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 | d1kbla1 | Pyruvate phosphate dikinase, C-terminal domain | 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 <-- 1.066 --> HitDALI alignment (Z-score: 9.7 Raw score:1168.90) d1j93a_ 1 --------tqpllldavrgkeveRPPVWLMRqagrymksyqllcekyplfrdrsenvdlV 52 :::::::: : d1kbla1 1 ietqeasvsgsferimvwadkfrTLKVRTNA---------------------------dT 33 d1j93a_ 53 VEISLQPWKvFRPDGVilfSDILTPLS----gmNIPFdiikgkgpvifdplrtAADVEK- 107 ::::::::: :::::: :::::::: :::: :::::: d1kbla1 34 PEDTLNAVK-LGAEGI-glCRTEHMFFeadrimKIRK-------------milSDSVEAr 78 d1j93a_ 108 -VREF-IPEKSVPYVGEALTILRkevnnqaAVLG-FVGApftlasYVVEGG--------- 155 :::: ::::::::::::::::: :::: :::: :::::: d1kbla1 79 eEALNeLIPFQKGDFKAMYKALE-------GRPMtVRYL-----dPPLHEFvphteeeqa 126 d1j93a_ 156 -----------------------sSKNFtkikrlafaepkvlHALLqKFATSMAKYIRYQ 192 :::: :::: ::::::::::::: d1kbla1 127 elaknmgltlaevkakvdelhefnPMMG-------hrgcrlaVTYP-EIAKMQTRAVMEA 178 d1j93a_ 193 ADSG------aQAVQIFDSWATelspvDFEEfSLPYLKQIVDSVKLTH-----PNLPLIL 241 :::: ::::::::::: :::: :::::::::::::::: ::::::: d1kbla1 179 AIEVkeetgidIVPEIMIPLVG-----EKKE-LKFVKDVVVEVAEQVKkekgsDMQYHIG 232 d1j93a_ 242 YASGSGGL---LERLPLTgVDVVSLDWT-------------------------------- 266 :::::::: ::::::: ::::::::: d1kbla1 233 TMIEIPRAaltADAIAEE-AEFFSFGTNdltqmtfgfsrddagkfldsyykakiyesdpf 291 d1j93a_ 267 ---------vDMADGRRRLG---PNVAIQGnvdpgvlfgskefITNRINDTVKKAgkgkH 314 :::::::::: ::::::: :::::::::::: : d1kbla1 292 arldqtgvgqLVEMAVKKGRqtrPGLKCGI-------cgehggDPSSVEFCHKVG---lN 341 d1j93a_ 315 ILNlghgikvgtpeenFAHFFEIAKGLRY-- 343 ::: ::::::::::::: d1kbla1 342 YVS--------cspfrVPIARLAAAQAALnn 364 FAST alignment (Normalized score: 4.75 Raw score:1677.00) d1j93a_ 1 TQPLLLDAVRGKEVE-----------------------RPPVWLMRQAGRYMKSYQLLCE 37 :::::: d1kbla1 1 ---------------IETQEASVSGSFERIMVWADKFRTLKVRT---------------- 29 d1j93a_ 38 KYPLFRDRSENVDL---VVEISLQPWKVFRPDG--VILFSDILTPLSGMNIPFDIIKGKG 92 :::::::::: :::: :::: ::::: d1kbla1 30 --------------NADTPEDTLNAVK-LGAE-GIGLCR--TEHMF-------------- 57 d1j93a_ 93 PVIFDPLR-----------------TAADVEKVREFIPEKS----VPYVGEALTILRKEV 131 ::::::: ::::::::::::::: d1kbla1 58 --------FEADRIMKIRKMILSDSVEAREEA---------LNELIPFQKGDFKAMYKAL 100 d1j93a_ 132 NNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV------------------ 173 : :::::: d1kbla1 101 E-GRPMTV----------------------------------RYLDPPLHEFVPHTEEEQ 125 d1j93a_ 174 --------------------------------------LHALLQKFATSMAKYIRYQADS 195 ::::::::::::::::::::: d1kbla1 126 AELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKE- 184 d1j93a_ 196 GA-----QAVQIFDSWATE-LSPVDFEEFSLPYLKQIVDSVKLTH-PNLPLILYA----S 244 ::::::::: :::::::: :::::::::::::::: ::::::::: : d1kbla1 185 --ETGIDIVPEIMIPL---VGEKKELKF-VKDVVVEVAEQVKKEKGSDMQYHIGTMIEIP 238 d1j93a_ 245 GSGGLLERLPLT-GVDVVSLDWTV------------------------------------ 267 :::::::::: ::::::: d1kbla1 239 