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 <-- 0.743 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1eswa_) 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 d1eswa_ Amylomaltase MalQ(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 <-- 0.743 --> Hit
DALI alignment (Z-score: 9.0 Raw score:1269.70) d1j93a_ 1 tqpllldaVRGKeverPPVWLMRQAGRYmkSYQLLCekyplfrdrsenvdLVVEISLQPW 60 :::: :::::::::::: :::::: :::::::::: d1eswa_ 1 --------MELP----RAFGLLLHPTSL--PGPYGV-------------gVLGREARDFL 33 d1j93a_ 61 KVFR---PDGVILFS---------DILT-------------------------------- 76 :::: :::::::: :::: d1eswa_ 34 RFLKeagGRYWQVLPlgptgygdsPYQSfsafagnpylidlrplaergyvrledpgfpqg 93 d1j93a_ 77 -----------------------------------------plSGMN---ipfdiikgkg 92 :::: d1eswa_ 94 rvdygllyawkwpalkeafrgfkekaspeereafaafrereawWLEDyalfmalkgahgg 153 d1j93a_ 93 pVIFD-----------plrtaadvekvrefipeksVPYVGEALTILRKEVNN-QAAVLGF 140 :::: ::::::::::::::::: ::::::: d1eswa_ 154 lPWNRwplplrkreekalreaksalaeevafhaftQWLFFRQWGALKAEAEAlGIRIIGD 213 d1j93a_ 141 VGApftLASYV----------------------------veggssKNFTkikrlafaepk 172 ::: ::::: :::: d1eswa_ 214 MPI---FVAEDsaevwahpewfhldeegrptvvagvppdyfsetgQRWG----------n 260 d1j93a_ 173 vLHAL---lqkfATSMAKYIRYQADsGAQAVQIFDswatelspvdFEEF----------- 218 :::: ::::::::::::: ::::::::: :::: d1eswa_ 261 pLYRWdvleregFSFWIRRLEKALE-LFHLVRIDH------frgfEAYWeipascptave 313 d1j93a_ 219 ---slpYLKQIVDSVKLTHPNLPLILYASGSggLLERLPLT---GVDVVSLDW------- 265 ::::::::::::::::::::::::: :::::::: ::::::::: d1eswa_ 314 grwvkaPGEKLFQKIQEVFGEVPVLAEDLGV--ITPEVEALrdrFGLPGMKVLqfafddg 371 d1j93a_ 266 ---TVDMADGRrrlgPNVAIQGNVD----pGVLF-------------------------g 293 :::::::: :::::::::: :::: d1eswa_ 372 menPFLPHNYP----AHGRVVVYTGthdndTTLGwyrtatphekafmaryladwgitfre 427 d1j93a_ 294 SKEFITNRINDTVKKAgkgkHILNLghGIKV--------------------------gtp 327 :::::::::::::::: ::::: :::: d1eswa_ 428 EEEVPWALMHLGMKSV---aRLAVY--PVQDvlalgsearmnypgrpsgnwawrllpgel 482 d1j93a_ 328 EENFAHFFEIAKGLRY-- 343 :::::::::::::::: d1eswa_ 483 SPEHGARLRAMAEATErl 500 FAST alignment (Normalized score: 4.11 Raw score:1700.00) d1j93a_ 1 TQPLLLDAVRGKEVER----PPVWLMR-QAGRYMKSYQLLCEKYPLFRDRSENVDL---- 51 ::::: :::: d1eswa_ 1 ----------------MELPRAFGL--LLHPT------------------------SLPG 18 d1j93a_ 52 ------VVEISLQPWK---VFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTA 102 :::::::::: ::::::::: d1eswa_ 19 PYGVGVLGREARDFLRFLKEAGGRYWQV-------------------------------- 46 d1j93a_ 103 ADVEKVREF--------------------------------------------------- 111 d1eswa_ 47 ---------LPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDY 97 d1j93a_ 112 --------------------------------------IPEKS----------------- 116 :::: d1eswa_ 98 GLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLE-DYALFMALKGAHGGLPW 156 d1j93a_ 117 --------------------------------VPYVGEALTILRKEVNN----QAAVLGF 140 :::::::::::::: ::::::: d1eswa_ 157 NRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAE---AEALGIRIIGD 213 d1j93a_ 141 VGAPFTLASYVVE--------------------------GGSSKNFTKIKRLAFAE---- 170 :: :::: d1eswa_ 