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 | d1vhna_ | Putative flavin oxidoreducatase TM0096 | 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 <-- 2.280 --> HitDALI alignment (Z-score: 16.2 Raw score:1711.90) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlghkfrNPV 60 ::: d1vhna_ 1 ---------------------------------------------------------VKV 3 d1d3ga_ 61 GIAAG--FDKHgEAVDGLYKMGFGFVEIGSVTPKPqegnprprvfrlpedqavinrygfn 118 ::::: :::: ::::::::::::::::::::::: d1vhna_ 4 GLAPMagYTDS-AFRTLAFEWGADFAFSEMVSAKG---------------------flmn 41 d1d3ga_ 119 shGLSVVEhrlrarQQKQakltedgLPLGVNLGKnktsvdAAEDYAEGVRVLGPLADYLV 178 :::::: :::: ::::::::: :::::::::::::::::::: d1vhna_ 42 sqKTEELL-----pQPHE-------RNVAVQIFG-----sEPNELSEAARILSEKYKWID 84 d1d3ga_ 179 VNVSSPN---TAGL-------GKAELRRLLTKVLQERdglrrvhRPAVLVKIAPDLTSqD 228 ::::::: :::: :::::::::::::::: :::::::::::::: : d1vhna_ 85 LNAGCPVrkvVKEGaggallkDLRHFRYIVRELRKSV-------SGKFSVKTRLGWEKnE 137 d1d3ga_ 229 KEDIASVVKELGIDGLIVTnTTVSrpaglqgalrsetGGLSgkPLRDlsTQTIREMyalt 288 ::::::::::::::::::: :::: :::: :::: ::::::: d1vhna_ 138 VEEIYRILVEEGVDEVFIHtRTVV-------------QSFT--GRAE--WKALSVL---- 176 d1d3ga_ 289 QGRVPIIGVGGVSSGQDALEKIR-AGASLVQLYTALTFwGPPVVGKVKRELEAL------ 341 ::::::::::::::::::::::: :::::::::::::: ::::::::::::::: d1vhna_ 177 EKRIPTFVSGDIFTPEDAKRALEeSGCDGLLVARGAIG-RPWIFKQIKDFLRSGkyseps 235 d1d3ga_ 342 ---------------------------------------------------lkeqgfggv 350 d1vhna_ 236 reeilrtferhlelliktkgerkavvemrkflagytkdlkgarrfrekvmkieevqilke 295 d1d3ga_ 351 tdaigadhrr 360 d1vhna_ 296 mfynfikeve 305 FAST alignment (Normalized score: 9.51 Raw score:3152.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPV 60 ::: d1vhna_ 1 ---------------------------------------------------------VKV 3 d1d3ga_ 61 GIAAGFD-----KHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRY 115 ::: :::::::::::::::::::::::: d1vhna_ 4 GLA----PMAGYTDSAFRTLAFEWGADFAFSEMVSA------------------------ 35 d1d3ga_ 116 GFNSH--------GLSVVEHRLRARQQKQAKLTEDG-------LPLGVNLGKNKTSVD-- 158 :::: ::::::: d1vhna_ 36 -----KGFLMNSQKTEE-------------------LLPQPHERNVAVQI--------FG 63 d1d3ga_ 159 -AAEDYAEGVRVLGPLADYLVVNVSSPNTAG--------------LGKAELRRLLTKVLQ 203 :::::::::::::::::::::::::: ::::::::::::::: d1vhna_ 64 SEPNELSEAARILSEKYKWIDLNAGCP----VRKVVKEGAGGALLKDLRHFRYIVRELRK 119 d1d3ga_ 204 ERDGLRRVH-RPAVLVKIAPDLTSQ------DKEDIASVVKELGIDGLIVTNTTVSRPAG 256 : ::::::::: :::::::::::::::::: d1vhna_ 120 S--------VSGKFSVKTR------LGWEKNEVEEIYRILVEEGVDEVF----------- 154 d1d3ga_ 257 LQGALRSETGGLSGKPLRDL--------------STQTIREMYALTQGRVPIIGVGGVSS 302 ::::::: ::::::::::::::: d1vhna_ 155 --------------------IHTRTVVQSFTGRAEWKALSV----LEKRIPTFVSGDIFT 190 d1d3ga_ 303 