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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1kbia1 | Flavocytochrome b2, C-terminal domain | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 0.837 --> HitDALI alignment (Z-score: 9.7 Raw score:1214.20) d1j93a_ 1 ------------------------------------------------------------ 1 d1kbia1 1 apgetkediarkeqlksllppldniinlydfeylasqtltkqawayyssgandevthren 60 d1j93a_ 1 ------------------tqplllDAVRgkeverpPVWLMRQAGRymksYQLLCekyplf 42 :::: :::::::::: ::::: d1kbia1 61 hnayhriffkpkilvdvrkvdistDMLG--shvdvPFYVSATALC----KLGNP------ 108 d1j93a_ 43 rdrsenvDLVVEISLQPWK-VFRPdGVILFSDiltplsgmnipfdiikgkgpvifdplrt 101 :::::::::::: :::: ::::::: d1kbia1 109 ------lEGEKDVARGCGQgVTKV-PQMISTL---------------------------- 133 d1j93a_ 102 aadvekvrefipeksvpYVGEALTILrkEVNNqAAVLGFVGAPftlasyvveggssknft 161 ::::::::: :::: :::::::::: d1kbia1 134 --------------ascSPEEIIEAA--PSDK-QIQWYQLYVN----------------- 159 d1j93a_ 162 kikrlafaepkvlhallqKFATSMAKYIRYQADSGAQAVQIFDSWAT------------- 208 ::::::::::::::::::::::::::::: d1kbia1 160 ------------------SDRKITDDLVKNVEKLGVKALFVTVDAPSlgqrekdmklkfs 201 d1j93a_ 209 ---------------elspvdfeEFSLPYLKQIVDSVklthpNLPLILYASGSGGLLERL 253 :::::::::::::: :::::::::::::::::: d1kbia1 202 ntkktnveesqgasralskfidpSLTWKDIEELKKKT-----KLPIVIKGVQRTEDVIKA 256 d1j93a_ 254 PLTGVDVVSLD------------WTVDMADGRRRL-----GPNVAIQGNvDPGVlfgske 296 ::::::::::: :::::::::::: ::::::::: :::: d1kbia1 257 AEIGVSGVVLSnhggrqldfsraPIEVLAETMPILeqrnlKDKLEVFVD-GGVR------ 309 d1j93a_ 297 fITNRINDTVKKAgkgkHILNLghGIKV---------gtpeENFAHFFEIAK-------- 339 :::::::::::: ::::: :::: ::::::::::: d1kbia1 310 -RGTDVLKALCLG---aKGVGL--GRPFlyanscygrngveKAIEILRDEIEmsmrllgv 363 d1j93a_ 340 -GLRY--------------------------------------- 343 :::: d1kbia1 364 tSIAElkpdlldlstlkartvgvpndvlynevyegptltefeda 407 FAST alignment (Normalized score: 5.14 Raw score:1921.00) d1j93a_ 1 TQPLLLDAV--------------------------------------------------- 9 d1kbia1 1 ---------APGETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGA 51 d1j93a_ 10 -----------------------------------RGKEVERPPVWLMRQ-----AGRYM 29 ::::::: :::: ::::: d1kbia1 52 NDEVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDV-PFYV---SATALCKLGN 107 d1j93a_ 30 KSYQLLCEKYPLFRDRSENVDLVV--EISLQPWKVFRP-------DGVILFSDILTPLSG 80 ::::::::: :::::: d1kbia1 108 ------------------------PLEGEKDVARG---CGQGVTKVPQMIS--------- 131 d1j93a_ 81 MNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGE-----ALTILRKEV-NNQ 134 ::::::::: ::: d1kbia1 132 ------------------------------------------TLASCSPEEIIEAAPSDK 149 d1j93a_ 135 AAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK--FATSMAKYIRYQ 192 ::::::::: :::::::::::: d1kbia1 150 QIQWYQLYV-------------------------------------NSDRKITDDLVKNV 172 d1j93a_ 193 ADSGAQAVQIFDSWATELSPVDFEEF---------------------------------- 218 ::::::::::::: d1kbia1 173 EKLGVKALFVTVD-------------APSLGQREKDMKLKFSNTKKTNVEESQGASRALS 219 d1j93a_ 219 -------SLPYLKQIVDSVKLTHPNLPLIL-YASGSGGLLERLPLTGVDVVSLDWTV--- 