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 | d1tvla_ | Putative monooxygenase YtnJ | 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 <-- 1.150 --> HitDALI alignment (Z-score: 11.0 Raw score:1325.70) d1j93a_ 1 tqpllldavrgkEVERPPVWLMrQAGRY------mksyQLLCekyplfrdrsenVDLVvE 54 :::::::::: ::::: :::: :::: : d1tvla_ 1 ------------RADFIQFGAM-IHGVGgttdgwrhpdVDPS-----------aSTNI-E 35 d1j93a_ 55 ISLQPWKV---FRPDGVILfSDILtplsgmnipfdIIKGKGpvifdplrtaadvekvref 111 :::::::: :::::::: :::: :::::: d1tvla_ 36 FYMKKAQTaekGLFSFIFI-ADGL----------fISEKSI------------------- 65 d1j93a_ 112 ipeksvpyvGEALTILRKEVNnQAAVLGFVGaPFTLasyvveggssknftkikrlafaep 171 :::::::::::: ::::::::: :::: d1tvla_ 66 phflnrfepITILSALASVTK-NIGLVGTFS-TSFT------------------------ 99 d1j93a_ 172 kvlhallqkFATSMAKYIRYQADSG--AQAVQIFDSW----------atELSPVDFEEFS 219 :::::::::::::::: :::::::::: ::::::::::: d1tvla_ 100 ---------EPFTISRQLMSLDHISggRAGWNLVTSPqegaarnhsksnLPEHTERYEIA 150 d1j93a_ 220 LPYLKQIVDSVKL------------------------------------------tHPNL 237 ::::::::::::: :::: d1tvla_ 151 QEHLDVVRGLWNSwehdafihnkktgqffdqaklhrlnhkgkyfqvegplnigrskQGEP 210 d1j93a_ 238 PLILYAsgSGGL-LERLPLtGVDVVSLDWT--vDMADGRRRLG----------PNVAIQG 284 :::::: :::: :::::: :::::::::: :::::::::: ::::::: d1tvla_ 211 VVFQAG--SSETgRQFAAK-NADAIFTHSNsleETKAFYADVKsraadegrdpSSVRIFP 267 d1j93a_ 285 NVdPGVL------------------------------------------------FGSKE 296 :: :::: ::::: d1tvla_ 268 GI-SPIVadteeeaekkyrefaelipienavteakarnltlrevaqemafprtlfIGTPE 326 d1j93a_ 297 FITNRINDTVKKAGkgkHILNLghGIKVGTP-EENFAHFFEIAK--GLRY---------- 343 :::::::::::::: ::::: ::::::: :::::::::::: :::: d1tvla_ 327 RVASLIETWFNAEA--aDGFIV--GSDIPGTlDAFVEKVIPILQerGLYRqdyrggtlre 382 d1j93a_ 344 -------- 344 d1tvla_ 383 nlglgipq 390 FAST alignment (Normalized score: 6.20 Raw score:2266.00) d1j93a_ 1 TQPLLLDAVRGKEV--ERPPVWLMRQAGRYMKSYQLLCEKYPLFR--------------- 43 ::::::: :::: d1tvla_ 1 --------------RADFIQFGA-MIHG-----------------VGGTTDGWRHPDVDP 28 d1j93a_ 44 DRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAA 103 ::::::::::::::::: :::::::::: d1tvla_ 29 SASTNIEFYMKKAQTAE-KGLFSFIFIA-------------------------------- 55 d1j93a_ 104 DVEKVREFIPEKSVP-----------------YVGEALTILRKEVNNQAAVLGFVGAPFT 146 ::::::::::::: ::::::::: :::: d1tvla_ 56 ---------------DGLFISEKSIPHFLNRFEPITILSALASVT-KNIGLVGTF-STSF 98 d1j93a_ 147 LASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK-FATSMAKYIRYQADSGA-----QAV 200 :::::::::::::: ::: d1tvla_ 99 ----------------------------------TEPFTISRQLMSLDH---ISGGRAGW 121 d1j93a_ 201 QIFDSWAT---------------ELSPVDFEEFSLPYLKQIVDSVK-------------- 231 ::: ::::::::::::::::::::::: d1tvla_ 122 NLV-----TSPQEGAARNHSKSNLPEHTERYEIAQEHLDVVRGLWNSWEHDAFIHNKKTG 