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 | d1rqba2 | Transcarboxylase 5S subunit, N-terminal domain | Aldolase | 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 <-- 0.910 --> HitDALI alignment (Z-score: 9.8 Raw score:1197.00) d1j93a_ 1 tqpllldavrgkeVERPPVWLM---RQAGRYMKsyqllcekyplfrdrseNVDLvveisl 57 ::::::::: :::::::: :::: d1rqba2 1 ------reievsePREVGITELvlrDAHQSLMA--------------trmAMEDmvgaca 40 d1j93a_ 58 QPWKvFRPDGVILFSDIltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksv 117 :::: :::::::::::: d1rqba2 41 DIDA-AGYWSVECWGGA---------------------------------tydscirfln 66 d1j93a_ 118 PYVGEALTILRKEVNNqAAVLGFVGAPF-tLASYvveggssknftkikrlafaepkvlha 176 :::::::::::::::: ::::::::::: :::: d1rqba2 67 EDPWERLRTFRKLMPN-SRLQMLLRGQNllGYRH-------------------------- 99 d1j93a_ 177 llqKFATSMAKYIRYQADSGAQAVQIFDSWAtelspvdfeefSLPYLKQIVDSVKLTHpn 236 :::::::::::::::::::::::::::: :::::::::::::::: d1rqba2 100 ---YNDEVVDRFVDKSAENGMDVFRVFDAMN-----------DPRNMAHAMAAVKKAG-- 143 d1j93a_ 237 LPLILYASG----------SGGLLERLPLTGVDVVSLDW------tvDMADGRRRLG--- 277 ::::::::: :::::::::::::::::::: :::::::::: d1rqba2 144 KHAQGTICYtispvhtvegYVKLAGQLLDMGADSIALXDmaallkpqPAYDIIKAIKdty 203 d1j93a_ 278 -PNVAIQGNVDPGVLfgskefitNRINDTVKKAGkGKHILNlghgikvgtpEENF----a 332 :::::::::::::: ::::::::::: :::::: :::: d1rqba2 204 gQKTQINLHCHSTTG--------VTEVSLMKAIEaGVDVVD-------taiSSMSlgpgh 248 d1j93a_ 333 hFFEIAKGLR--------------------------------------------y 343 ::::::::: d1rqba2 249 nPTESVAEMLegtgyttnldydrlhkirdhfkairpkykkfesktlvdtsifksq 303 FAST alignment (Normalized score: 6.60 Raw score:2126.00) d1j93a_ 1 TQPLLLDAVRGKEV--------ERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS------ 46 :::::::: d1rqba2 1 --------------REIEVSEPREVGITEL------------------------VLRDAH 22 d1j93a_ 47 -------ENVDLVVEISLQPWKVFRPDGVILFSD----ILTPLSGMNIPFDIIKGKGPVI 95 ::::::::::::::: :::::: ::::: d1rqba2 23 QSLMATRMAMEDMVGACADIDA-AGYWSV-----ECWGGATYD----------------- 59 d1j93a_ 96 FDPLRTAADVEKVREFIPEKSVP--------YVGEALTILRKEVNNQAAVLGFVGAPFTL 147 ::::::::::::: ::::::::::: d1rqba2 60 -----------------------SCIRFLNEDPWERLRTFRKLM-PNSRLQMLLRG---- 91 d1j93a_ 148 ASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK---------FATSMAKYIRYQADSGAQ 198 :::::::::::::::::: d1rqba2 92 ---------------------------------QNLLGYRHYNDEVVDRFVDKSAENGMD 118 d1j93a_ 199 AVQIFDSWATELSPVDFEEF--SLPYLKQIVDSVKLTHPNLPLILYASG----------- 245 ::::::: :::::::::::::: ::::::::: d1rqba2 119 VFRVFDA-------------MNDPRNMAHAMAAVKK--AGKHAQGTI--CYTISPVHTVE 161 d1j93a_ 246 -SGGLLERLPLTGVDVVSLDWTV--------------DMADGRRRLGPNVAIQGNVDPGV 290 :::::::::::::::::: ::::::::::::::: :::: d1rqba2 162 GYVKLAGQLLDMGADSIAL----ADMAALLKPQPAYDIIKAIKDTYGQKTQI-NLHC--- 213 d1j93a_ 291 LFGSK----EFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAH------------- 333 :::::::::::: d1rqba2 214 -----HSTTGVTEVSLMKAIE--------------------------AGVDVVDTAISSM 242 d1j93a_ 334 -------FFEIAKGLRY------------------------------------------- 343 ::::::: d1rqba2 243 SLGPGHNPTESVAE---MLEGTGYTTNLDYDRLHKIRDHFKAIRPKYKKFESKTLVDTSI 299 d1j93a_ 344 ---- 344 d1rqba2 300 FKSQ 303 TMalign alignment (TM-score: 0.47 Raw score:160.37) d1j93a_ 1 ------TQPLLLDAVRGKEVERPPVWLMRQ---A----GRYMKS---------------- 31 :::: ::::::::: : :::::: d1rqba2 1 REIEVS----------EPRE-VGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWS 49 d1j93a_ 32 --------Y-QLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMN 82 : ::::::: : :::::::::::::::::::::: : :::: d1rqba2 50 VECWGGATYDSCIRFLN----E------DPWERLRTFRKLMPNSRLQMLL-R-GQNL--- 94 d1j93a_ 83 IPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVG 142 ::: : : ::: :::::::::::::: : :::::: d1rqba2 95 --LGY-------R-------------H-YND-EVVDRFVDKSAENG--M-----DVFRVF 123 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQI 202 : :: : :::::::::::::::::::::: d1rqba2 124 D--AM------------------------------N--DPRNMAHAMAAVKKAGKHAQGT 149 d1j93a_ 203 FDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS-GSGG--LLERLP-LT-- 256 :: :: :: :::::::::::::::::: :: :::::::: :::: :::::: :: d1rqba2 150 IC--YT-IS-PVHTVEGYVKLAGQLLDM--GA--DSIALADMAALLKPQPAYDIIKAIKD 201 d1j93a_ 257 -G---VDV-VSLDW--TVDMADGRRRLGPNVAIQGNVDPGVLFG-----SKEFITNRIND 304 : ::: ::::: ::::::::::::::::::::: :::::: ::::::: d1rqba2 202 TYGQKTQINLHCHSTTGVTEVSLMKAIEAGVDVVDTA-ISSMSLGPGHN----PTESVAE 256 d1j93a_ 305 TVK-KAGKGKHIL-------NLGHGIKVGTPEENFAH--------------------FFE 336 ::: ::::: ::: :::::::: d1rqba2 257 MLEGTGYTT-NLDYDRLHKI---------RDHFKAIRPKYKKFESKTLVDTSIFKSQ--- 303 d1j93a_ 337 IAKGLRY 343 d1rqba2 304 ------- 304 HHsearch alignment (Probability: 0.88 E-value:0.00) d1j93a_ 185 MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHP-NLPLILYA 243 ::::::::::::::::::::::::: ::::: :::::::::::: :::::::: d1rqba2 163 YVKLAGQLLDMGADSIALXDMAALL-KPQPA--------YDIIKAIKDTYGQKTQINLHC 213 d1j93a_ 244 SGSGG 248 ::::: d1rqba2 214 HSTTG 218