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 | d1muma_ | 2-methylisocitrate lyase | Phosphoenolpyruvate/pyruvate domain | 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 <-- 1.140 --> HitDALI alignment (Z-score: 11.5 Raw score:1264.40) d1j93a_ 1 ---tqPLLLDAvrGKEVeRPPVWLMrqagrymksyqllcekyplfrdrsenvdlVVEISL 57 :::::: :::: ::::::: :::::: d1muma_ 1 lhspgKAFRAA--LTKE-NPLQIVG---------------------------tiNANHAL 30 d1j93a_ 58 QPWKVFrPDGVILFSD-----------iLTPLsgmnipfdiikgkgpvifdplrtaadve 106 :::::: ::::::::: :::: d1muma_ 31 LAQRAG-YQAIYLSGGgvaagslglpdlGIST---------------------------- 61 d1j93a_ 107 kvrefipeksVPYVGEALTILRKEVNnqAAVLGFVGApftlasyvveggssknftkikrl 166 :::::::::::::::: ::::::::: d1muma_ 62 ----------LDDVLTDIRRITDVCS--LPLLVDADI----------------------- 86 d1j93a_ 167 afaepkvlhallqKFATSMAKYIRYQADSGAQAVQIFDSW-----------ATELspvdf 215 ::::::::::::::::::::::::::: :::: d1muma_ 87 ----------gfgSSAFNVARTVKSMIKAGAAGLHIEDQVgakrcghrpnkAIVS----- 131 d1j93a_ 216 EEFSLPYLKQIVDSVklTHPNLPLILYASG--------SGGLLERLPLTGVDVVSLDWT- 266 ::::::::::::::: ::::::::::::: ::::::::::::::::::::: d1muma_ 132 KEEMVDRIRAAVDAK--TDPDFVIMARTDAlavegldaAIERAQAYVEAGAEMLFPEAIt 189 d1j93a_ 267 --vDMADGRRRLGpnVAIQGNVDPGVlfgskefitNRIN--DTVKKAgkgkHILNlghgi 322 :::::::::: ::::::::::: :::: :::::: :::: d1muma_ 190 elaMYRQFADAVQ--VPILANITEFG-------atPLFTtdELRSAH---vAMAL--ypl 235 d1j93a_ 323 kvgTPEE---------------------------------nfahffeiakglry 343 :::: d1muma_ 236 safRAMNraaehvynvlrqegtqksvidtmqtrnelyesinyyqyeekldnlfa 289 FAST alignment (Normalized score: 6.49 Raw score:2044.00) d1j93a_ 1 TQP------LLLDAVRGKEVE----RPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD 50 ::::: :::::: d1muma_ 1 ---LHSPGKAFRAA-------LTKENPLQIV----------------------------- 21 d1j93a_ 51 L---VVEISLQPWKVFRPDGVILF------------SDILTPLSGMNIPFDIIKGKGPVI 95 :::::::::: ::::::::: :::: d1muma_ 22 -GTINANHALLAQR-AGYQAIYLSGGGVAAGSLGLPDLGI-------------------- 59 d1j93a_ 96 FDPLRTAADVEKVREFIPEK-SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEG 154 :::::::::::::::: :::::::: d1muma_ 60 --------------------STLDDVLTDIRRITDVC--SLPLLVDA------------- 84 d1j93a_ 155 GSSKNFTKIKRLAFAEPKVLHALLQK------FATSMAKYIRYQADSGAQAVQIFDSWAT 208 :::::::::::::::::::::::: d1muma_ 85 --------------------------DIGFGSSAFNVARTVKSMIKAGAAGLHIED---- 114 d1j93a_ 209 ELSPVDF-----------------EEFSLPYLKQIVDSVK-LTHPNLPLILYASG----- 245 ::::::::::::: :::::::::::: d1muma_ 115 -------QVGAKRCGHRPNKAIVSKEEMVDRIRAAVD---AKTDPDFVIMART--DALAV 162 d1j93a_ 246 -----SGGLLERLPLTGVDVVSLDWTV------DMADGRRRLGP-NVAIQGNVDPGVLFG 293 ::::::::::::::::::: :::::::: :::: d1muma_ 163 EGLDAAIERAQAYVEAGAEMLFPE---AITELAMYRQFADA---VQVPI----------- 205 d1j93a_ 294 SKEFITN-------------RINDTVKKAGKGK---HILNLGHGIKVGTPEENFAHFFEI 337 ::::::: :::: d1muma_ 206 -------LANITEFGATPLFTTDELRS------AHVAMAL-------------------- 232 d1j93a_ 338 AKGLRY------------------------------------------------------ 343 d1muma_ 233 ------YPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 286 d1j93a_ 344 --- 344 d1muma_ 287 LFA 289 TMalign alignment (TM-score: 0.49 Raw score:166.42) d1j93a_ 1 -T-Q-PLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 57 : : ::::::: :::::::::: : ::: d1muma_ 1 LHSPGKAFRAAL---TKENPLQIVG-T------------------------------INA 26 d1j93a_ 58 QPWKVFR---PDGVILFSDILT---PLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREF 111 ::::::: :::::::::::: ::::::::: : d1muma_ 27 NHALLAQRAGYQAIYLSGGGVAAGS----------LGLPDLGIS---------------T 61 d1j93a_ 112 IPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEP 171 : : :::::::::::::: :::::::::: :: d1muma_ 62 -L---D-DVLTDIRRITDVCS--LPLLVDADIG--FG----------------------- 89 d1j93a_ 172 KVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWA---------TELSPVDFEEFSLPY 222 : : :::::::::::::::::::::::::: ::: ::::::::: d1muma_ 90 ------S-S-AFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAI---VSKEEMVDR 138 d1j93a_ 223 LKQIVDSVKLTHPNLPLILYASGS----G-GLL---ERLPLTGVDVVSLD-WTV--DMAD 271 ::::: ::: :::::::::::::: : ::: :::::::::::::: ::: :::: d1muma_ 139 IRAAV-DAK-TDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQ 196 d1j93a_ 272 GRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPE--- 328 :::: :: :::::::::::::: : ::::::::::: ::::: ::::::::: d1muma_ 197 FADA-VQ-VPILANITEFGATP----L-FTTDELRSAHV---AMALY-PLSAFRAMNRAA 245 d1j93a_ 329 --------------------------------------------ENFAHFFEIAKGLRY 343 d1muma_ 246 EHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA--------------- 289 HHsearch alignment (Probability: 0.48 E-value:0.00) d1j93a_ 59 PWKVFRPDGVILFSD 73 ::::::::::::::: d1muma_ 31 LAQRAGYQAIYLSGG 45