------SFVKDFKPQALGDT 14 d1d3ga_ 47 ---LEVRVLGHKFRNPVGIAAGFDKHG--------------------EAVDGLYKMGF-- 81 ::::::::::::::::: ::::::: d1oyba_ 15 NLFKPIKIGNNELLHRAVIP-------PLTRMRALHPGNIPNRDWAVEYYTQRA----QR 63 d1d3ga_ 82 --GFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHG-------------LSVVE 126 ::::::::::: ::::: d1oyba_ 64 PGTMIITEGAFIS-----------------------------PQAGGYDNAPGVWSEEQM 94 d1d3ga_ 127 HRLRARQQKQAKLTEDGLPLGVNLGKNKTSV----------------------------- 157 :::::::::::: ::::::::::: d1oyba_ 95 VEWTKIFNAIHE---KKSFVWVQLWV-----LGWAAFPDNLARDGLRYDSASDNVFMDAE 146 d1d3ga_ 158 ---------------------DAAEDYAEGVRVLGP-LADYLVVNVSSPNTAGL------ 189 ::::::::::::::: ::::::::: :::: d1oyba_ 147 QEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHS-ANGY---LLNQFL 202 d1d3ga_ 190 -----------------GKAELRRLLTKVLQERDGLRRVHRP----AVLVKIAPDL---- 224 ::::::::::::::: :::::: d1oyba_ 203 DPHSNTRTDEYGGSIENRARFTLEVVDALVEA----------IGHEKVGLRL----SPYG 248 d1d3ga_ 225 ------------TSQDKEDIASVVKE-----LGIDGLIVTNTTVSRPAGLQGALRSETGG 267 :::::::::::::: ::::::: d1oyba_ 249 VFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVH---------------------- 286 d1d3ga_ 268 ----------LSGKPLRDLSTQ-----TIREMYALTQGRVPIIGVGG-VSSGQDALEKIR 311 :::::: ::::::::: ::::::::: :::::::::::: d1oyba_ 287 LVEPRVTNPFLTEGEG------EYEGGSNDFVYSIW--KGPVIRAGNFALHPEVVREEVK 338 d1d3ga_ 312 AGA--SLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR--------- 360 : ::::::::::: ::::::::: d1oyba_ 339 D--KRTLIGYGRFFIS-NPDLVDRLE-------------------------KGLPLNKYD 370 d1d3ga_ 361 ----------------------------- 361 d1oyba_ 371 RDTFYQMSAHGYIDYPTYEEALKLGWDKK 399 TMalign alignment (TM-score: 0.59 Raw score:213.24) d1d3ga_ 1 MATGDERFYAEH----LMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDM-LEVRVL-GH 54 ::::: :::::: :::::: :: d1oyba_ 1 -------SFVKDFKPQ----------------------------ALGDTNLFKPIKIGNN 25 d1d3ga_ 55 KFRNPVGIAAGFDK-H------G----E--AVDGLYKMGFGFVEIGSVTPKP--QEGNPR 99 :::::::::::::: : : : :::::::::::::::::::::: :::: d1oyba_ 26 ELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYD-- 83 d1d3ga_ 100 PRVFRLPEDQAVINRYGFNSHGL-S-VVEHRLRARQQKQAKLTEDGLPLGVNLGKNK--- 154 ::::: : :::::::::::::::: : ::::::::::: d1oyba_ 84 ------------------NAPGVWSEEQMVEWTKIFNAIHEK--K-SFVWVQLWVLGWAA 122 d1d3ga_ 155 ----------T-S-----------------------------VD--AAEDYAEGVRVLGP 172 : : :: :::::::::::::: d1oyba_ 123 FPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIA 182 d1d3ga_ 173 -LADYLVVNVSSPNT-AGL-----------------G-KAELRRLLTKVLQERDGLRRVH 212 :::::::::::::: ::: : :::::::::::::::: d1oyba_ 183 AGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIG------ 236 d1d3ga_ 213 RPAVLVKIAPD-------L-----TSQDKEDIASVVKEL-----GIDGLIVTNTTVSRPA 255 ::::::::::: : ::::::::::::::: :::::::::::::: d1oyba_ 237 HEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTN-- 294 d1d3ga_ 256 GLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVS-SGQDALEKIRAGA 314 ::::::::::::::: ::::::: ::::::::::: ::::::::::::: d1oyba_ 295 ----------PFLTEGEGEYEGGSN-DFVYSIW--KGPVIRAGNFALHPEVVREEVKDKR 341 d1d3ga_ 315 SLVQLYTALTFWGPPVVGKVKREL-----------------------------------E 339 :::::::::: ::::::::::::: d1oyba_ 342 TLIGYGRFFI-SNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWDKK- 399 d1d3ga_ 340 ALLKEQGFGGVTDAIGADHRR 360 d1oyba_ 400 --------------------- 400 HHsearch alignment (Probability: 1.00 E-value:0.00) d1d3ga_ 48 EVRVLGHKFRNPVGIAAG---F---D---KHGE----AVDGLYKMGFGFVEIGSVTPKPQ 94 :::::::::::::::::: : : :::: ::::::::::::::::::::::: d1oyba_ 19 PIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQ 78 d1d3ga_ 95 EGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLG--K 152 ::::::::::::::: : :::::::::: :::::::::::: : d1oyba_ 79 -AGGYDNAPGVWSEEQ-M-------VEWTKIFNAI----------HEKKSFVWVQLWVLG 119 d1d3ga_ 153 ---------------------------------------NKTSV----DAAEDYAEGVRV 169 ::::: :::::::::::: d1oyba_ 120 WAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKN 179 d1d3ga_ 170 -LGPLADYLVVN---------VSSPNTAGLGKAELR----RLLTKVLQERDGLRRVH-RP 214 ::::::::::: ::::::: ::::::: ::::::::::::::::: :: d1oyba_ 180 SIAAGADGVEIHSANGYLLNQFLDPHSN-TRTDEYGGSIENRARFTLEVVDALVEAIGHE 238 d1d3ga_ 215 AVLVKIAPDLTS------------QDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALR 262 :::::::::::: :::::::::::::::::::::::::::::::::::: d1oyba_ 239 KVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLT 298 d1d3ga_ 263 SETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAG-ASLVQLYT 321 ::: :::::::::::::::: :::::::::::::::::::::: :::::::: d1oyba_ 299 EGE--------GEYEGGSNDFVYSIWK--GPVIRAGNFALHPEVVREEVKDKRTLIGYGR 348 d1d3ga_ 322 ALTFWGPPVVGKVKREL 338 ::: ::::::::::::: d1oyba_ 349 FFI-SNPDLVDRLEKGL 364