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 | d1o5ka_ | Dihydrodipicolinate synthase | 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 <-- 1.941 --> HitDALI alignment (Z-score: 11.9 Raw score:1379.50) d1j93a_ 1 tqplLLDAvrgkeverpPVWLMRQagrymksyqllcekyPLFRdrsENVDLvVEISLQ-P 59 :::: ::::::: :::: ::::: :::::: : d1o5ka_ 1 ----HMFR---------GVGTAIV------------tpfKNGE---LDLES-YERLVRyQ 31 d1j93a_ 60 WKVFrPDGVILF---SDILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipekS 116 :::: ::::::: :::::: : d1o5ka_ 32 LENG-VNALIVLgttGESPTV--------------------------------------N 52 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlha 176 :::::::::::::::::::::::::::: d1o5ka_ 53 EDEREKLVSRTLEIVDGKIPVIVGAGTN-------------------------------- 80 d1j93a_ 177 llqkFATSMAKYIRYQADSGAQAVQIFDSWATElspvDFEEfSLPYLKQIVDSVKlthpn 236 ::::::::::::::::::::::::::::: :::: ::::::::::::: d1o5ka_ 81 ----STEKTLKLVKQAEKLGANGVLVVTPYYNK---pTQEG-LYQHYKYISERTD----- 127 d1j93a_ 237 LPLILYAS------GSGG-LLERLPLTG--VDVVSLDWTV--DMADGRRRLG---PNVAI 282 :::::::: :::: ::::::::: :::::::::: :::::::::: ::::: d1o5ka_ 128 LGIVVYNVpgrtgvNVLPeTAARIAADLknVVGIXEANPDidQIDRTVSLTKqarSDFMV 187 d1j93a_ 283 QGNVDPgvlfgskefitnRINDTVKKAgkgkHILNLghgikvgtpeeNFAHFFEIAKGLR 342 :::::: ::::::::: ::::: ::::::::::::: d1o5ka_ 188 WSGNDD------------RTFYLLCAG---gDGVIS------vvsnvAPKQMVELCAEYF 226 d1j93a_ 343 Y----------------------------------------------------------- 343 : d1o5ka_ 227 Sgnleksrevhrklrplmkalfvetnpipvkaalnlmgfienelrlplvpasektvellr 286 d1j93a_ 344 --------- 344 d1o5ka_ 287 nvlkesgll 295 FAST alignment (Normalized score: 7.13 Raw score:2269.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----PVWLMRQAGRYMKSYQLLCEKYPLFRDRS---------- 46 :::: d1o5ka_ 1 -----------------HMFRGVGT-------------------------AIVTPFKNGE 18 d1j93a_ 47 ENVDLVVEISLQPWKVFRPDGVIL----FSDILTPLSGMNIPFDIIKGKGPVIFDPLRTA 102 ::::::::::::::: ::::::: :::: d1o5ka_ 19 LDLESYERLVRYQLE-NGVNALI-VLGTTGES---------------------------- 48 d1j93a_ 103 ADVEKVREFIPEKS----VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 :::::::::::::::::::::::: d1o5ka_ 49 --------------PTVNEDEREKLVSRTLEIVDGKIPVIVG------------------ 76 d1j93a_ 159 NFTKIKRLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQI-FDSWAT-ELSP 212 :::::::::::::::::::::: :::: :::: d1o5ka_ 77 ----------------------AGTNSTEKTLKLVKQAEKLGANGVLVVTPYY--NKPTQ 112 d1j93a_ 213 VDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGG---------LLERLPLT------G 257 ::::::::::::: ::::::::: ::::::: : d1o5ka_ 113 ----EGLYQHYKYISER-----TDLGIVVYN-----VPGRTGVNVLPETAAR-IAADLKN 157 d1j93a_ 258 VDVVSLDWTV------DMADGRRR---LGPNVAIQGNVDPGVLFGSKEFI----TNRIND 304 :::::: :::::::: ::::::: :::::: d1o5ka_ 158 VVGIAE----ANPDIDQIDRTVSLTKQARSDFMV----------------WSGNDDRTFY 197 d1j93a_ 305 TVKKAGKGKHILNLGHGIKVGTPE------------ENFAHFFEIAKGLRY--------- 343 ::: :::::::::::: d1o5ka_ 198 LLC---------------------AGGDGVISVVSNVAPKQMVELCAE---YFSGNLEKS 233 d1j93a_ 344 ------------------------------------------------------------ 344 d1o5ka_ 234 REVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVLKESG 293 d1j93a_ 344 -- 344 d1o5ka_ 294 LL 295 TMalign alignment (TM-score: 0.50 Raw score:172.86) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :: : :::::: ::: : : ::: : ::::::::::::: d1o5ka_ 1 ----HM-F--------RGVGTA-IVT-----P---F-KNG---E---LDLESYERLVRYQ 31 d1j93a_ 61 KVFRPDGVILF---SDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV 117 ::::::::::: :::::: : : d1o5ka_ 32 LENGVNALIVLGTTGESPTV-N-------------------------------------E 53 d1j93a_ 118 PYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL 177 ::::::::::::::::::::::::::: d1o5ka_ 54 DEREKLVSRTLEIVDGKIPVIVGAGTN--------------------------------- 80 d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNL 237 ::::::::::::::::::::::::::: :: ::::::::::::::::: : : d1o5ka_ 81 ---STEKTLKLVKQAEKLGANGVLVVTPYY-NK---PTQEGLYQHYKYISERT---D--L 128 d1j93a_ 238 PLILYASG----SGGLLERLPLT---G--VDVVSLD-WTVD-MADGRRRL-GPN-VAIQG 284 :::::::: ::::::::::: : ::::::: :::: :::::::: ::: ::::: d1o5ka_ 129 GIVVYNVPGRTGVNVLPETAARIAADLKNVVGIAEANPDIDQIDRTVSLTKQARSDFMVW 188 d1j93a_ 285 NVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG-LRY 343 :::::: :: :::::: ::::: :::: : :: :::::::::: ::: d1o5ka_ 189 SGNDDR----------TF-YLLCAG----GDGVI-SVVS--N-VA-PKQMVELCAEYFSG 228 d1j93a_ 344 ------------------------------------------------------------ 344 d1o5ka_ 229 NLEKSREVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNV 288 d1j93a_ 344 ------- 344 d1o5ka_ 289 LKESGLL 295 HHsearch alignment (Probability: 0.95 E-value:0.00) d1j93a_ 182 ATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLIL 241 :::::::::::::::::::::::::::::: ::::::::::::::: :::::: d1o5ka_ 82 TEKTLKLVKQAEKLGANGVLVVTPYYNKPT----QEGLYQHYKYISERT-----DLGIVV 132 d1j93a_ 242 YAS----GS---GGLLERLPLTGVDVVSLDWT-VDMAD------GRRRLGPNVAIQGNVD 287 ::: :: :::::::::::::::::::: ::::: :::::::::::::::: d1o5ka_ 133 YNVPGRTGVNVLPETAARIAADLKNVVGIXEANPDIDQIDRTVSLTKQARSDFMVWSGND 192 d1j93a_ 288 PGV 290 ::: d1o5ka_ 193 DRT 195