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 | d1j6oa_ | Hypothetical protein TM0667 | Metallo-dependent hydrolases | 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 <-- 0.684 --> HitDALI alignment (Z-score: 8.4 Raw score:994.10) d1j93a_ 1 tqpllldavrgkEVERPPVWLMRQAGRYMK--------syqllcekyplfrdrSENVdlV 52 :::::::::::::::::: :::: : d1j6oa_ 1 ------------HHHHMVDTHAHLHFHQFDddrnavissfeenniefvvnvgvNLED--S 46 d1j93a_ 53 VEISLQPWKVFRPdGVILfSDIL-TPLSGmnipfdiikgkgpvifdplrtaadvekvref 111 ::::::::::::: :::: :::: ::::: d1j6oa_ 47 KKSLDLSKTSDRI-FCSV-GVHPhDAKEV------------------------------- 73 d1j93a_ 112 ipEKSV-PYVGEALTILRkevnnqaaVLGF-VGAPFtlASYVveggssknftkikrlafa 169 :::: ::::::::::: :::: ::::: :::: d1j6oa_ 74 --PEDFiEHLEKFAKDEK-------vVAIGeTGLDF--FRNI------------------ 104 d1j93a_ 170 epkvlhaLLQKFATSMAKYIRYQADSgaQAVQIFDSWatelspvdfeefSLPYLKQIVDS 229 ::::::::::::::::::: ::::::::: ::::::::::: d1j6oa_ 105 ------sPAEVQKRVFVEQIELAGKL-nLPLVVHIRD------------AYSEAYEILRT 145 d1j93a_ 230 VklTHPNLPLILYASGSggLLERLPLT--GVDVVSLDWTVD------mADGRRRLGPNVa 281 : :::::::::::::: :::::::: :::::::::::: ::::::::::: d1j6oa_ 146 E--SLPEKRGVIHAFSS--DYEWAKKFidLGFLLGIGGPVTypknealREVVKRVGLEY- 200 d1j93a_ 282 IQGN-----VDPG-VLFGskefitnRINDTVKKA----------GKGKHIlnlghgikvg 325 :::: :::: :::: ::::::::: :::::: d1j6oa_ 201 IVLEtdcpfLPPQpFRGK--rnepkYLKYVVETIsqvlgvpeakVDEATT---------- 248 d1j93a_ 326 tpeenfahffeiakglry 343 d1j6oa_ 249 ------enarriflevke 260 FAST alignment (Normalized score: 4.11 Raw score:1228.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVE------ 54 d1j6oa_ 1 ------------------------------------------------------HHHHMV 6 d1j93a_ 55 -------------ISLQPWKVFRP---------DGVILFSDILTPLSGMNIPFDIIKGKG 92 ::::::: :::: d1j6oa_ 7 DTHAHLHFHQFDDDRNAVIS----SFEENNIEFVVNV----------------------- 39 d1j93a_ 93 PVIFDPLRTAADVEKVREFIPEKSV---PYVGEALTILRKEVNNQAAVLGFVGAPFTLAS 149 :::::::::::::: ::::::::: d1j6oa_ 40 -------------------------GVNLEDSKKSLDLSKTS-DRIFCSVGV-------- 65 d1j93a_ 150 YVVEGGSSKNFTKIKRLAFAEPKVLHALLQKF--------ATSMAKYIRYQAD-SGAQA- 199 ::::::::::::: ::::: d1j6oa_ 66 --------------------------------HPHDAKEVPEDFIEHLEKFAKDEKVVAI 93 d1j93a_ 200 VQIFDSWA----TELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPL 255 ::::: :::: ::::::::::::::::: :::::::::: :::::::: d1j6oa_ 94 GETGL---DFFRNISP----AEVQKRVFVEQIELAGK--LNLPLVVHIR---DAYSEAYE 141 d1j93a_ 256 TG----------VDVVSLDWTVD-----MADGRRRLG---PNVAIQGNVDPGVLFGSKEF 297 :::: ::::::: ::::: d1j6oa_ 142 --ILRTESLPEKRGVI-------HAFSSDYEWAKK--FIDLGFLL--------------- 175 d1j93a_ 298 I----------TNRINDTVKKAGKGKHILNLGHGIKVGTPEEN----------------- 330 ::::::::::::::::::: d1j6oa_ 176 -GIGGPVTYPKNEALREVVKRVGLEYIVLE-------------TDCPFLPPQPFRGKRNE 221 d1j93a_ 331 ---FAHFFEIAKGLRY-------------------------- 343 :::::::::: d1j6oa_ 222 PKYLKYVVETISQ---VLGVPEAKVDEATTENARRIFLEVKE 260 TMalign alignment (TM-score: 0.48 Raw score:164.54) d1j93a_ 1 --TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQ 58 :::::::::::: :::::: : ::::: d1j6oa_ 1 HH---------------HHMVDTHAHLHF--HQFDDD---------------R--NAVIS 26 d1j93a_ 59 PWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP 118 ::::::::::::::::::: : : d1j6oa_ 27 SFEENNIEFVVNVGVNLED-----------------------------------S---K- 47 d1j93a_ 119 YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALL 178 ::::::::: :: :::::::: ::::: : : d1j6oa_ 48 KSLDLSKTS--DR----IFCSVGVH-PHDAK-E--------------------------V 73 d1j93a_ 179 QKFATSMAKYIRYQADSGAQAVQIFDSWATEL--SPVDFEEFSLPYLKQIVDSVKLTHPN 236 :: :::::::::::::::::::::::::::: :: :::::::::::::::: :: d1j6oa_ 74 PE--DFIEHLEKFAKDEKVVAIGETGLDFFRNIS---PA-EVQKRVFVEQIELAGK-LN- 125 d1j93a_ 237 LPLILYASGSGGLLERLPL-T-GV--DVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLF 292 ::::::::::::::::::: : :: :::::::::: ::::::::::::::::: ::::: d1j6oa_ 126 LPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSD-YEWAKKFIDLGFLLGIG-GPVTY 183 d1j93a_ 293 GSKEFI-TNRINDTVKKAGKGKHILNLGH-GIK----VGTPE--ENFAHFFE--I----- 337 :: :: :: ::::::::::::::::: ::: ::::: :::::::: : d1j6oa_ 184 PK--NEA-LR--EVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGV 238 d1j93a_ 338 -AKGL-RY-------------- 343 :::: :: d1j6oa_ 239 PEAKVDEATTENARRIFLEVKE 260 HHsearch alignment (Probability: 0.89 E-value:0.00) d1j93a_ 236 NLPLILYASGS-GGLLERLPLTGVD---VVSLDWTVDMADGRRRLGPNVAIQGNVDPGVL 291 ::::::::::: ::::::::::::: :::::::::::::::::::::: :::::::: d1j6oa_ 125 NLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFIDLGFL--LGIGGPVT 182 d1j93a_ 292 FGSKEFITNRINDTVKKAGKGKHILNLGHGIK-------VGTPEENFAHFFEIAKGL 341 ::::: ::::::::::::::::::::::: :::::::::::::::::: d1j6oa_ 183 YPKNE----ALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQV 235