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 | d1j18a2 | Bacterial beta-amylase | (Trans)glycosidases | 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 <-- 1.386 --> HitDALI alignment (Z-score: 12.9 Raw score:1542.30) d1j93a_ 1 tqpllldavrgkeVERPPVWLMRQAGrymKSYQllcekyplfrdrsenvdlvveisLQPW 60 ::::::::::::: :::: :::: d1j18a2 1 ------avngkgmNPDYKAYLMAPLKkipEVTN-------------------wetfENDL 35 d1j93a_ 61 KVFR---PDGVILFSDILTPLSGMnipfdiikgkgpvifdplrtaadvekvREFIpekSV 117 :::: ::::::::::::::::: :::: :: d1j18a2 36 RWAKqngFYAITVDFWWGDMEKNG---------------------------DQQF---DF 65 d1j93a_ 118 PYVGEALTILRKEVnnqAAVLGFVGA-----------pftlasyVVEGgssknfTKIKR- 165 :::::::::::::: ::::::::: :::: ::::: d1j18a2 66 SYAQRFAQSVKNAG---MKMIPIISThqcggnvgddcnvpipswVWNQ---ksdDSLYFk 119 d1j93a_ 166 ------lafaepkvLHALLQKFATSMAK-YIRYQADSG--AQAVQIFDS---WATE---- 209 :::::::::::::: ::::::::: ::::::::: :::: d1j18a2 120 setgtvnketlnplASDVIRKEYGELYTaFAAAMKPYKdvIAKIYLSGGpagELRYpsyt 179 d1j93a_ 210 ------------------------------------------------------------ 210 d1j18a2 180 tsdgtgypsrgkfqaytefakskfrlwvlnkygslnevnkawgtkliselailppsdgeq 239 d1j93a_ 210 ----------------lSPVDFEEfSLPYL-KQIVDSVKLTHpNLPLILYASG------- 245 ::::::: ::::: ::::::::::: :::::::::: d1j18a2 240 flmngylsmygkdylewYQGILEN-HTKLIgELAHNAFDTTF-QVPIGAKIAGvhwqynn 297 d1j93a_ 246 ---------------sgGLLERLPLTGVdVVSLDW---------------tvDMADGRRR 275 ::::::::::: :::::: :::::::: d1j18a2 298 ptiphgaekpagyndysHLLDAFKSAKL-DVTFTClemtdkgsypeysmpktLVQNIATL 356 d1j93a_ 276 L-GPNVAIQGNVDPGVlfGSKEfITNRINDTVKKAGkgKHILNLghGIKV--gTPEENFA 332 : :::::::::::::: :::: ::::::::::::: :::::: :::: ::::::: d1j18a2 357 AnEKGIVLNGENALSI--GNEE-EYKRVAEMAFNYN--FAGFTL--LRYQdvmYNNSLMG 409 d1j93a_ 333 HFFEIAKGlry 343 :::::::: d1j18a2 410 KFKDLLGV--- 417 FAST alignment (Normalized score: 5.33 Raw score:2018.00) d1j93a_ 1 TQPLLLDAVRGKEVE---------RPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS----- 46 :::::: d1j18a2 1 ---------------AVNGKGMNPDYKAYL-------------------------MAPLK 20 d1j93a_ 47 -----ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRT 101 ::::::::::::::: ::::::::::::::: d1j18a2 21 KIPEVTNWETFENDLRWAKQ-NGFYAITVDFWWGDM------------------------ 55 d1j93a_ 102 AADVEKVREFIPEKS---------VPYVGEALTILRKEVNN-QAAVLGFVGAPFTLASYV 151 ::::::::::::: :::::::: d1j18a2 56 ---------------EKNGDQQFDFSYAQRFAQSVKN----AGMKMIPII---------- 86 d1j93a_ 152 VEGGSSKNFTKIKRLAF------------------------------------------- 168 d1j18a2 87 -----------------STHQCGGNVGDDCNVPIPSWVWNQKSDDSLYFKSETGTVNKET 129 d1j93a_ 169 ---AEPKVLHALLQKFATSMAKYIRYQAD--SGAQAVQIFDSWATEL------------- 210 :::::::::::::::: ::::::: ::::::::: d1j18a2 130 LNPLASDVIRKEYGELYTA---FAAAMKPYKDVIAKIYLS-------GGPAGELRYPSYT 179 d1j93a_ 211 ------------------------------------------------------------ 211 d1j18a2 180 TSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQ 