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 | d1ezwa_ | Coenzyme F420 dependent tetrahydromethanopterin reductase | 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 <-- 1.126 --> HitDALI alignment (Z-score: 11.4 Raw score:1316.30) d1j93a_ 1 tqpllldavrgkeveRPPVWLMRqagrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 :::::::: ::::::::::::::: d1ezwa_ 1 --------------aEVSFGIEL--------------------lpDDKPTKIAHLIKVAE 26 d1j93a_ 61 KvFRPDGVILfsdILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyV 120 : :::::::: :::: : d1ezwa_ 27 D-NGFEYAWI--cDHYN---------------------------------------nysY 44 d1j93a_ 121 GEALTILRKEVNnQAAVLGFVGAPFTlasyvveggssknftkikrlafaepkvlhallqK 180 :::::::::::: ::::::::::::: : d1ezwa_ 45 MGVLTLAAVITS-KIKLGPGITNPYT---------------------------------R 70 d1j93a_ 181 FATSMAKYIRYQADSG--AQAVQIFDSW---------------atelspvdfeEFSLPYL 223 :::::::::::::::: :::::::::: ::::::: d1ezwa_ 71 HPLITASNIATLDWISggRAIIGMGPGDkatfdkmglpfpckipiwnpeaedeVGPATAI 130 d1j93a_ 224 KQIVDSVKLTH--------------------------PNLPLILYAsgSGGL-LERLPLt 256 ::::::::::: ::::::::: :::: :::::: d1ezwa_ 131 REVKEVIYQYLeggpveyegkyvktgtadvkarsiqgSDIPFYMGA--QGPImLKTAGE- 187 d1j93a_ 257 GVDVVSLDW--tvDMADGRRRLG----------PNVAIQGNVDP---------------- 288 ::::::::: :::::::::: ::::::::::: d1ezwa_ 188 IANGVLVNAsnpkDFEVAVPKIEegakeagrslDEIDVAAYTCFsidkdedkaieatkiv 247 d1j93a_ 289 --------------------------------------------------GVLFgSKEFI 298 :::: ::::: d1ezwa_ 248 vafivmgspdvvlerhgidtekaeqiaeaigkgdfgtaiglvdedmieafSIAG-DPDTV 306 d1j93a_ 299 TNRINDTVKKAgkgkHILNlghGIKVG---tpEENFAHFFEIAKglry 343 ::::::::::: :::: ::::: :::::::::::: d1ezwa_ 307 VDKIEELLKAG---vTQVVvgsPIGPDkekaiELVGQEVIPHFK---- 347 FAST alignment (Normalized score: 6.80 Raw score:2346.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS-----ENVDLVVEI 55 ::::::: ::::::::: d1ezwa_ 1 --------------AEVSFGI-------------------------ELLPDDKPTKIAHL 21 d1j93a_ 56 SLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEK 115 :::::: ::::::::: d1ezwa_ 22 IKVAED-NGFEYAWIC-------------------------------------------- 36 d1j93a_ 116 SVP------YVGEALTILRKEVNNQAAVLGF-VGAPFTLASYVVEGGSSKNFTKIKRLAF 168 ::::::::::::: ::::::: :::::: d1ezwa_ 37 ---DHYNNYSYMGVLTLAAVIT-SKIKLGP-GITNPYT---------------------- 69 d1j93a_ 169 AEPKVLHALLQK-FATSMAKYIRYQADSGA-----QAVQIFDSWATELSPVDFE------ 216 :::::::::::::: :::::: d1ezwa_ 70 ------------RHPLITASNIATLDW---ISGGRAIIGMG-------------PGDKAT 101 d1j93a_ 217 ----------------------EFSLPYLKQIVDSVKLT--------------------- 233 ::::::::::::::::: d1ezwa_ 102 FDKMGLPFPCKIPIWNPEAEDEVGPATAIREVKEVIYQYLEGGPVEYEGKYVKTGTADVK 161 d1j93a_ 234 -----HPNLPLILYASGSGGLLERLPLTGVDVVSLDWTV------DMADGRRRL------ 276 ::::::::::: :::::::::: ::::::: :::::::: d1ezwa_ 162 ARSIQGSDIPFYMGAQ-GPIMLKTAGE-IANGVLV----NASNPKDFEVAVPK-IEEGAK 214 d1j93a_ 277 -----GPNVAIQG--NVDPGV--------------------------------------- 290 :::::: :::: d1ezwa_ 215 EAGRSLDEIDV--AAYTCF--SIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGIDTEKA 270 d1j93a_ 291 ----------------------------LFGSKEFITNRINDTVKKAGKGK---HILNLG 319 ::::::::::::::::: :::: d1ezwa_ 271 EQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGDPDTVVDKIEELLK------AGVTQVV-- 322 d1j93a_ 320 HGIKVGT--------PEENFAHFFEIAKGLRY---- 343 ::::::::::::: d1ezwa_ 323 -------VGSPIGPDKEKAIELVGQEVI----PHFK 347 TMalign alignment (TM-score: 0.48 Raw score:164.01) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQL------------------LCEKYPLF 42 :: :::::::::::::::::: :: d1ezwa_ 1 ------AE--------VSFGIELLPDDKPTKIAHLIKVAEDNGFEYAWICDH------YN 40 d1j93a_ 43 RDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTA 102 :::::: :::::::: :: : :::::::::::::: d1ezwa_ 41 NYSYMG--VLTLAAVI-TS--K--IKLGPGITNPYTRH---------------------- 71 d1j93a_ 103 ADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTK 162 ::: :::::::::::::: : ::::::: :: ::::::::: : d1ezwa_ 72 --------PLI--TASNIATLDWISGG-R-----AIIGMGP--GD-KATFDKMGL----P 108 d1j93a_ 163 IKRL--------AFAEPKVLHALLQKFATSMAKYIRYQAD-------------------- 194 :::: :::::::::::::::::::::: d1ezwa_ 109 FPCKIPIWNPEA------EDEVGPATAIREVKEVIYQYLEGGPVEYEGKYVKTGTADVKA 162 d1j93a_ 195 -S-G--AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGS-GGL 249 : : :::::::: : :: : ::::::: : :::::::::: ::: d1ezwa_ 163 RSIQGSDIPFYMGA---Q------GP---I-MLKTAGE-I------ANGVLVNASNPKDF 202 d1j93a_ 250 LERLPLTG-VD-----VVSLDWTVDMADGRRRLGPN-VAIQGNVDPGVLFGS-KE----- 296 :::::::: :: ::: ::::::::::::::: :: d1ezwa_ 203 EVAVPKIEEGAKEAGR-----------------SLDEIDVAAYTCFSIDKDEDKAIEATK 245 d1j93a_ 297 -------------------------------------------------------FITNR 301 ::::: d1ezwa_ 246 IVVAFIVMGSPDVVLERHGIDTEKAEQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGDPDT 305 d1j93a_ 302 INDTVKK-AGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 343 ::::::: :::::::::: :::::::::::::::::::::::: d1ezwa_ 306 VVDKIEELLKAGVTQVVV-GSPIGPDKEKAIELVGQEVIPHFK 347 HHsearch alignment (Probability: 0.17 E-value:0.01) d1j93a_ 287 DPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIA 338 :::::::::::::::::::::: :::::::::: :::::::::::::::: d1ezwa_ 295 EAFSIAGDPDTVVDKIEELLKA-GVTQVVVGSP---IGPDKEKAIELVGQEV 342