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 | d1bd0a2 | Alanine racemase | PLP-binding barrel | 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 <-- 1.561 --> HitDALI alignment (Z-score: 6.6 Raw score:806.80) d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 d1bd0a2 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeKSVPYV 120 :::::: d1bd0a2 1 ------------------------------------------------------VDLDAI 6 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhallqk 180 :::::::::::::::::::::::: d1bd0a2 7 YDNVENLRRLLPDDTHIMAVVKAN-----------------------------------a 31 d1j93a_ 181 fatSMAKYIRYQADSGAQAVQIFDswatelspvdfeefslPYLKQIV-DSVKlthpnLPL 239 ::::::::::::::::::::: ::::::: :::: ::: d1bd0a2 32 yghGDVQVARTALEAGASRLAVAF---------------lDEALALReKGIE-----API 71 d1j93a_ 240 ILYASGSGGLLERLPLTGVdVVSLDWtvDMADGRRR--lgpNVAIQGNVDPGvlfgskeF 297 ::::::::::::::::::: :::::: :::::::: ::::::::::: : d1bd0a2 72 LVLGASRPADAALAAQQRI-ALTVFRsdWLEEASALysgpfPIHFHLKMDTG-mgrlgvK 129 d1j93a_ 298 ITNRINDTVKKAGK----GKHILNLghGIKV-------GTPE--ENFAHFFEIAKGL--- 341 :::::::::::::: ::::::: :::: :::: ::::::::::::: d1bd0a2 130 DEEETKRIVALIERhphfVLEGLYT--HFATadevntdYFSYqyTRFLHMLEWLPSRppl 187 d1j93a_ 342 --------------------------------------------ry 343 d1bd0a2 188 vhcansaaslrfpdrtfnmvrfgiamyglapspgikpllpyplkea 233 FAST alignment (Normalized score: 3.92 Raw score:1108.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSE-NVDLVVEISLQP 59 :::::::::::: d1bd0a2 1 -----------------------------------------------VDLDAIYDNVENL 13 d1j93a_ 60 WKVFRP-----DGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPE 114 :: :::::: d1bd0a2 14 RR----LLPDDTHIMAV------------------------------------------- 26 d1j93a_ 115 KSVP--------YVGEALTILRKEVNNQAA---VLGFVGAPFTLASYVVEGGSSKNFTKI 163 ::::::::::: ::::: d1bd0a2 27 ----VKANAYGHGDVQVARTALE-------AGASRLAV---------------------- 53 d1j93a_ 164 KRLAFAEPKVLHALLQKFATS-MAKYIRYQADSGA-QAVQIFDSWATELSPVDFEEFSLP 221 ::::::::::::: ::::: d1bd0a2 54 ---------------------AFLDEALALREKGIEAPILV------------------- 73 d1j93a_ 222 Y----LKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGV-------DVVSLDWTV--- 267 ::::::::: ::::::::: :::::::::: :::::: d1bd0a2 74 -LGASRPADAALAA----QQRIALTVF-RSDWLEEASA---LYSGPFPIHFHLK---MDT 121 d1j93a_ 268 -----------DMADGRRRL---GPNVAIQGNVDPGVLF-------GSKEFITNRINDTV 306 :::::::: ::::::::::: :::::::::::::: d1bd0a2 122 GMGRLGVKDEEETKRIVAL-IERHPHFVLEGLYT-----HFATADEVNTDYFSYQYTRFL 175 d1j93a_ 307 ---KKAGKGKHILNLGHGIKVGTP---------EENFAHFFEIAKGLRY----------- 343 ::::: ::::::::: d1bd0a2 176 HMLEWLPS----------------RPPLVHCANSAASLRFPD-------RTFNMVRFGIA 212 d1j93a_ 344 --------------------- 344 d1bd0a2 213 MYGLAPSPGIKPLLPYPLKEA 233 TMalign alignment (TM-score: 0.39 Raw score:132.65) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1bd0a2 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 : ::: ::::: d1bd0a2 1 -------------------V-------------------------------DLD-AIYDN 9 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 ::::::: ::: ::::::::::: ::: d1bd0a2 10 VENLRRL--LPD-DTHIMAVVKAN-AYG-------------------------------- 33 d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLI 240 : ::::::::::::::::::::: :: :::::::::: : :::: d1bd0a2 34 H--GDVQVARTALEAGASRLAVAF--------------LD-EALALREKGI---E-APIL 72 d1j93a_ 241 LYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGP-N-VAIQGNVDP--G---VLFG 293 :::: ::::::::::::::::::::::::::::::::: : ::::::::: : :: d1bd0a2 73 VLGA-SRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVK-- 129 d1j93a_ 294 SKEFITNRINDTVKKAGK---GKHILNLGHGIKV-------G--TPEENFAHFFEIAKGL 341 :: :::::::::::: ::::::: ::::: : ::::::::::::: :: d1bd0a2 130 ---DE-EETKRIVALIERHPHFVLEGLY-THFATADEVNTDYFSYQYTRFLHMLEWL-PS 183 d1j93a_ 342 RY------------------------------------------------ 343 :: d1bd0a2 184 RPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEA 233 HHsearch alignment (Probability: 0.31 E-value:0.05) d1j93a_ 123 ALTILRKEVNNQAAV 137 ::::::::::::::: d1bd0a2 9 NVENLRRLLPDDTHI 23