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 <-- 0.742 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1ecea_) 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 d1ecea_ Endocellulase E1(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 <-- 0.742 --> Hit
DALI alignment (Z-score: 10.6 Raw score:1294.90) d1j93a_ 1 TQPL----lldAVRG--KEVErPPVWLMRQ----agrymkSYQLLcekyplfrdrsenvd 50 :::: :::: :::: :::::::: ::::: d1ecea_ 1 AGGGywhtsgrEILDanNVPV-RIAGINWFgfetcnyvvhGLWSR--------------- 44 d1j93a_ 51 LVVEISLQPWKvFRPDGVILfSDILTPLSgmniPFDIIkgkgpvifdplrtaadvekvre 110 ::::::::::: :::::::: :::::::: ::::: d1ecea_ 45 DYRSMLDQIKS-LGYNTIRLpYSDDILKP----GTMPN------------sinfyqmnqd 87 d1j93a_ 111 fipeksVPYVGEALTILRKEVnnqAAVLGFVG-------apFTLAsyvveggssknftki 163 ::::::::::::::: :::::::: :::: d1ecea_ 88 lqgltsLQVMDKIVAYAGQIG---LRIILDRHrpdcsgqsaLWYT--------------- 129 d1j93a_ 164 krlafaepkvlhaLLQKFATSMAKYIRYQADS-GAQAVQIFDSWaTELSpvDFEE----- 217 ::::::::::::::::::: ::::::::::: :::: :::: d1ecea_ 130 ----------ssvSEATWISDLQALAQRYKGNpTVVGFDLHNEP-HDPA--CWGCgdpsi 176 d1j93a_ 218 FSLPYLKQIVDSVKLTHPNLPLILYA-----------SGSGGLLERlPLTG----vDVVS 262 :::::::::::::::::::::::::: ::::::::: :::: :::: d1ecea_ 177 DWRLAAERAGNAVLSVNPNLLIFVEGvqsyngdsywwGGNLQGAGQyPVVLnvpnrLVYS 236 d1j93a_ 263 LDWT--------------------vDMAD-GRRRL-GPNVAIQGNVDPGvlFGSKEFITN 300 :::: :::: ::::: ::::::::::::: ::::::::: d1ecea_ 237 AHDYatsvypqtwfsdptfpnnmpgIWNKnWGYLFnQNIAPVWLGEFGT--TLQSTTDQT 294 d1j93a_ 301 RINDTVKKAG------kGKHILNLgHGIKVG--------------tPEENFAHFfEIAK- 339 :::::::::: ::::::: :::::: :::::::: :::: d1ecea_ 295 WLKTLVQYLRptaqygaDSFQWTF-WSWNPDsgdtggilkddwqtvDTVKDGYL-APIKs 352 d1j93a_ 340 --glry 343 d1ecea_ 353 sifdpv 358 FAST alignment (Normalized score: 5.13 Raw score:1798.00) d1j93a_ 1 TQPLLLDAVRGKEV-------------------ERPPVWLMRQAGRYMKSYQLLCEKYPL 41 ::::::: d1ecea_ 1 --------------AGGGYWHTSGREILDANNVPVRIAGI-------------------- 26 d1j93a_ 42 FRDRSENVD------------------LVVEISLQPWKVFRPDGVILFSDILTPLSGMN- 82 ::::::::::: ::::::::::::::: d1ecea_ 27 ---------NWFGFETCNYVVHGLWSRDYRSMLDQIKS-LGYNTIRLPYSDDIL-----K 71 d1j93a_ 83 IPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS-----------------VPYVGEALT 125 ::::: ::::::::: d1ecea_ 72 PGTMP-----------------------------NSINFYQMNQDLQGLTSLQVMDKIVA 102 d1j93a_ 126 ILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK----- 180 :::: :::::::: d1ecea_ 103 YAGQ---IGLRIILD----------------------------------------RHRPD 119 d1j93a_ 181 -------------FATSMAKYIRYQADS------GAQAVQIFDSWATELSPVDFEE---- 217 :::::::::::::: :::::: d1ecea_ 120 CSGQSALWYTSSVSEATWISDLQALAQ-RYKGNPTVVGFD----------------LHNE 162 d1j93a_ 218 --------------FSLPYLKQIVDSVKLTHPNLPLILY------------ASGSGGLLE 251 ::::::::::::::::::::::::: ::::: d1ecea_ 163 PHDPACWGCGDPSIDWRLAAERAGNAVLSVNPNLLIFVEGVQSYNGDSYWWGGNLQ---- 218 d1j93a_ 252 RLPLTGV--------------DVVSLDWTV------------------------DMADGR 273 ::::: :::: d1ecea_ 219 -------GAGQYPVVLNVPNRLVYSA----HDYATSVYPQTWFSDPTFPNNMPGIWNK-- 265 d1j93a_ 274 RR------LGPNVAIQGNVDPGVLFGS----------KEFITNRINDTVKKAGKG----- 312 ::::::: :::::::::::::::: d1ecea_ 266 --NWGYLFNQNIAPV------------WLGEFGTTLQSTTDQTWLKTLVQYLR--PTAQY 309 d1j93a_ 313 ---KHILNLGHGIKVGTPEEN----------------------FAHFFEIAKGLRY---- 343 ::::: ::::::::: d1ecea_ 310 GADSFQWT-------------FWSWNPDSGDTGGILKDDWQTVDTVKDGYLA----PIKS 352 d1j93a_ 344 ------ 344 d1ecea_ 353 SIFDPV 358 TMalign alignment (TM-score: 0.59 Raw score:201.14) d1j93a_ 1 TQPLLLD----AVRG--KEVERPPVWLMRQAG---RYMKSYQLLCEKYPLFRDRSEN-VD 50 ::::::: :::: ::: ::::::: ::: :::::::: : d1ecea_ 1 AGGGYWHTSGREILDANNVP-VRIAGIN-WFGFET--------------CNYVVHGLW-S 43 d1j93a_ 51 LVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDII------------KGKGPVIFDP 98 :::::::::::::::::::: ::::::::: : ::::: d1ecea_ 44 RDYRSMLDQIKSLGYNTIRL-PYSDDILKP-G-TMPNSINFYQMNQDLQG---------- 90 d1j93a_ 99 LRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 :::::::::::::::::: : ::::::: :: :: :::: d1ecea_ 91 ---------------LTSLQVMDKIVAYAGQIG---L-RIILDRH--RP--DC---SGQS 124 d1j93a_ 159 NF-TKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSP--VDF 215 :: :: : :: :::::::::::::::::::::::::::::::::::: ::: d1ecea_ 125 ALW-YT--S------SV--SEATWISDLQALAQRYKGNPTVVGFDLHNEPHDPACWGCGD 173 d1j93a_ 216 EEF-SLPYLKQIVDSVKLTHPNLPLILYA---------SGSGGLLER--LPLTG----VD 259 ::: ::::::::::::::::::::::::: ::::::::: ::::: :: d1ecea_ 174 PSIDWRLAAERAGNAVLSVNPNLLIFVEGVQSYNGDSYWWGGNLQGAGQYPVVLNVPNRL 233 d1j93a_ 260 VVSLDWT------------------V--DMAD-GRRRL-GPNVAIQGNVDPGVLF-G-SK 295 ::::::: : :::: ::::: :::::::::::::::: : :: d1ecea_ 234 VYSAHDYATSVYPQTWFSDPTFPNNMPGIWNKNWGYLFNQNIAPVWLGEFGTTLQSTTDQ 293 d1j93a_ 296 EFITNRINDTVK---KAG-KGKHILNLGHGI------KVGT-P------EENFAHFFEIA 338 :::::::::::: : :::::::: ::: :::: : ::::::::::: d1ecea_ 294 TWLKTLVQYLRPTAQ--YGADSFQWTF-WSWNPDSGDTGGILKDDWQTVDTVKDGYLAPI 350 d1j93a_ 339 KGL-----RY 343 ::: d1ecea_ 351 KSSIFDPV-- 358 HHsearch alignment (Probability: 0.13 E-value:0.13) d1j93a_ 116 SVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLH 175 ::::::::::::::: : ::::::::::::::::: :::::::::: d1ecea_ 93 SLQVMDKIVAYAGQI-G-LRIILDRHRPDCSGQSA---------------LWYTSSVSEA 135 d1j93a_ 176 ALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELS-----PVDFEEFSLPYLKQIVDSV 230 :::::::::::::::: :::::::::::::: ::::::::::::::::::: d1ecea_ 136 TWISDLQALAQRYKGN------PTVVGFDLHNEPHDPACWGCGDPSIDWRLAAERAGNAV 189 d1j93a_ 231 KLTHPNLPLILYA 243 ::::::::::::: d1ecea_ 190 LSVNPNLLIFVEG 202