176 d1j93a_ 232 -----------------------LTHP-----NLPLILYASGSG--GLLERLPLTGVDVV 261 :::: ::::::::: :::::::: ::::: d1tvla_ 177 QFFDQAKLHRLNHKGKYFQVEGPLNIGRSKQGEPVVFQAGS---SETGRQFAAK-NADAI 232 d1j93a_ 262 SLDWTV---DMADGRRRL-----------GPNVAIQGNVDP------------------- 288 ::::: :::::::: :::::: d1tvla_ 233 FTHSN-SLEETKAFYAD-VKSRAADEGRDPSSVRI------FPGISPIVADTEEEAEKKY 284 d1j93a_ 289 ----------------------------------GVLFGSKEFITNRINDTVKKAGKGKH 314 ::::::::::::::::::: d1tvla_ 285 REFAELIPIENAVTEAKARNLTLREVAQEMAFPRTLFIGTPERVASLIETWFN------- 337 d1j93a_ 315 ILNLGHGIKVG-----------TPEENF----AHFFEIAKGLRY---------------- 343 :::::: ::::::::: d1tvla_ 338 -----------AEAADGFIVGSDIPGTLDAFVEKVIPILQE---RGLYRQDYRGGTLREN 383 d1j93a_ 344 ------- 344 d1tvla_ 384 LGLGIPQ 390 TMalign alignment (TM-score: 0.54 Raw score:183.66) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRY-----M-KSYQLLCEKYPLFRDRSENVDLVVE 54 ::::::::::::::: : :::::::: : :: : ::::: d1tvla_ 1 -------------RADFIQFGAMIHGVGGTTDGWRHPDVDPSA---S--TN--I-EFYMK 39 d1j93a_ 55 ISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGK---GPV----IFDPLRTAADVEK 107 ::::::: :::::::: ::: : : ::::: ::: d1tvla_ 40 KAQTAEK--GLFSFIFI-ADG--L------F-ISEKSIPHFLNRFEP------------- 74 d1j93a_ 108 VREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLA 167 : : :::::::::: ::::::::::: : d1tvla_ 75 -----I---T-ILSALASVTK------NIGLVGTFSTS--F------------------- 98 d1j93a_ 168 FAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATE------------LSPVDF 215 : : :::::::::::::::::::::::::::: :::::: d1tvla_ 99 ----------T-E-PFTISRQLMSLDHISGGRAGWNLVTSPQEGAARNHSKSNLPEHTER 146 d1j93a_ 216 EEFSLPYLKQIVDSVKL---------------------------------------TH-- 234 ::::::::::::::::: :: d1tvla_ 147 YEIAQEHLDVVRGLWNSWEHDAFIHNKKTGQFFDQAKLHRLNHKGKYFQVEGPLNIGRSK 206 d1j93a_ 235 PNLPLILYASGSGGLLERLPLTGVDVVSLDW----TVD--MADGRRRLG----PN-VAIQ 283 :::::::::::::::::::::: :::::::: ::: ::::::::: :: :::: d1tvla_ 207 QGEPVVFQAGSSETGRQFAAKN-ADAIFTHSNSLEETKAFYADVKSRAADEGRDPSSVRI 265 d1j93a_ 284 GNVDP------------------------------------------------GVLFGSK 295 ::::: ::::::: d1tvla_ 266 FPGISPIVADTEEEAEKKYREFAELIPIENAVTEAKARNLTLREVAQEMAFPRTLFIGTP 325 d1j93a_ 296 EFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFA-HFFEIAKGLRY----------- 343 ::::::::::::::: ::::: ::::::::::::: ::::::::::: d1tvla_ 326 ERVASLIETWFNAEA---ADGFI-VGSDIPGTLDAFVEKVIPILQERGLYRQDYRGGTLR 381 d1j93a_ 344 --------- 344 d1tvla_ 382 ENLGLGIPQ 390 HHsearch alignment (Probability: 0.33 E-value:0.01) d1j93a_ 286 VDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIA 338 ::::::::::::::::::::::::::::::::: ::::::::::::: d1tvla_ 316 FPRTLFIGTPERVASLIETWFNAEAADGFIVGS-------DIPGTLDAFVEKV 361