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 | d1hl2a_ | N-acetylneuraminate lyase | 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 <-- 1.746 --> HitDALI alignment (Z-score: 11.1 Raw score:1298.90) d1j93a_ 1 tqpllLDAVrgkeverpPVWLMRQagrymksyqllcekyPLFRdrsENVDLVVEISLQPW 60 :::: ::::::: :::: :::::::::::::: d1hl2a_ 1 -----TNLR--------GVMAALL-----------tpfdQQQA---LDKASLRRLVQFNI 33 d1j93a_ 61 KvFRPDGVIL---fSDILTPLsgmnipfdiikgkgpvifdplrtaadvekvrefipEKSV 117 : :::::::: ::::::: :::: d1hl2a_ 34 Q-QGIDGLYVggstGEAFVQS-----------------------------------LSER 57 d1j93a_ 118 -PYVGEALTILRkevnNQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlha 176 ::::::::::: :::::::::::: d1hl2a_ 58 eQVLEIVAEEAK----GKIKLIAHVGCV-------------------------------- 81 d1j93a_ 177 llqkFATSMAKYIRYQADSGAQAVQIFDSWatelspVDFEeFSLPYLKQIVDSVKlthpN 236 :::::::::::::::::::::::::: :::: :::::::::::::: : d1hl2a_ 82 ----STAESQQLAASAKRYGFDAVSAVTPF---yypFSFE-EHCDHYRAIIDSAD----G 129 d1j93a_ 237 LPLILYAS------GSGG-LLERLPLTG-VDVVSLDWTV--DMADGRRRlGPNVAIQGNV 286 :::::::: :::: ::::::::: :::::::::: :::::::: :::::::::: d1hl2a_ 130 LPMVVYNIparsgvKLTLdQINTLVTLPgVGALKQTSGDlyQMEQIRRE-HPDLVLYNGY 188 d1j93a_ 287 DPgvlfgskefitnRINDTVKKAgkgkHILNLghgikvgtpeeNFAHFFEIAKGLR---- 342 :: ::::::::: ::::: ::::::::::::: d1hl2a_ 189 DE------------IFASGLLAG---aDGGIG------styniMGWRYQGIVKALKegdi 227 d1j93a_ 343 ------------------------------------------------------------ 343 d1hl2a_ 228 qtaqklqtecnkvidlliktgvfrglktvlhymdvvsvplcrkpfgpvdekylpelkala 287 d1j93a_ 343 -------y 343 d1hl2a_ 288 qqlmqerg 295 FAST alignment (Normalized score: 6.64 Raw score:2112.00) d1j93a_ 1 TQPLLLDAVRGKEVERP----PVWLMRQAGRYMKSYQLLCEK-------YPLFRDRSENV 49 :::: :::: ::: d1hl2a_ 1 -----------------TNLRGVMA-----------------ALLTPFDQQQA----LDK 22 d1j93a_ 50 DLVVEISLQPWKVFRPDGVILFSDIL------TPLSGMNIPFDIIKGKGPVIFDPLRTAA 103 :::::::::::: ::::::: :::: d1hl2a_ 23 ASLRRLVQFNIQ-QGIDGLY------VGGSTGEAFV------------------------ 51 d1j93a_ 104 DVEKVREFIPEKS--VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFT 161 :::::::::::::::::::::::: d1hl2a_ 52 -------------QSLSEREQVLEIVAEEAKGKIKLIAH--------------------- 77 d1j93a_ 162 KIKRLAFAEPKVLHALLQK----FATSMAKYIRYQADSGAQAVQIFDSWAT------ELS 211 :::::::::::::::::::::: ::: d1hl2a_ 78 -------------------VGCVSTAESQQLAASAKRYGFDAVSA------VTPFYYPFS 112 d1j93a_ 212 PVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG---------SGGLLERLPLT-GVDVV 261 : ::::::::::::: :::::::::: ::::::::::: ::::: d1hl2a_ 113 F----EEHCDHYRAIIDS----ADGLPMVVYN--IPARSGVKLTLDQINTLVTLPGVGAL 162 d1j93a_ 262 SLDWTV------DMADGRRRLGPNVAIQGN--VDPGVLFGSKEFITNRINDTVKKAGKGK 313 :: :::::::: :::::: :::: ::::::: d1hl2a_ 163 KQ----TSGDLYQMEQIRRE-HPDLVL---YNGYDE-----------IFASGLL------ 197 d1j93a_ 314 HILNLGHGIKVGTPE------------ENFAHFFEIAKGLRY------------------ 343 :::::::::::: d1hl2a_ 198 ---------------AGADGGIGSTYNIMGWRYQGIVKA---LKEGDIQTAQKLQTECNK 239 d1j93a_ 344 -------------------------------------------------------- 344 d1hl2a_ 240 VIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 295 TMalign alignment (TM-score: 0.50 Raw score:170.28) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :: : ::::::::: : : ::::::: : ::::::::::: d1hl2a_ 1 -----TN-L--------RGVMAALLT-----P---F-DQQQALD---K-ASLRRLVQFNI 33 d1j93a_ 61 KVFRPDGVILF---SDIL-TPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS 116 : ::::::::: :::: ::::: : : d1hl2a_ 34 Q-QGIDGLYVGGSTGEAFVQSLSE------------------------------R-E--- 58 d1j93a_ 117 VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHA 176 : ::::::::::: : ::::::::: : : d1hl2a_ 59 Q-VLEIVAEEAKG-K---IKLIAHVGC--V-S---------------------------- 82 d1j93a_ 177 LLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPN 236 : :::::::::::::: :::: :::::::::: :::: ::::::::::::: : d1hl2a_ 83 -T-AESQQLAASAKRYG---FDAV-SAVTPFYYPF--SFEE-HCDHYRAIIDSAD--G-- 129 d1j93a_ 237 LPLILYASG-----SGG--LLERLPLTG-VDVVSLDWTVD--MADGRRRLGPNVAIQGNV 286 ::::::::: ::: ::::::::: ::::::::::: ::::::: ::: :::::: d1hl2a_ 130 LPMVVYNIPARSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRRE-HPD-LVLYNG 187 d1j93a_ 287 DPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKG-LRY-- 343 ::::: : ::::: :: : ::: ::::: : : :::::::::: ::: d1hl2a_ 188 YDEIF------A--SGLLA--GA----D-GGI-GSTYN-I-M--GWRYQGIVKALKEGDI 227 d1j93a_ 344 ------------------------------------------------------------ 344 d1hl2a_ 228 QTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALA 287 d1j93a_ 344 -------- 344 d1hl2a_ 288 QQLMQERG 295 HHsearch alignment (Probability: 0.94 E-value:0.00) d1j93a_ 123 ALTILRKEVNNQAAVLGFVGAPFT 146 :::::::::::::::::::::::: d1hl2a_ 60 VLEIVAEEAKGKIKLIAHVGCVST 83