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 <-- 1.344 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1xyza_) 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 d1xyza_ 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 <-- 1.344 --> Hit
DALI alignment (Z-score: 11.5 Raw score:1373.50) d1j93a_ 1 tqpllldavrgkeVERPPVWLMrQAGRymkSYQLlcekyplfrdrsenvdlvveisLQPW 60 ::::::::: :::: :::: :::: d1xyza_ 1 -----nalrdyaeARGIKIGTC-VNYP-fyNNSD-------------------ptyNSIL 34 d1j93a_ 61 KVFrPDGVILF-SDIL-TPLSGmnipfdiikgkgpvifdplrtaadvekvREFIpekSVP 118 ::: ::::::: :::: ::::: :::: ::: d1xyza_ 35 QRE-FSMVVCEnEMKFdALQPR----------------------------QNVF---DFS 62 d1j93a_ 119 YVGEALtILRKEVnnQAAVLGFVGAPFTLA-syVVEGgssknftkikrlafaepKVLHAL 177 :::::: :::::: ::::::::::::::: :::: :::::: d1xyza_ 63 KGDQLL-AFAERN--GMQMRGHTLIWHNQNpswLTNG----------------nWNRDSL 103 d1j93a_ 178 LQKFATSMAKYIRYQADsGAQAVQIFDSwATELSPVDFEEF------slPYLKQIVDSVK 231 ::::::::::::::::: :::::::::: :::::::::::: ::::::::::: d1xyza_ 104 LAVMKNHITTVMTHYKG-KIVEWDVANE-CMDDSGNGLRSSiwrnvigqDYLDYAFRYAR 161 d1j93a_ 232 LTHPNLPLILYASGS------GGLLE-RLPLT-----GVDVVSLDW----------tvDM 269 ::::::::::::::: ::::: ::::: ::::::::: :: d1xyza_ 162 EADPDALLFYNDYNIedlgpkSNAVFnMIKSMkergvPIDGVGFQChfingmspeylaSI 221 d1j93a_ 270 ADGRRRLGP-NVAIQGnvDPGV----------lfGSKEFITNRINDTVKkaGKGKHILNL 318 ::::::::: :::::: :::: ::::::::::::::: ::::::::: d1xyza_ 222 DQNIKRYAEiGVIVSFteIDIRipqsenpatafqVQANNYKELMKICLA--NPNCNTFVM 279 d1j93a_ 319 gHGIKVG---------------------tPEENFAHFFEIAkglry 343 :::::: :::::::::::: d1xyza_ 280 -WGFTDKytwipgtfpgygnpliydsnynPKPAYNAIKEAL----m 320 FAST alignment (Normalized score: 4.39 Raw score:1455.00) d1j93a_ 1 TQPLLLDAVRGKEVE----------RPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD 50 :::::: d1xyza_ 1 ---------------NALRDYAEARGIKIGT----------------------------- 16 d1j93a_ 51 L-------------VVEISLQPWKVF-RPDGVILF---SDILTPLSGMNIPFDIIKGKGP 93 :::::: ::::::: :::::: d1xyza_ 17 -CVNYPFYNNSDPTYNSILQ------REFSMVVC-ENEMKFDAL---------------- 52 d1j93a_ 94 VIFDPLRTAADVEKVREFIPEKS--------VPYVGEALTILRKEVNNQAAVLGFVGAPF 145 ::::::::::::: ::::::::: d1xyza_ 53 -----------------------QPRQNVFDFSKGDQLLAFAER---NGMQMRGHT---- 82 d1j93a_ 146 TLASYVVEGGSSKN-------FTKIKRLAFA----EPKVLHALLQKFATSMAKYIRYQAD 194 ::::: ::::::::::::: :::::: d1xyza_ 83 --------------LIWHNQNPSWLT-----NGNWNRDSLLAVMKNHI---TTVMTH--- 117 d1j93a_ 195 --SGAQAVQIFDSWATELSPVDFEEFS-----------------------LPYLKQIVDS 229 ::::::: :::::::::: d1xyza_ 118 YKGKIVEWD------------------VANECMDDSGNGLRSSIWRNVIGQDYLDYAFRY 159 d1j93a_ 230 VKLTHPNLPLILYASG--------SGGLLERLPL-----TGVDVVSLDWTVDMADGRRRL 276 ::::::::::::::: :::::::::: ::::::::: d1xyza_ 160 AREADPDALLFYNDY-NIEDLGPKSNAVFNMIKSMKERGVPIDGVGFQ------------ 206 d1j93a_ 277 GPNVAIQGNVDPGVL-----FGSKEFITNRINDTVKKAGKG------KHILNLGHGIKVG 325 :::::: :::::::::: :::: d1xyza_ 207 ---------------CHFINGMSPEY-LASIDQNIKR----YAEIGVIVSF--------- 237 d1j93a_ 326 T-------------------PEENFAHFFEIAKGLRY----------------------- 343 ::::::::::::::: d1xyza_ 238 -TEIDIRIPQSENPATAFQVQANNYKELMKICLAN--PNCNTFVMWGFTDKYTWIPGTFP 294 d1j93a_ 344 -------------------------- 344 d1xyza_ 295 GYGNPLIYDSNYNPKPAYNAIKEALM 320 TMalign alignment (TM-score: 0.57 Raw score:196.31) d1j93a_ 1 ---TQPLL-LDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEIS 56 :: : :::::::::: ::: :: :: ::: d1xyza_ 1 NAL---RDY--A----EARGIKIGTC-VNY----PF-----------------YN--NSD 27 d1j93a_ 57 LQPWKVF--RPDGVILF-SDI-LTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::: :::::::: ::: ::::::: : d1xyza_ 28 PTYNSILQREFSMVVCENEMKFDALQPRQ-----------------------------N- 57 d1j93a_ 113 PEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEG-GSSKNFTKIKRLAFAEP 171 ::::::::::::::::: : :::::::::::::::::::: : d1xyza_ 58 --VFDFSKGDQLLAFAERN-G-MQMRGHTLIWHNQNPSWLTNG-----------N----- 97 d1j93a_ 172 KVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFE--EF---SLPYLKQI 226 :: :::::::::::::::::::::::::::::::::::::::::: :: :::::::: d1xyza_ 98 WN-RDSLLAVMKNHITTVMTHYKGKIVEWDVANECMDDSGNGLRSSIWRNVIGQDYLDYA 156 d1j93a_ 227 VDSVKLTHPNLPLILYASGS-----GG-LLE-RLP-L----TGVDVVSLDW-T------- 266 :::::::::::::::::::: :: ::: ::: : :::::::::: : d1xyza_ 157 FRYAREADPDALLFYNDYNIEDLGPKSNAVFNMIKSMKERGVPIDGVGFQCHFINGMSPE 216 d1j93a_ 267 V--DMADGRRRLGP-NVAIQG-NVDPGVL----F-GSKEFITNRINDTVKKA-GKG-KHI 315 : ::::::::::: :::::: ::::::: : ::::::::::::::::: ::: ::: d1xyza_ 217 YLASIDQNIKRYAEIGVIVSFTEIDIRIPQSENPATAFQVQANNYKELMKICLANPNCNT 276 d1j93a_ 316 LNLGH-----GIKV------GT----PE-ENFAHFFEIAKGLRY 343 ::::: :::: :: :: ::::::::::::::: d1xyza_ 277 FVMWGFTDKYTWIPGTFPGYGNPLIYDSNYNPKPAYNAIKEALM 320 HHsearch alignment (Probability: 0.62 E-value:0.01) d1j93a_ 187 KYIRYQADSGAQAVQIFDSWATEL--------SPVDFEEFSLPYLKQIVDSVKLTHPNLP 238 :::::::::::::::::::::::: :::::::::::::::::::::::::::: d1xyza_ 109 NHITTVMTHYKGKIVEWDVANECMDDSGNGLRSSIWRNVIGQDYLDYAFRYAREADPDAL 168 d1j93a_ 239 LIL 241 ::: d1xyza_ 169 LFY 171