HorA Server Transitive Detail

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


Query <-- 0.875 --> Intermediate <-- 0.913 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1ur1a_) through the intermediate protein (d1j93a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1j93a_ Uroporphyrinogen decarboxylase,​ URODUROD/​MetE-​likeTIM beta/​alpha-​barrelα/β
Hit d1ur1a_ Xylanase(Trans)glycosidasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.875 --> Intermediate
DALI 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 <-- 0.913 --> Hit
DALI alignment (Z-score: 11.7 Raw score:1399.40) d1j93a_ 1 tqpllldavrgkevERPPVWLMRQagrymksyqllcekyplfrdrsenVDLVVE---isL 57 :::::::::: :::::: : d1ur1a_ 1 --------glksayKDNFLIGAAL-----------------------nATIASGaderlN 29 d1j93a_ 58 QPWKVFrPDGVILF-SDIL-TPLSgmNIPFdiikgkgpvifdplrtaadvekvrefipeK 115 :::::: ::::::: :::: :::: :::: : d1ur1a_ 30 TLIAKE-FNSITPEnCMKWgVLRD--AQGQ-----------------------------W 57 d1j93a_ 116 SVPYVGEALTILRKEVnnqAAVLGFVGAPFTlasYVVEggssknftkikrlafAEPKVlH 175 :::::::::::::::: :::::::::::: :::: ::::: : d1ur1a_ 58 NWKDADAFVAFGTKHN---LHMVGHTLVWHS--qIHDE---------vfknadGSYIS-K 102 d1j93a_ 176 ALLQKFATSMAK-YIRYQADsGAQAVQIFDSwATELSPVdFEEF------sLPYLKQIVD 228 :::::::::::: ::::::: :::::::::: ::::::: :::: ::::::::: d1ur1a_ 103 AALQKKMEEHITtLAGRYKG-KLAAWDVVNE-AVGDDLK-MRDShwykimgDDFIYNAFT 159 d1j93a_ 229 SVKLTHPNLPLILYASGS-----GGLLERLPL------TGVDVVSLDWT--------vDM 269 :::::::::::::::::: ::::::::: ::::::::::: :: d1ur1a_ 160 LANEVDPKAHLMYNDYNIertgkREATVEMIErlqkrgMPIHGLGIQGHlgidtppiaEI 219 d1j93a_ 270 ADGRRRL-GPNVAIQGnvDPGV------------------------------lfGSKEFI 298 ::::::: :::::::: :::: :::::: d1ur1a_ 220 EKSIIAFaKLGLRVHFtsLDVDvlpsvweevstrfeykperdpytkglpqemqdKLAKRY 279 d1j93a_ 299 TNRINDTVKkaGKGKHILNLghGIKVG------------------------tPEENFAHF 334 ::::::::: ::::::::: ::::: :::::::: d1ur1a_ 280 EDLFKLFIK--HSDKIDRAT-fWGVSDdaswlngfpipgrtnypllfdrklqPKDAYFRL 336 d1j93a_ 335 FEI-akglry 343 ::: d1ur1a_ 337 LDLkrlehhh 346 FAST alignment (Normalized score: 5.46 Raw score:1882.00) d1j93a_ 1 TQPLLLDAVRGKE------VERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVE 54 :::::::: d1ur1a_ 1 -------------GLKSAYKDNFLIGA--------------------------------- 14 d1j93a_ 55 ISLQPWKVF--------------------RPDGVILFSD-----ILTPLSGMNIPFDIIK 89 ::::::: :::: d1ur1a_ 15 ---------ALNATIASGADERLNTLIAKEFNSITP---ENCMKWGVL------------ 50 d1j93a_ 90 GKGPVIFDPLRTAADVEKVREFIPEK-------SVPYVGEALTILRKEVNN-QAAVLGFV 141 :::::::::::::: ::::::: d1ur1a_ 51 --------------------------RDAQGQWNWKDADAFVAFGTK----HNLHMVGH- 79 d1j93a_ 142 GAPFTLASYVVEGGSSKN--------FTKIKRLAF--------AEPKVLHALLQKFATSM 185 :::: ::::::::::::::: d1ur1a_ 80 ------------------TLVWHSQIHDEV-----FKNADGSYISKAALQKKMEEHIT-- 114 d1j93a_ 186 AKYIRYQAD--SGAQAVQIFDSWATELSPVDFEEF---------------------SLPY 222 ::::: ::::::: :::: d1ur1a_ 115 -TLAGR---YKGKLAAWD-----------------VVNEAVGDDLKMRDSHWYKIMGDDF 153 d1j93a_ 223 LKQIVDSVKLTHPNLPLILYASGS--GGLLERLP---------LTGVDVVSLDWTV---- 267 :::::::::::::::::::::::: :::::::: :::::::::: d1ur1a_ 154 IYNAFTLANEVDPKAHLMYNDYNIERTGKREATVEMIERLQKRGMPIHGLGIQ---GHLG 210 d1j93a_ 268 -------DMADGRRRLG---PNVAIQGNVDPGVLFG------------------------ 293 :::::::: ::::: d1ur1a_ 211 IDTPPIAEIEKSIIA--FAKLGLRV-----------HFTSLDVDVLPSVWEEVSTRFEYK 257 d1j93a_ 294 -------------SKEFITNRINDTVKKAGKGK--------HILNLGHGIKVGTPEENF- 331 ::::::::::::::: :::: d1ur1a_ 258 PERDPYTKGLPQEMQDKLAKRYEDLFKL-----FIKHSDKIDRAT--------------F 298 d1j93a_ 332 -------------------------------AHFFEIAKGLRY-------- 343 ::::::::: d1ur1a_ 299 WGVSDDASWLNGFPIPGRTNYPLLFDRKLQPKDAYFRLLD---LKRLEHHH 346 TMalign alignment (TM-score: 0.58 Raw score:199.74) d1j93a_ 1 --TQPLL-LDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 57 :: : ::::::::: ::: : ::::::: d1ur1a_ 1 GL---KSA--Y-----KDNFLIGAA-LNA-----T------------------IASGADE 26 d1j93a_ 58 QPWKVF--RPDGVILF-SDI-LTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIP 113 :::::: :::::::: ::: ::::: :: : : d1ur1a_ 27 RLNTLIAKEFNSITPENCMKWGVLRD---AQ------------------------G-Q-- 56 d1j93a_ 114 EKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKI--KRLAFAEP 171 ::::::::::::::::: :::::::::::::: ::::: :: : : d1ur1a_ 57 --WNWKDADAFVAFGTKHN--LHMVGHTLVWHSQI-HDEVF-------KNAD--G---S- 98 d1j93a_ 172 KVLHALLQKFATSMAK-YIRYQADSGAQAVQIFDSWATELSPVDFE-EF---SLPYLKQI 226 :::::::::::::::: ::::::: ::::::::::::::::::::: :: :::::::: d1ur1a_ 99 YISKAALQKKMEEHITTLAGRYKG-KLAAWDVVNEAVGDDLKMRDSHWYKIMGDDFIYNA 157 d1j93a_ 227 VDSVKLTHPNLPLILYASGS-G--G--LLE-RLP-L----TGVDVVSLDW------TV-- 267 :::::::::::::::::::: : : ::: ::: : :::::::::: :: d1ur1a_ 158 FTLANEVDPKAHLMYNDYNIERTGKREATVEMIERLQKRGMPIHGLGIQGHLGIDTPPIA 217 d1j93a_ 268 DMADGRRRL-GPNVAIQGN-VDPGV----------------------------LF-GSKE 296 ::::::::: ::::::::: ::::: :: :::: d1ur1a_ 218 EIEKSIIAFAKLGLRVHFTSLDVDVLPSVWEEVSTRFEYKPERDPYTKGLPQEMQDKLAK 277 d1j93a_ 297 FITNRINDTVKKAGKGKHILNLGHG-----I-KV--------GT---PE-----ENFAHF 334 ::::::::::: :::::::::: :: : :: :: :: :::::: d1ur1a_ 278 RYEDLFKLFIK-HSDKIDRATF-WGVSDDASWLNGFPIPGRTNYPLLFDRKLQPKDAYFR 335 d1j93a_ 335 FEIAKG-LRY- 343 :::::: ::: d1ur1a_ 336 LLDLKRLEHHH 346 HHsearch alignment (Probability: 0.20 E-value:0.02) d1j93a_ 187 KYIRYQADSGAQAVQIFDSWATELSP-------VDFEEFSLPYLKQIVDSVKLTHPNLPL 239 :::::::::::::::::::::::::: ::::::::::::::::::::::::::: d1ur1a_ 111 EHITTLAGRYKGKLAAWDVVNEAVGDDLKMRDSHWYKIMGDDFIYNAFTLANEVDPKAHL 170 d1j93a_ 240 ILYA------SGS---GGLLERLPLTG--VDVVSLDWTV 267 :::: ::: ::::::::::: :::::::::: d1ur1a_ 171 MYNDYNIERTGKREATVEMIERLQKRGMPIHGLGIQGHL 209