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 | d1luca_ | Bacterial luciferase alpha chain, LuxA | Bacterial luciferase-like | 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 <-- 1.238 --> HitDALI alignment (Z-score: 10.4 Raw score:1258.20) d1j93a_ 1 tqpllldavrgkeverPPVWLMRQagrymksyQLLCekypLFRDRSenvdLVVEISLQPW 60 :::::::: :::: :::::: :::::::::: d1luca_ 1 ----------------MKFGNFLL-----tyqPPEL----SQTEVM---kRLVNLGKASE 32 d1j93a_ 61 kVFRPDGVILfsdiltplsgmniPFDIikgkgpvifdplrtaadvekvrefipeksvpyv 120 ::::::::: :::: d1luca_ 33 -GCGFDTVWL----------lehHFTE--------------------------fgllgnp 55 d1j93a_ 121 gEALTILRKEVNNqAAVLG-FVGAPFtlasyvveggssknftkikrlafaepkvlhallq 179 :::::::::::: ::::: :::::: d1luca_ 56 yVAAAHLLGATET-LNVGTaAIVLPT---------------------------------- 80 d1j93a_ 180 KFATSMAKYIRYQADSG--AQAVQIFDSW------atelspvDFEEFSLPYLKQIVDSVK 231 ::::::::::::::::: :::::::::: :::::::::::::::::: d1luca_ 81 AHPVRQAEDVNLLDQMSkgRFRFGICRGLydkdfrvfgtdmdNSRALMDCWYDLMKEGFN 140 d1j93a_ 232 LT----------------------HPNLPLILYAsgSGGL-LERLPLTGVdVVSLDWTV- 267 :: :::::::::: :::: ::::::::: :::::::: d1luca_ 141 EGyiaadnehikfpkiqlnpsaytQGGAPVYVVA--ESAStTEWAAERGL-PMILSWIIn 197 d1j93a_ 268 --DMADGRRRLG----------PNVAIQGNVDPG-------------------------- 289 :::::::::: :::::::::::: d1luca_ 198 thEKKAQLDLYNevatehgydvTKIDHCLSYITSvdhdsnrakdicrnflghwydsyvna 257 d1j93a_ 290 ------------VLFGSKEFITNRINDTVKKAGkgKHILNLghGIKVG----tpEENFAH 333 ::::::::::::::::::::: :::::: ::::: :::::: d1luca_ 258 tkifridysyeiNPVGTPEECIAIIQQDIDATG--IDNICC--GFEANgseeeiIASMKL 313 d1j93a_ 334 FFE-IAKGLRY-- 343 ::: ::::::: d1luca_ 314 FQSdVMPYLKEkq 326 FAST alignment (Normalized score: 5.75 Raw score:1924.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYP----------LFRDRSENVD 50 ::::: :::: ::: d1luca_ 1 ----------------MKFGN-------------------FLLTYQPPELSQTE---VMK 22 d1j93a_ 51 LVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 :::::::::: :::::::::: d1luca_ 23 RLVNLGKASE-GCGFDTVWLL--------------------------------------- 42 d1j93a_ 111 FIPEKSVP-----------YVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKN 159 ::::::::::::: ::::::: d1luca_ 43 --------EHHFTEFGLLGNPYVAAAHLLGAT-ETLNVGT-------------------- 73 d1j93a_ 160 FTKIKRLAFAEPKVLHALLQK--------FATSMAKYIRYQADSGA-----QAVQIFDSW 206 :::::::::::::: :::::: d1luca_ 74 ---------------------AAIVLPTAHPVRQAEDVNLLDQ---MSKGRFRFGIC--- 106 d1j93a_ 207 ATELSPVDFEE----------------FSLPYLKQIVDSVKLTH---------------- 234 :::::::::::::::: d1luca_ 107 -----------RGLYDKDFRVFGTDMDNSRALMDCWYDLMKEG-FNEGYIAADNEHIKFP 154 d1j93a_ 235 -----------PNLPLILYASGSGGLLERLPLTGVDVVSLDWTV---DMADGRRRL---- 276 :::::::::: :::::::::::: ::::::::: :::::::: d1luca_ 155 KIQLNPSAYTQGGAPVYVVAE-SASTTEWAAERG-LPMILSWIINTHEKKAQLDL-YNEV 211 d1j93a_ 277 -------GPNVAIQG--NVDPG-------------------------------------- 289 :::::: :::: d1luca_ 212 ATEHGYDVTKIDH--CLSYIT-SVDHDSNRAKDICRNFLGHWYDSYVNATKIFRIDYSYE 268 d1j93a_ 290 -VLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVG-------------TPEENFAHFF 335 ::::::::::::::::::: :::::::::: d1luca_ 269 INPVGTPEECIAIIQQDIDA-----------------TGIDNICCGFEANGSEEEIIASM 311 d1j93a_ 336 EIAKGLRY----------- 343 :::: d1luca_ 312 KLFQ----SDVMPYLKEKQ 326 TMalign alignment (TM-score: 0.53 Raw score:181.56) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRY-MKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 :::::::::::: : ::::: ::: ::::::::: d1luca_ 1 ----------------MKFGNFLLTYQPP-E--LSQTE------VMK----RLVNLGKAS 31 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF-IPEKSVP 118 :: ::::::: ::::: :: :::::: : : : d1luca_ 32 EG-CGFDTVW-LLEHH-----------FT-EFGLLG---------------NP-Y---V- 57 d1j93a_ 119 YVGEALTILRKEVNNQAAVLGF-VGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 :::::::::: : ::::: ::::: : d1luca_ 58 AAAHLLGATE----T--LNVGTAAIVLP--T----------------------------- 80 d1j93a_ 178 LQKFATSMAKYIRYQADSG-AQAVQIFDSWATE--L-------SPVDFEEFSLPYLKQIV 227 ::::::::::::::::: ::::::::::::: : ::::::::::::::: d1luca_ 81 --AHPVRQAEDVNLLDQMSKGRFRFGICRGLYDKDFRVFGTDM--DNSRALMDCWYDLMK 136 d1j93a_ 228 DSVKL--------------------T-HPN-LPLILYASGSGGLLERLPLTGVDVVSLDW 265 ::::: : ::: ::::::: ::::::::::: ::::::::: d1luca_ 137 EGFNEGYIAADNEHIKFPKIQLNPSAYTQGGAPVYVVA-ESASTTEWAAE-RGLPMILSW 194 d1j93a_ 266 -TV--DMADGRRRLG---------P-NVAIQGNVDP------------------------ 288 :: :::::::::: : :::::::::: d1luca_ 195 IINTHEKKAQLDLYNEVATEHGYDVTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSY 254 d1j93a_ 289 ------------G--VLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGT---PE-EN 330 : ::::::::::::::::::::: :::::: :::::: :: :: d1luca_ 255 VNATKIFRIDYSYEINPVGTPEECIAIIQQDIDATG--IDNICC--GFEANGSEEEIIAS 310 d1j93a_ 331 FAHFF-EIAKGLRY-- 343 ::::: :::::::: d1luca_ 311 MKLFQSDVMPYLKEKQ 326 HHsearch alignment (Probability: 0.76 E-value:0.00) d1j93a_ 288 PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIA 338 ::::::::::::::::::::::::::::::::::::::::::::::::::: d1luca_ 268 EINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEEEIIASMKLFQSDV 318