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 | d1vlwa_ | KDPG aldolase | 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 <-- 1.152 --> HitDALI alignment (Z-score: 10.9 Raw score:1133.00) d1j93a_ 1 tqpllLDAVrgkeverPPVWLMRQagrymksyqllcekyplfrdrSENVDLVVEISLQPW 60 :::: :::::::: ::::::::::::::: d1vlwa_ 1 -hhmkMEEL-----fkKHKIVAVL--------------------rANSVEEAKEKALAVF 34 d1j93a_ 61 KVFrPDGVILFSDiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvPYV 120 ::: ::::::::: ::: d1vlwa_ 35 EGG-VHLIEITFT-------------------------------------------vPDA 50 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGApftlasyvveggssknftkikrlafaepkvlhallqk 180 ::::::::::::::::::::::: d1vlwa_ 51 DTVIKELSFLKEKGAIIGAGTVT------------------------------------- 73 d1j93a_ 181 fatsMAKYIRYQADSGAQAVQIFDswatelspvdfeefslpyLKQIVDSVKLthPNLPLI 240 :::::::::::::::::::: :::::::::: :::::: d1vlwa_ 74 ----SVEQCRKAVESGAEFIVSPH-----------------lDEEISQFCKE--KGVFYM 110 d1j93a_ 241 LYAsgSGGL-LERLPLTGVDVVSL--DWTVDMADGRRR--lGPNVAIQGNVDPgvlfgsk 295 ::: :::: :::::::::::::: :::::::::::: :::::::::::: d1vlwa_ 111 PGV--MTPTeLVKAMKLGHTILKLfpGEVVGPQFVKAMkgpFPNVKFVPTGGV------- 161 d1j93a_ 296 efITNRINDTVKKAgkgkHILNlgHGIK-----vgtpeENFAHFFEIAKGLry 343 :::::::::::: :::: :::: ::::::::::::: d1vlwa_ 162 --NLDNVCEWFKAG---vLAVG--VGSAlvkgtpdevrEKAKAFVEKIRGC-- 205 FAST alignment (Normalized score: 6.59 Raw score:1747.00) d1j93a_ 1 TQPLLLDAVRGKEVERP------------PVWLMRQAGRYMKSYQLLCEKYPLFRDR--- 45 :::: d1vlwa_ 1 -----------------HHMKMEELFKKHKIVA------------------------VLR 19 d1j93a_ 46 SENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADV 105 ::::::::::::::: :::::::::: d1vlwa_ 20 ANSVEEAKEKALAVF-EGGVHLIEIT---------------------------------- 44 d1j93a_ 106 EKVREFIPEKSVP----YVGEALTILRKEVNN--QAAVLGFVGAPFTLASYVVEGGSSKN 159 ::::::::::::: :::::: d1vlwa_ 45 -------------FTVPDADTVIKELSFLK--EKGAIIGA-------------------- 69 d1j93a_ 160 FTKIKRLAFAEPKVLHALLQKFATS----MAKYIRYQADSGAQAVQIFDSWATELSPVDF 215 :::::::::::::::::: d1vlwa_ 70 -------------------------GTVTSVEQCRKAVESGAEFIVS------------- 91 d1j93a_ 216 EEFSLPY---LKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSL--DWTV--- 267 :::::::::: :::::::::: :::::::::::::::::: :::: d1vlwa_ 92 -------PHLDEEISQFCKE--KGVFYMPGVM-TPTELVKAMKLGHTILKLFPGEVVGPQ 141 d1j93a_ 268 DMADGRRRLGPNVAIQGNVDPGVLFGSKEF------ITNRINDTVKKAGKGKHILNLGHG 321 :::::::: :::::: :::::::::: d1vlwa_ 142 FVKAMKGP-FPNVKF---------------VPTGGVNLDNVCEWFK-------------- 171 d1j93a_ 322 IKVG--------------TPEENFAHFFEIAKGLRY------ 343 :::::::::::::: d1vlwa_ 172 ----AGVLAVGVGSALVKGTPDEVREKAKAFV----EKIRGC 205 TMalign alignment (TM-score: 0.39 Raw score:133.65) d1j93a_ 1 TQPLLLDAVRGKEV-----------------------ERPPVWLMRQAGRYMKSYQLLCE 37 ::::::::: :::: :::::::::::: : d1vlwa_ 1 HHMKMEELF-KKHKIVAVLRANSVEEAKEKALAVFEG-GVHLIEITFTVP---D------ 49 d1j93a_ 38 KYPLFRDRSENVDLVVEISLQPWKVFR------PDGVILFSDILTPLSGMNIPFDIIKGK 91 : :::::::: ::::::::: : d1vlwa_ 50 -----------------A-DTVIKELSFLKEKGAIIGAGTVT--S--------------- 74 d1j93a_ 92 GPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYV 151 ::::: :::::: ::::::::: d1vlwa_ 75 ----------------------------VEQCR-KAVESG---AEFIVSPHL-------- 94 d1j93a_ 152 VEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSG-AQAVQIFDSWATEL 210 : :::::::::: :::::: : d1vlwa_ 95 ---------------------------------D-EEISQFCKEKGVFYMPG-V------ 113 d1j93a_ 211 SPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLP-LT--G--VDVVSLDW 265 :::::::::::: :: :::::::::: ::::::: :: : ::::::: d1vlwa_ 114 --------MTPTELVKAMKL---GH-TILKLFPGEV-VGPQFVKAMKGPFPNVKFVPTG- 159 d1j93a_ 266 TVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVG 325 :::::::::::::::::::::::::::::: :::::::::::::::: d1vlwa_ 160 GVNLDNVCEWFKAGVLAVGVGSALVKGTPD-EVREKAKAFVEKIRGC------------- 205 d1j93a_ 326 TPEENFAHFFEIAKGLRY 343 d1vlwa_ 206 ------------------ 206 HHsearch alignment (Probability: 0.81 E-value:0.00) d1j93a_ 279 NVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVG---TPEENFAHFF 335 :::::::::: ::::::::: :::::::::::::: :::::::::: d1vlwa_ 154 KFVPTGGVNL-----------DNVCEWFKA---GVLAVGVGSALVKGTPDEVREKAKAFV 199 d1j93a_ 336 EIAKG 340 ::::: d1vlwa_ 200 EKIRG 204