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 | d1k87a2 | Proline dehydrohenase domain of bifunctional PutA protein | FAD-linked oxidoreductase | 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 <-- 0.934 --> HitDALI alignment (Z-score: 9.8 Raw score:1212.10) d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvDLVVEIsLQPW 60 :::::: :::: d1k87a2 1 ------------------------------------------------gETIAEA-LANA 11 d1j93a_ 61 KVFR--PDGVILFSDilTPLSgMNIPfdiikgkgpvifdplrtaadvekvrefipeKSVP 118 :::: ::::::::: :::: :::: :::: d1k87a2 12 RKLEekGFRYSYDML--GEAA-LTAA----------------------------daQAYM 40 d1j93a_ 119 -YVGEALTILRKEVNNQ---AAVLGFVGA-pftlaSYVVeggssknftkikrlafaepkv 173 :::::::::::::::: ::::::::: :::: d1k87a2 41 vSYQQAIHAIGKASNGRgiyEGPGISIKLsalhprYSRA--------------------- 79 d1j93a_ 174 LHALLQ-KFATSMAKYIRYQADsGAQAVQIFDSWAtelspvdfeefSLPYLKQIVDSvkL 232 :::::: ::::::::::::::: :::::::::::: ::::::::::: : d1k87a2 80 QYDRVMeELYPRLKSLTLLARQ-YDIGINIDAEEA------drleiSLDLLEKLCFE--P 130 d1j93a_ 233 THPNL-PLILYASG----SGGLLERLPLTG-----vDVVSLD------------------ 264 ::::: :::::::: :::::::::::: :::::: d1k87a2 131 ELAGWnGIGFVIQAyqkrCPLVIDYLIDLAtrsrrrLMIRLVkgaywdseikraqmdgle 190 d1j93a_ 265 ------------WTVD--MADGRRrlGPNV-AIQGNVdpgvlfgskefITNRINDTVKKA 309 :::: :::::: :::: :::::: :::::::::::: d1k87a2 191 gypvytrkvytdVSYLacAKKLLA--VPNLiYPQFAT----------hNAHTLAAIYQLA 238 d1j93a_ 310 G----KGKHILNLghGIKVgtpeenFAHFFEIAK------GLRY---------------- 343 : :::::::: :::: ::::::::: :::: d1k87a2 239 GqnyyPGQYEFQC--LHGM------GEPLYEQVTgkvadgKLNRpcriyapvgthetlla 290 d1j93a_ 344 ------------------------------------------------------------ 344 d1k87a2 291 ylvrrllengantsfvnriadtslpldelvadpvtaveklaqqegqtglphpkiplprdl 350 d1j93a_ 344 - 344 d1k87a2 351 y 351 FAST alignment (Normalized score: 5.22 Raw score:1812.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS-ENVDLVVEISLQP 59 ::::::::::::: d1k87a2 1 ----------------------------------------------GETIAEALANARKL 14 d1j93a_ 60 WKVFRP--DGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS- 116 :: :::::: d1k87a2 15 EE----KGFRYSYD---------------------------------------------M 25 d1j93a_ 117 --------------VPYVGEALTILRKEVNNQ---AAVLGFVGAPFTLASYVVEGGSSKN 159 :::::::::::::::::: ::::::: ::::: d1k87a2 26 LGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISI-KLSAL------------ 72 d1j93a_ 160 FTKIKRLAFAEPKV-------LHALL-QKFATSMAKYIRYQADSGA-QAVQIFDSWATEL 210 ::::: ::::::::::::::::: ::::: d1k87a2 73 --------------HPRYSRAQYDRVMEELYPRLKSLTLLARQY--DIGINI-------- 108 d1j93a_ 211 SPVDFEE-----FSLPYLKQIVDSVK--LTHPNL-PLILYASG------SGGLLERLPLT 256 :::::::::::::: :::::: :::::: :::::::::: d1k87a2 109 -------DAEEADRLEISLDLLEKLCFEPELAGWNGIGFVI--QAYQKRCPLVIDYLID- 158 d1j93a_ 257 GV--------DVVSLDWTV--------------------------------DMADGRRRL 276 ::::: :::::::: d1k87a2 159 --LATRSRRRLMIRL----VKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKK- 211 d1j93a_ 277 G-----PNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKG------KHILNLGHGIKVG 325 ::::: ::::: ::::::::::::: :::: d1k87a2 212 -LLAVPNLIYP-QFATH---------NAHTLAAIYQLAG--QNYYPGQYEF--------- 249 d1j93a_ 326 T------PEENFAHFFEIAKGLRY------------------------------------ 343 :::::::: d1k87a2 250 -QCLHGMGEPLYEQV---------TGKVADGKLNRPCRIYAPVGTHETLLAYLVRRLLEN 299 d1j93a_ 344 ---------------------------------------------------- 344 d1k87a2 300 GANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRDLY 351 TMalign alignment (TM-score: 0.41 Raw score:139.67) d1j93a_ 1 ---------------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQ-LLCEKYPLFRD 44 :::::::::: : :: ::::::::: d1k87a2 1 GETIAEALANARKLE---------------EKGFRYSYDM-L----GEA--ALTAADAQA 38 d1j93a_ 45 RSENVDLVVEISLQPWKVFR-P---DGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLR 100 :: ::::::::::::::: : ::::::::::: :::: ::::: d1k87a2 39 YM---VSYQQAIHAIGKASNGRGIYEGPGISIKLSA--------LHPR----YSRAQ--- 80 d1j93a_ 101 TAADVEKVR---EFIP--EKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVE-- 153 : : :::::::::::::::: :::::: :: ::::: d1k87a2 81 --------YDRV---MEE--LYPRLKSLTLLARQYD-----IGINID---AE-EADRLEI 118 d1j93a_ 154 --------------------------GGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAK 187 : :: ::::::::::: d1k87a2 119 SLDLLEKLCFEPELAGWNGIGFVIQA-------------Y------QK-RCPLVIDYLID 158 d1j93a_ 188 YIRYQADSGAQAVQIFDSWATE-----------------L-SPVDFEEFSLPYLKQIVDS 229 ::::::: : ::::::::::: : :::::::::::::::::: d1k87a2 159 LATRSRR--R-LMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLA- 214 d1j93a_ 230 VKLTHPNLPLILYASGSGGLLERLPLTG-------VDVVSL----DWTVDMADGRRRLGP 278 ::: : ::::::: ::::::::::::: :::::: ::::::: : d1k87a2 215 VPN-L--IYPQFAT-HNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQ--V----- 263 d1j93a_ 279 NVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGT------------ 326 : : ::::::: :::: :: ::::::: d1k87a2 264 ---T-G-------------------KVADGKL-NRPC-RI-YAPVGTHETLLAYLVRRLL 297 d1j93a_ 327 ------------------------------------------------------PEENFA 332 d1k87a2 298 ENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRDLY------ 351 d1j93a_ 333 HFFEIAKGLRY 343 d1k87a2 352 ----------- 352 HHsearch alignment (Probability: 0.02 E-value:0.87) d1j93a_ 292 FGSKEFI-TNRINDTVKKAGKGKHIL 316 ::::::: :::::::::::::::::: d1k87a2 282 VGTHETLLAYLVRRLLENGANTSFVN 307