267 ::::::::::: ::::::: ::: ::::::::::::::::: d1kbia1 220 KFIDPSLTWKDIEELKKK-----TKLPIVIKGVQ-RTEDVIKAAEIGVSGVV-----LSN 268 d1j93a_ 268 --------------DMADGRRRL------GPNVAIQGNVDPGVLFGSKEF-------ITN 300 :::::::: :::::: ::: d1kbia1 269 HGGRQLDFSRAPIEVLAETMPI-LEQRNLKDKLEV---------------FVDGGVRRGT 312 d1j93a_ 301 RINDTVKKAGKGKHILNLGHGIKVGT-------------------PEENFAHFFEIAKGL 341 ::::::: ::::::::::::: d1kbia1 313 DVLKALC-------------------LGAKGVGLGRPFLYANSCYGRNGVEKAIEILR-- 351 d1j93a_ 342 RY-------------------------------------------------------- 343 d1kbia1 352 --DEIEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA 407 TMalign alignment (TM-score: 0.44 Raw score:151.38) d1j93a_ 1 ------------------------------------------------------------ 1 d1kbia1 1 APGETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEVTHREN 60 d1j93a_ 1 ----------------------TQPLLLDAVRGKEVERPPVWLMRQ-AGR--YMKSYQ-- 33 ::::::: ::::::::::: ::: :::::: d1kbia1 61 HNAYHRIFFKPKILVDVRKVDI-----STDMLGS-HVDVPFYVSATALCKLGNPLEGEKD 114 d1j93a_ 34 ----------------LLCEKYPLFRDRSENVDLVVEISLQPWKV-FR-PDGVILFSDIL 75 ::: :: ::::::::: :: :::::::: : d1kbia1 115 VARGCGQGVTKVPQMI-----------STL---AS-CSPEEIIEAAPSDKQIQWYQL-Y- 157 d1j93a_ 76 TPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQA 135 :: :: : :::::::::::::: d1kbia1 158 VN-SD--------------------------------R-KITDDLVKNVEKLG------- 176 d1j93a_ 136 AVLGFVGAPFTLASYVVEGGSSKN-------------------FTKI--------KRLAF 168 :::::::: ::: : ::::: :: d1kbia1 177 VKALFVTV-DAP--S----LGQREKDMKLKFSNTKKTNVEESQ--GASRALSKFI----- 222 d1j93a_ 169 AEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVD 228 :: :::::::::::: ::::::::::: :::::::::: d1kbia1 223 --------DP-SLTWKDIEELKK--KTKLPIVIKGV--------------QRTEDVIKAA 257 d1j93a_ 229 SVKLTHPNLPLILYA-SG-----SGGLLERLP-LT--G--------VDVVSLDWTVDMAD 271 ::: : ::::::: :: ::::::::: :: : :::::::::::::: d1kbia1 258 EIG--V--SGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTD 313 d1j93a_ 272 GRRRLGPNVAIQGNV-DP-GVL-FG--SK-EFI-TNRINDTVKKA-----GKGKH----- 314 ::::::::::::::: :: ::: :: :: ::: ::::::::::: ::::: d1kbia1 314 VLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDL 373 d1j93a_ 315 ----------------------------------ILNLGHGIKVGTPEENFAHFFEIAKG 340 d1kbia1 374 LDLSTLKARTVGVPNDVLYNEVYEGPTLTEFEDA-------------------------- 407 d1j93a_ 341 LRY 343 d1kbia1 408 --- 408 HHsearch alignment (Probability: 0.14 E-value:0.02) d1j93a_ 185 MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS 244 :::::::::::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1kbia1 249 RTEDVIKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQR-NLKDKLEVF-VDG 306 d1j93a_ 245 GSGGLLERLP--LTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVD-PGVLFGSKEFITNR 301 :::::::::: :::::::::: ::: :::::::::::::: d1kbia1 307 GVRRGTDVLKALCLGAKGVGLG--------------------RPFLYANSCYGRNGVEKA 346 d1j93a_ 302 INDTVKKAGKGKHILNLGHGIKVGTPEENFA 332 :::::::::: ::::::::::::::::::: d1kbia1 347 IEILRDEIEM--SMRLLGVTSIAELKPDLLD 375