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 | d1l6sa_ | 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) | 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 <-- 1.696 --> HitDALI alignment (Z-score: 11.6 Raw score:1332.40) d1j93a_ 1 -----------tqpllldavrgkeverpPVWLMRqagrymksyqLLCEkyplfrdrseNV 49 :::::: :::: :: d1l6sa_ 1 tdliqrprrlrkspalramfeettlslnDLVLPI---fveeeidDYKAveampgvmriPE 57 d1j93a_ 50 DLVVEISLQPWKVFrPDGVILFSDiltplSGMNipfdiikgkgpvifdplrtaadvekVR 109 :::::::::::::: ::::::::: :::: :: d1l6sa_ 58 KHLAREIERIANAG-IRSVMTFGI---shHTDE-------------------------TG 88 d1j93a_ 110 EF-IPEKsVPYVGEaLTILRKEVNNqAAVLGFVG------apfTLASyvveggssknftk 162 :: :::: :::::: :::::::::: :::::::: :::: d1l6sa_ 89 SDaWRED-GLVARM-SRICKQTVPE-MIVMSDTCfceytshghCGVL------------- 132 d1j93a_ 163 ikrlafaePKVLhaLLQKFATSMAKYIRYQADSGAQAVQIFDSwatelspvdfeefSLPY 222 :::: ::::::::::::::::::::::::::::: :::: d1l6sa_ 133 --------XEHG-vDNDATLENLGKQAVVAAAAGADFIAPSAA-------------MDGQ 170 d1j93a_ 223 LKQIVDSVKLT-HPNLPLILY-ASGS-----------------------------gGLLE 251 ::::::::::: ::::::::: :::: :::: d1l6sa_ 171 VQAIRQALDAAgFKDTAIMSYsTKFAssfygpfreaagsalkgdrksyqmnpmnrrEAIR 230 d1j93a_ 252 ---RLPLTGVDVVSLD--WTVD--MADGRRRlgPNVAIQGNVDPGVLFG----------- 293 ::::::::::::: :::: ::::::: :::::::::::::::: d1l6sa_ 231 eslLDEAQGADCLMVKpaGAYLdiVRELRER--TELPIGAYQVSGEYAMikfaalagaid 288 d1j93a_ 294 SKEFITNRINDTVKKAgkgkHILNLghgikvgtpEENFAhffeiakglry 343 :::::::::::::::: ::::: ::::: d1l6sa_ 289 EEKVVLESLGSIKRAG---aDLIFS-yfaldlaeKKILR----------- 323 FAST alignment (Normalized score: 6.81 Raw score:2265.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----------------------------PVWLMRQAGRYMKSY 32 :::: d1l6sa_ 1 -----------------TDLIQRPRRLRKSPALRAMFEETTLSLNDLVL----------- 32 d1j93a_ 33 QLLCEKYPLFRDRS----------------------ENVDLVVEISLQPWKVFRPDGVIL 70 ::::::::::::::: :::::::: d1l6sa_ 33 --------------PIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIAN-AGIRSVMT 77 d1j93a_ 71 FSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV------------- 117 :: d1l6sa_ 78 FG---------------------------------------------ISHHTDETGSDAW 92 d1j93a_ 118 ---PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVL 174 :::::::::::::: :::::::: d1l6sa_ 93 REDGLVARMSRICKQTV-PEMIVMSD---------------------------------- 117 d1j93a_ 175 HA--------------------LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD 214 ::::::::::::::::::::::::::::: d1l6sa_ 118 --TCFCEYTSHGHCGVLAEHGVDNDATLENLGKQAVVAAAAGADFIAPSAA--------- 166 d1j93a_ 215 FEEFSLPYLKQIVDSVKL-THPNLPLILYASG---------------------------- 245 :::::::::::::: :::::::::: d1l6sa_ 167 ----MDGQVQAIRQALDAAGFKDTAIMSY---STKFASSFYGPFREAAGSALKGDRKSYQ 219 d1j93a_ 246 --------SGGLLERLPLTGVDVVSLDWTV--------DMADGRRRLGPNVAIQG--NVD 287 :::::::::::::::::: :::::::: ::::: ::: d1l6sa_ 220 MNPMNRREAIRESLLDEAQGADCLMV----KPAGAYLDIVRELRER--TELPI--GAYQV 271 d1j93a_ 288 PGVLFG------------SKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEE------ 329 ::::: :::::::::::::: d1l6sa_ 272 SGEYA-MIKFAALAGAIDEEKVVLESLGSIKR----------------------AGADLI 308 d1j93a_ 330 ---NFAHFFEIAKGLRY------ 343 :::::: d1l6sa_ 309 FSYFALDLA--------EKKILR 323 TMalign alignment (TM-score: 0.54 Raw score:184.27) d1j93a_ 1 ------------------------TQPLLLDAVRGKEVERPPVWLMRQAG---RYMKSYQ 33 ::::::::::::: :::: d1l6sa_ 1 TDLIQRPRRLRKSPALRAMFEETT-------------LSLNDLVLPIFVEEEI---DDYK 44 d1j93a_ 34 L-------LCEKYPLFRDRSENVDLVVEISLQPWKV--FRPDGVILFSDILTPLSGMNIP 84 : :: ::::::::::::: :::::::::::::: :: :: d1l6sa_ 45 AVEAMPGV----------MR---IPEKHLAREIERIANAGIRSVMTFGISHH-TD---ET 87 d1j93a_ 85 FDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAP 144 : :::::: ::::::::::::::::: ::::::::: d1l6sa_ 88 G-----------------------SDAWRE--DGLVARMSRICKQTVPE-MIVMSDTCF- 120 d1j93a_ 145 FTLASYVVEGGSS--KNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQI 202 ::: :: :::: ::::: : :::::::::::::::::::::::::: d1l6sa_ 121 -CEY-TS--HGHCGV-----LAEHG------V--DNDATLENLGKQAVVAAAAGADFIAP 163 d1j93a_ 203 FDSWATELSPVDFEEFSLPYLKQIVDSVKLT--HPNLPLILY--AS-G------------ 245 :: : ::: ::::::::::: ::::::::: :: : d1l6sa_ 164 SA--A-----------MDG-QVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGS 209 d1j93a_ 246 ----------S-G-G--LLERLP-LT--G-V-DVVSLDWTVDMADGRRRL-GPNVAIQGN 285 : : : :::::: :: : : :::::::::::::::::: ::::::::: d1l6sa_ 210 ALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAY 269 d1j93a_ 286 V---DP-GVL--F----GS-KEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHF 334 : :: ::: : :: :::::::::::::::: ::::: :: ::::: d1l6sa_ 270 QVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGA---DLIFS--YF-------ALDLA 317 d1j93a_ 335 FEIAKGLRY 343 :::::: d1l6sa_ 318 EKKILR--- 323 HHsearch alignment (Probability: 0.61 E-value:0.00) d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 ::::::::::::::::::::::::::::::::: :::: ::: : :: d1l6sa_ 96 GLVARMSRICKQTVPEMIVMSDTCFCEYTSHGH----------CGVL---XEH-G---VD 138 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 :::::::::::::::::::::::::::::::: ::::::::::: ::::: d1l6sa_ 139 NDATLENLGKQAVVAAAAGADFIAPSAAMDGQ----------VQAIRQALDAA--GFKDT 186 d1j93a_ 238 PLILY 242 ::::: d1l6sa_ 187 AIMSY 191