GQDALEKIR-AGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR- 360 ::::::::: :::::::::::::: ::::::::::::: d1vhna_ 191 PEDAKRALEESGCDGLLVARGAIG-RPWIFKQIKDFLR---------------------S 228 d1d3ga_ 361 ------------------------------------------------------------ 361 d1vhna_ 229 GKYSEPSREEILRTFERHLELLIKTKGERKAVVEMRKFLAGYTKDLKGARRFREKVMKIE 288 d1d3ga_ 361 ----------------- 361 d1vhna_ 289 EVQILKEMFYNFIKEVE 305 TMalign alignment (TM-score: 0.52 Raw score:186.96) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPV 60 : :: d1vhna_ 1 ------------------------------------------------V---------KV 3 d1d3ga_ 61 GIAAGFDKHGEA-VDGLYKMGFGFVEIGSVTPKPQ---EGNPRPRVFRLPEDQAVINRYG 116 :::::::::::: :::::::::::::::::::::: d1vhna_ 4 GLAPMAGYTDSAFRTLAFEWGADFAFSEMVSAKGFLMN---------------------- 41 d1d3ga_ 117 FNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADY 176 :::: :::: ::: : : : :::::::: ::::::::::::::::::: d1vhna_ 42 -SQKT-EELL-PQP--H--E---R----NVAVQIFG-----SEPNELSEAARILSEKYKW 82 d1d3ga_ 177 LVVNVSSPN--T-A-G---L---GKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDL-T 225 ::::::::: : : : : :::::::::::::::: : : :::::::::: : d1vhna_ 83 IDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVRELRKSV--S----G-KFSVKTRLGWEK 135 d1d3ga_ 226 SQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMY 285 : :::::::::::::::::::::::::: ::: ::: : :::::: d1vhna_ 136 N-EVEEIYRILVEEGVDEVFIHTRTVVQ-------------SFT--GRA-E-WKALSV-- 175 d1d3ga_ 286 ALTQGRVPIIGVGGVSSGQDALEKIR-AGASLVQLYTALTFWGPPVVGKVKRELEALL-- 342 : ::::::::::::::::::::::: ::::::::::::: ::::::::::::::::: d1vhna_ 176 L--EKRIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAI-GRPWIFKQIKDFLRSGKYS 232 d1d3ga_ 343 ------------------------------------------------------------ 343 d1vhna_ 233 EPSREEILRTFERHLELLIKTKGERKAVVEMRKFLAGYTKDLKGARRFREKVMKIEEVQI 292 d1d3ga_ 343 -------------KEQGFGGVTDAIGADHRR 360 d1vhna_ 293 LKEMFYNFIKEVE------------------ 305 HHsearch alignment (Probability: 1.00 E-value:0.00) d1d3ga_ 140 TEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPN---TAGLGKAELRR 196 ::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1vhna_ 51 QPHERNVAVQIFGSE-----PNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALLK 105 d1d3ga_ 197 LLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAG 256 :::::::::::::::::::::::::::::::::::::::::::::::::::::: d1vhna_ 106 DLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRT------ 159 d1d3ga_ 257 LQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIR-AGAS 315 ::::::::: :::::::::: ::::::::::::::::::::: :::: d1vhna_ 160 -------VVQSFTGRA----EWKALSVLEK----RIPTFVSGDIFTPEDAKRALEESGCD 204 d1d3ga_ 316 LVQLYTALTFWGPPVVGKVKREL 338 :::::::: :::::::::::::: d1vhna_ 205 GLLVARGA-IGRPWIFKQIKDFL 226