RAALTADAIA--EEAEFFSF----GTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFA 292 d1j93a_ 268 ---------DMADGRRRL----GPNVAIQGNVDPGVLFGSKEF--------ITNRINDTV 306 :::::::: :::::: ::::::::: d1kbla1 293 RLDQTGVGQLVEMAVKK-GRQTRPGLKC---------------GICGEHGGDPSSVEFCH 336 d1j93a_ 307 KKAGKGKHILNLGHGIKVGTP---------EENFAHFFEIAKGLRY----- 343 : ::::::::::::: d1kbla1 337 K--------------------VGLNYVSCSPFRVPIARLAAAQ---AALNN 364 TMalign alignment (TM-score: 0.55 Raw score:188.30) d1j93a_ 1 ----------------------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEK 38 :::::::: : d1kbla1 1 IETQEASVSGSFERIMVWADKF--------------RTLKVRTN-A-------------- 31 d1j93a_ 39 YPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 : :::::::::: ::::::::::::::::::::::: :::: d1kbla1 32 -------D-----TPEDTLNAVK-LGAEGIGLCRTEHMFFEADRIMK---------IRKM 69 d1j93a_ 99 LRTAADVEKV-R-EFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGG- 155 ::: :::::: : :::::::::::::::::::: : :::::::: :: ::::::: d1kbla1 70 ILS-DSVEAREEALNELIPFQKGDFKAMYKALE---G--RPMTVRYL--DP-PLHEFVPH 120 d1j93a_ 156 --------------------------SS-KNFTKIK--RLAFAEPKVLHALLQKFATSMA 186 :: ::::::: : : :: :::::::::: d1kbla1 121 TEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGC--R---L--AV-TYPEIAKMQT 172 d1j93a_ 187 KYIRYQAD-SG-----AQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKL-T----HP 235 :::::::: :: ::::::::: :: :: ::: :::::::::::::: : :: d1kbla1 173 RAVMEAAIEVKEETGIDIVPEIMIP-LV--GE--KKE-LKFVKDVVVEVAEQVKKEKGSD 226 d1j93a_ 236 NLPLILYASGSGGL---LERLPLTGVDVVSLDW--------------------------- 265 :::::::::::::: ::::::: :::::::: d1kbla1 227 MQYHIGTMIEIPRAALTADAIAEE-AEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKI 285 d1j93a_ 266 -------------TVD-MADGRRRL--GPNVAIQGNVDPGVLFGSKEFITNRINDTVKKA 309 ::: :::::::: :::::::::::::::: :: ::::::::: d1kbla1 286 YESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGD-----PS-SVEFCHKVG 339 d1j93a_ 310 GKGKHILNLGHGIKVGTPEENFAHFFEIAKG-LR-Y 343 ::::: :: : : ::::::::::: :: : d1kbla1 340 ----LNYVS--CS---P-F-RVPIARLAAAQAALNN 364 HHsearch alignment (Probability: 0.07 E-value:0.04) d1j93a_ 130 EVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYI 189 :::::::::::::::::: :::::::::::::::::: d1kbla1 145 ELHEFNPMMGHRGCRLAV---------------------TYPEIAKMQTRAVMEAAI--- 180 d1j93a_ 190 RYQADSGAQA-VQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHP---NLPLILY-AS 244 :::::::::: ::::::::: :::::: :::::::::::::::::: ::::::: :: d1kbla1 181 EVKEETGIDIVPEIMIPLVG--EKKELK-FVKDVVVEVAEQVKKEKGSDMQYHIGTMIEI 237 d1j93a_ 245 GSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNV-------AIQGNVDPGVLFG--SK 295 ::::::::::::::::::::: :::::::::::::: ::::::::::::: :: d1kbla1 238 PRAALTADAIAEEAEFFSFGT-NDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQ 296 d1j93a_ 296 EFITNRINDTVKKAGKG---KHILNLGHGIKVGTPEENFAHFFE 336 ::::::::::::::::: :::: ::::::: :::::::::: d1kbla1 297 TGVGQLVEMAVKKGRQTRPGLKCG--ICGEHGG-DPSSVEFCHK 337