239 d1j93a_ 211 --------------SPVDFEEFSLPYLKQIVD----SVKLTHPNLPLILYASG------- 245 ::::: :::::::::::: :::::: :::::::: d1j18a2 240 FLMNGYLSMYGKDYLEWYQ-GILENHTKLIGELAHNAFDTTF-QVPIGAKI--AGVHWQY 295 d1j93a_ 246 -----------------SGGLLERLPLTGVDVVSLDWTV-------------------DM 269 :::::::::::: ::::: :: d1j18a2 296 NNPTIPHGAEKPAGYNDYSHLLDAFKSAK-LDVTF----TCLEMTDKGSYPEYSMPKTLV 350 d1j93a_ 270 ADGRRRLG---PNVAIQGNVDPGVLF--------GSKEFITNRINDTVKKAGKGK---HI 315 :::::: ::::: ::::::::::::::: :: d1j18a2 351 QNIATL--ANEKGIVL----------NGENALSIGNEEEYKRVAEMAFN------YNFAG 392 d1j93a_ 316 LNLGHGIKVG-----TPEENFAHFFEIAKGLRY-- 343 ::::: ::::::::::::: d1j18a2 393 FTLLR-----YQDVMYNNSLMGKFKDLL-----GV 417 TMalign alignment (TM-score: 0.58 Raw score:200.55) d1j93a_ 1 ------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKS----------------------- 31 ::::: :::::::::: :::: d1j18a2 1 AVNGKG--------MNPDY---KAYLMAPLKK-IPEVTNWETFENDLRWAKQNGFYAITV 48 d1j93a_ 32 ----YQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR---PDGVILFSDIL--------- 75 :::::::::::: :::::::::::: ::::::::::: d1j18a2 49 DFWW--------GDMEKNGDQQFD-FSYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDC 99 d1j93a_ 76 ---T---PL-SG-MNIPFDIIKGKGPVIFDPLRT-------AADVEKVREFI-PEKSVPY 119 : :: :: ::::: : ::::: :::::: ::::::: d1j18a2 100 NVPIPSWVWNQKSDDSLY---------F-KSETGTVNKETL-----NPLASDVIRKEYGE 144 d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAP--FTLASYVVEGGSSKN-FTKIK------------ 164 ::::::::::::::::::::::::: ::::::::::::::: ::::: d1j18a2 145 LYTAFAAAMKPYKDVIAKIYLSGGPAGELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFR 204 d1j93a_ 165 --------------------------------RL-AFA-EP----K--VLHALLQKFATS 184 :: ::: :: : :::::::::::: d1j18a2 205 LWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILENH 264 d1j93a_ 185 MAKYIRYQADSGA----QAVQIFDSWATELSP----VDFEEF--SLPYLKQIVDSVKLTH 234 ::::::::::::: ::::::::::::::: :::::: :::::::::::::::: d1j18a2 265 TKLIGELAHNAFDTTFQVPIGAKIAGVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAK 324 d1j93a_ 235 PNLPLILYASGSG----------G--LLERLPLTG----VDVVSLD--WT---VDMADGR 273 ::::::::::: : ::::::::: ::::::: :: ::::::: d1j18a2 325 --LDVTFTCLEMTDKGSYPEYSMPKTLVQNIATLANEKGIVLNGENALSIGNEEEYKRVA 382 d1j93a_ 274 RRL-GPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFA 332 ::: :::::::::::::::::: :::::::::::: : d1j18a2 383 EMAFNYNFAGFTLLRYQDVMYN-NSLMGKFKDLLG--V---------------------- 417 d1j93a_ 333 HFFEIAKGLRY 343 d1j18a2 418 ----------- 418 HHsearch alignment (Probability: 0.63 E-value:0.00) d1j93a_ 262 SLDWTVDMADGRRRLGPNVAIQG----NVDPGVLFGSKEFITNRINDTVKKAGKGKHILN 317 ::::::::::::::::::::::: :::::::::::::::::: :::::::::::: d1j18a2 309 GYNDYSHLLDAFKSAKLDVTFTCLEMTDKGSYPEYSMPKTLVQNI---ATLANEKGIVLN 365 d1j93a_ 318 LGHGIKVGTPEENFAHFFEIAKGLR 342 :::::::::::::::::::::::: d1j18a2 366 -GENALSIGNEEEYKRVAEMAFNYN 389