214 MP-----------IFVAEDSAEVWAHPEWFHLDEEGRPTVVAG-------------VPPD 249 d1j93a_ 171 ---------------PKVLHALLQKF--ATSMAKYIRYQADSGAQAVQIF--DSWATELS 211 :::::: ::::::::::::: ::::::: :::: d1eswa_ 250 YFSETGQRWGNPLYRWDVLER-----EGFSFWIRRLEKALE-LFHLVRI-DHFRGF---- 298 d1j93a_ 212 PVDFEEFSLP---------------------YLKQIVDSVKLTHPNL--PLILYASGSGG 248 :::::::::::::: :::::::::: d1eswa_ 299 ----------EAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFG--EVPVLAEDLGVI- 345 d1j93a_ 249 ---LLERLPLTGVDVVSLDWT------------VDMADGRRRLGPNV-----AIQGNVDP 288 ::::::::: :::::: ::::: :::::: d1eswa_ 346 TPEVEALRDRFG-LPGMKV--LQFAFDDGMENPFLPHN---------YPAHGRVVVYT-- 391 d1j93a_ 289 GVLFG------------------------------------SKEFITNRINDTVKKAGKG 312 :::::::::::::: d1eswa_ 392 -----GTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMK----- 441 d1j93a_ 313 KHILNLGHGIKV---------------------------------------GTPEENFAH 333 ::::::::: d1eswa_ 442 ------------SVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGAR 489 d1j93a_ 334 FFEIAKGLRY---- 343 ::::::: d1eswa_ 490 LRAMAEA---TERL 500 TMalign alignment (TM-score: 0.53 Raw score:181.74) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 ::: : : ::::: :::: :: :: ::: :: ::::::::::::: d1eswa_ 1 -----MEL-----P-R-AFGLL-LHPT---SL-PG-PYG----VG--VLGREARDFLRFL 36 d1j93a_ 61 KVFRPDGVILFSDI----------L-T-PLS----------------------------- 79 :::::::::::::: : : ::: d1eswa_ 37 KEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVD 96 d1j93a_ 80 -----------------------------------------G-MN--IPFD-II--KGKG 92 : :: :::: : d1eswa_ 97 YGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALK-GAH---- 151 d1j93a_ 93 PVIFDPLR--T--AADVE--K---V------R---EF--IPEKSVPYVGEALTILRKEVN 132 ::::::: : ::::: : : : : :::::::::::::::::: : d1eswa_ 152 -GGLPWNRWPLPLRKREEKALREAKSALAEEVAFH-AFT-QWLFFRQWGALKAEAEAL-G 207 d1j93a_ 133 NQAAVLGFVGAPFTLASYVV-EG------GSSKNFTKI--KRLAFA-------------- 169 : :::::::: ::::::: :: ::: :::::: d1eswa_ 208 I--RIIGDMPI--FVAEDSAEVWAHPEWF------HLDEEGRPTVVAGVPPDYFSETGQR 257 d1j93a_ 170 ---EPKVLHA-LL----QKFATSMAKYIRYQADSGAQAVQIFDSWA---TELS------- 211 ::::: :: :::::::::::::: ::::::::::: :::: d1eswa_ 258 WGN--PLYRWDVLEREGFSFWIRRLEKALEL----FHLVRIDHFRGFEAYWEIPASCPTA 311 d1j93a_ 212 --PVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDM 269 ::::: :::::: :::::::::::::: :::: :: d1eswa_ 312 VEGRWVK---APGEKL-FQKIQEVFGEVPVL--------------------AEDL-GV-- 344 d1j93a_ 270 ADGRRRLG--PN-VAIQGNVDPGVLFGSKEFI-TNRINDTVKKAGKG-KHILNLGHGIKV 324 ::::::: :: ::::::::::: : :: ::::::::::::: :::::::::::: d1eswa_ 345 -ITPEVEALRDRFGLPGMKVLQFA--F---DDG-MENPFLPHNYPAHGRVVVYTGTHDND 397 d1j93a_ 325 GTP----------------------------EENFAHFFEIAKGLRY------------- 343 ::: :::::::::::::::: d1eswa_ 398 TTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLAL 457 d1j93a_ 344 ------------------------------------------- 344 d1eswa_ 458 GSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL 500 HHsearch alignment (Probability: 0.02 E-value:0.13) d1j93a_ 239 LILYASGSGGLLER 252 :::::::::::::: d1eswa_ 291 RIDHFRGFEAYWEI 304