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 | d1o94a1 | Trimethylamine dehydrogenase, N-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 <-- 1.564 --> HitDALI alignment (Z-score: 13.3 Raw score:1564.00) d1j93a_ 1 ------tqplllDAVRgkeverPPVWLMRQAGrymksyqllcekyplfrDRSE-NVDLVV 53 :::: :::::::::: :::: :::::: d1o94a1 1 ardpkhdilfepIQIG-pktlrNRFYQVPHCI-----------------GAGSdKPGFQS 42 d1j93a_ 54 EISLQPWKvFRPDGVILFsdILTPLSgmnipFDIIkgkgpvifdplrtaadvekvrefip 113 :::::::: ::::::::: :::::: :::: d1o94a1 43 AHRSVKAE-GGWAALNTE-yCSINPE---sdDTHR----------------------lsa 75 d1j93a_ 114 ekSVPYVGEALTILRKE-VNNQAAVLGFVGapftLASYvvEGGS--sknftkIKRL---- 166 ::::::::::::::: :::::::::::: :::: :::: :::: d1o94a1 76 riWDEGDVRNLKAMTDEvHKYGALAGVELW----YGGA--HAPNmesratprGPSQyase 129 d1j93a_ 167 ---afaepkVLHALLQKFATSMAKYIRYQADSGAQAVQIFDS------WATE-------- 209 ::::::::::::::::::::::::::::::::: :::: d1o94a1 130 fetlsyckeMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAhsylplQFLNpyynkrtd 189 d1j93a_ 210 ----lSPVDFEeFSLPYLKQIVDSVKlthPNLPLILYASG--------------SGGLLE 251 :::::: :::::::::::::: ::::::::::: :::::: d1o94a1 190 kyggsLENRAR-FWLETLEKVKHAVG---SDCAIATRFGVdtvygpgqieaevdGQKFVE 245 d1j93a_ 252 RLPLtGVDVVSLD---------------------WTVDMADGRRRLGpnVAIQgNVDPGV 290 :::: :::::::: ::::::::::::: :::: :::::: d1o94a1 246 MADS-LVDMWDITigdiaewgedagpsrfyqqghTIPWVKLVKQVSK--KPVL-GVGRYT 301 d1j93a_ 291 lfgskefITNRINDTVKKAGkgkHILNLghGIKV-gtpeenFAHFfeiakglry 343 ::::::::::::: ::::: :::: :::: d1o94a1 302 -------DPEKMIEIVTKGY--aDIIGC--ARPSiadpflpQKVE----qgryd 340 FAST alignment (Normalized score: 6.57 Raw score:2242.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----------------------PVWLMRQAGRYMKSYQLLCEK 38 :::::::: d1o94a1 1 -----------------ARDPKHDILFEPIQIGPKTLRNRFYQVPHC------------- 30 d1j93a_ 39 YPLFRDR----SENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPV 94 :::::::::::::::: :::::::: d1o94a1 31 -------IGAGSDKPGFQSAHRSVKAE-GGWAALNT------------------------ 58 d1j93a_ 95 IFDPLRTAADVEKVREFIPEKS------------------------VPYVGEALTILRKE 130 ::::::::::::: d1o94a1 59 ----------------------EYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHK- 95 d1j93a_ 131 VNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV---------------- 173 :::::::: d1o94a1 96 ---YGALAGVEL--------------------------------WYGGAHAPNMESRATP 120 d1j93a_ 174 -------------------LHALLQKFATSMAKYIRYQADSGAQAVQIFDS---WATELS 211 :::::::::::::::::::::::::::::::: :::: d1o94a1 121 RGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQ-- 178 d1j93a_ 212 PV---------------DFEEFSLPYLKQIVDSVKLT-HPNLPLILYASG---------- 245 :::: ::::::::::::::: :::::::::: d1o94a1 179 --FLNPYYNKRTDKYGGSLEN-RARFWLETLEKVKHAVGSDCAIATRF--GVDTVYGPGQ 233 d1j93a_ 246 ------SGGLLERLPLTGVDVVSLDWTV-------------------------DMADGRR 274 :::::::::: ::::::: ::::::: d1o94a1 234 IEAEVDGQKFVEMADS-LVDMWDI----TIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQ 288 d1j93a_ 275 RLGPNVAIQGNVDPGVLFGSKEF-------ITNRINDTVKKAGKGKHILNLGHGIKVGTP 327 :: :::: :::::::::: d1o94a1 289 VS--KKPV---------------LGVGRYTDPEKMIEIVT-------------------- 311 d1j93a_ 328 EENFAHFFEIAKGLRY----------------------------- 343 d1o94a1 312 ----------------KGYADIIGCARPSIADPFLPQKVEQGRYD 340 TMalign alignment (TM-score: 0.61 Raw score:208.16) d1j93a_ 1 ---------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL 51 ::::::::::: ::::::::::: : :::::::: d1o94a1 1 ARDPKHDIL---FEPIQIGPKTL-RNRFYQVPHCI-----G-----------AGSDKPGF 40 d1j93a_ 52 VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGP--VIFDPLRTAADVEKVR 109 :::::::::: ::::::::: ::: ::: :::::: :: d1o94a1 41 QSAHRSVKAE-GGWAALNTE-YCS-INP---ESDDTH---RLSA---------------- 75 d1j93a_ 110 EFIPEKSVPYVGEALTILRKE-VNNQAAVLGFVGAPFTLASY--------VV----EGGS 156 :: ::::::::::::::: ::::::::::::: ::::: :: :::: d1o94a1 76 --RI--WDEGDVRNLKAMTDEVHKYGALAGVELWY--GGAHAPNMESRATPRGPSQYASE 129 d1j93a_ 157 SKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDS-W---AT-ELS 211 ::::::: : : ::::::::::::::::::::::::::::::::: : :: ::: d1o94a1 130 FETLSYC--K---E--MDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNP 182 d1j93a_ 212 ---------PVDFEEFSLPYLKQIVDSVKLTHPN-LPLILYASGS---------G--GLL 250 ::::::: ::::::::::::::::: :::::::::: : ::: d1o94a1 183 YYNKRTDKYGGSLENR-ARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQ 241 d1j93a_ 251 ERLPLT--GVDVVSLD---------------------WTVDMADGRRRLGPNVAIQGNVD 287 :::::: :::::::: :::::::::::: : ::: :::: d1o94a1 242 KFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVS-K-KPV-LGVG 298 d1j93a_ 288 PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG---LRY 343 : :: ::::::::::::: :::::: ::: :::: :::::::::: d1o94a1 299 R-YT------DPEKMIEIVTKGY--ADIIGC--ARP--SIAD-PFLPQKVEQGRYD--- 340 HHsearch alignment (Probability: 0.83 E-value:0.00) d1j93a_ 176 ALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE--------EFS------LP 221 :::::::::::::::::::::::::::::::::::: :::: ::: :: d1o94a1 142 SDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPL-QFLNPYYNKRTDKYGGSLENRAR 200 d1j93a_ 222 YLKQIVDSVKLTHP-NLPLILYAS-------G------SGGLLERLPLTGVDVVSLDWTV 267 :::::::::::::: ::::::::: : :::::::::::::::::::::: d1o94a1 201 FWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGD 260 d1j93a_ 268 --------------------D-MADGRRRLGPNVAIQGNVD 287 : ::::::::::::::::::: d1o94a1 261 IAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYT 301