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 <-- 1.177 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1odza_) 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 d1odza_ Mannanase A,​ ManA(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 <-- 1.177 --> Hit
DALI alignment (Z-score: 10.2 Raw score:1267.60) d1j93a_ 1 ---------------tqplLLDAVrGKEV-ERPPVWLMRQagrYMKSYQllcekyplfrd 44 ::::: :::: :::::::::: :::::: d1odza_ 1 vkpvtvklvdsqatmetrsLFAFM-QEQRrHSIMFGHQHEttqGLTITR----------- 48 d1j93a_ 45 rsenvdLVVEIslQPWK---VFRPDGVILfsDILT-PLSGmnipfdiikgkgpvifdplr 100 ::::: :::: ::::::::: :::: :::: d1odza_ 49 ------TDGTQ--SDTFnavGDFAAVYGW--DTLSiVAPK-------------------- 78 d1j93a_ 101 taadvekvrefipeksvpYVGEALTILRKEVnnqaAVLGFVGapfTLASyVVEG------ 154 ::::::::::::: ::::::: :::: :::: d1odza_ 79 ---------------aegDIVAQVKKAYARG----GIITVSS---HFDN-PKTDtqkgvw 115 d1j93a_ 155 ----gSSKNFtkIKRLafaEPKVLhALLQKFATSMAKYIRYQA---dsgAQAVQIFDS-- 205 ::::: :::: ::::: :::::::::::::::::: ::::::::: d1odza_ 116 pvgtsWDQTP--AVVDslpGGAYN-PVLNGYLDQVAEWANNLKdeqgrlIPVIFRLYHen 172 d1j93a_ 206 -----WATE--LSPVDFEEFSLPYLKQIV--DSVKlthpnLPLILYASG---------SG 247 :::: :::::::::::::::::: :::: ::::::::: :: d1odza_ 173 tgswfWWGDkqSTPEQYKQLFRYSVEYLRdvKGVR-----NFLYAYSPNnfwdvteanYL 227 d1j93a_ 248 GLLeRLPLTgVDVVSLDW--------------tvDMADGRRRLGP-NVAIQG-nVDPG-- 289 ::: ::::: :::::::: ::::::::::: :::::: :::: d1odza_ 228 ERY-PGDEW-VDVLGFDTygpvadnadwfrnvvaNAALVARMAEArGKIPVIsgIGIRap 285 d1j93a_ 290 ----vlFGSKeFITNRINDTVK--KAGKgkHILNLghGIKV------------------- 324 :::: ::::::::::: :::: ::::: :::: d1odza_ 286 dieaglYDNQ-WYRKLISGLKAdpDARE-iAFLLV--WRNApqgvpggtqvphywvpanr 341 d1j93a_ 325 -----gtPEENFAHFFEiaKGLR----------------y 343 :::::::::: :::: d1odza_ 342 peninngTLEDFQAFYA--DEFTafnrdieqvyqrptliv 379 FAST alignment (Normalized score: 4.75 Raw score:1711.00) d1j93a_ 1 TQPLLLDAVRGKE----------------------------VERPPVWLMRQAGRYMKSY 32 :::::::::: d1odza_ 1 -------------VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQH--------- 38 d1j93a_ 33 QLLCEKYPLFRDRSENVDLVVEIS---------------LQPWKVF--RPDGVILFSDIL 75 ::::::: ::::: ::::: d1odza_ 39 ------------------------ETTQGLTITRTDGTQSDTFNAVGDFAAVY--GWDTL 72 d1j93a_ 76 TPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP-------YVGEALTILR 128 :: :::::::::: d1odza_ 73 SI-----------------------------------------VAPKAEGDIVAQVKKAY 91 d1j93a_ 129 KEVNN-QAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEP---------------- 171 : ::::::::: d1odza_ 92 A----RGGIITVSSH-----------------------------FDNPKTDTQKGVWPVG 118 d1j93a_ 172 ---------------KVLHALLQKFATSMAKYIRYQADSGA----------QAVQIFDSW 206 :::::::::::::::::::: :::: d1odza_ 119 TSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANN------LKDEQGRLIPVIFR----- 167 d1j93a_ 207 AT---------------ELSPVDFEEFSLPYLKQIVDSVK--LTHPNLPLILYASGSGGL 249 :::::: ::::::::::::: :::::::::::: d1odza_ 168 --LYHENTGSWFWWGDKQSTPEQ----YKQLFRYSVEYLRDVKGVRNFLYAYSP------ 215 d1j93a_ 250 LERLPLT-------------------GVDVVSLDWTV------------------DMADG 272 ::::::: ::::: d1odza_ 216 -------NNFWDVTEANYLERYPGDEWVDVLGF----DTYGPVADNADWFRNVVANAALV 264 d1j93a_ 273 RRRLG---PNVAI--QGN-VDPGVLF----GSKEFITNRINDTVKKAGKGK-------HI 315 ::: ::::: ::: :::::: ::::::::::::::: :: d1odza_ 265 ARM--AEARGKIPVISGIGIRAPDI-EAGLYDNQWYRKLISGLKA------DPDAREIAF 315 d1j93a_ 316 LNLGHGIKVGTPEE------------------------NFAHFFEIAKGLRY-------- 343 :: :::::: ::::::::::::: d1odza_ 316 LL-VWRNAP-----QGVPGGTQVPHYWVPANRPENINNGTLEDFQAFYADE-FTAFNRDI 368 d1j93a_ 344 ----------- 344 d1odza_ 369 EQVYQRPTLIV 379 TMalign alignment (TM-score: 0.56 Raw score:190.92) d1j93a_ 1 --------------TQP-LLLDAVRGKEVERPPVWLMRQAGRY----MKSY--------- 32 ::: ::::::::::::::::::::::::: :::: d1odza_ 1 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAV 60 d1j93a_ 33 ----------QLLCEKYPLFRDRSENVDLVVEISLQPWKV-FRPDGVILFSDILTPLSGM 81 :::::::::::::::::::: :::::::: ::::: :: d1odza_ 61 GDFAAVYGWD----------TLSIVAPKAEGDIVAQVKKAYARGGIITV-SSHFD-NP-- 106 d1j93a_ 82 NIPF-DIIKGKG-PVIFDPLRTAADVEKVRE----FI-PEKSVPYVGEALTILRKEVNNQ 134 ::: ::::::: ::::::: ::::::: :: :::::::::::::::::::::: d1odza_ 107 -KTDTQKGVWPVGTSWDQTP----AVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRL 161 d1j93a_ 135 AAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQA- 193 ::::::::::::::::::: : : : :::::::::::::::::: d1odza_ 162 IPVIFRLYHENTGSWFWWG---------D--K-------Q-STPEQYKQLFRYSVEYLRD 202 d1j93a_ 194 --DSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG------ 245 ::::::::::: :: :::::::: ::::: :::::: :::::::: d1odza_ 203 VKGVRNFLYAYSP--NN-FWDVTEAN-YLERY--PGDEWV------DVLGFDTYGPVADN 250 d1j93a_ 246 -----SG-GLLERLP-LT--G-VDVVSL-DW--------------T--VDMADGRRRLGP 278 :: ::::::: :: : :::::: :: : :::::::::::: d1odza_ 251 ADWFRNVVANAALVARMAEARGKIPVISGIGIRAPDIEAGLYDNQWYRKLISGLKADPDA 310 d1j93a_ 279 NVAIQGNVD----------------PGVLF---GS----KEFITNRINDTVKKAGKGKHI 315 ::::::::: ::::: :: :::::::::: ::: d1odza_ 311 REIAFLLVWRNAPQGVPGGTQVPHYWVPANRPENINNGTLEDFQAFYAD--EFT------ 362 d1j93a_ 316 LNLGHGIKVGTPEENFAHFFEIAKGLRY--------- 343 : : :::::: d1odza_ 363 A------------------F--NRDIEQVYQRPTLIV 379 HHsearch alignment (Probability: 0.03 E-value:0.45) d1j93a_ 170 EPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDS----------WA-TELSPVDFEEF 218 :::::::::::::::::: ::::::::::::::: :: ::::::::::: d1odza_ 136 YNPVLNGYLDQVAEWANN---LKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQL 192 d1j93a_ 219 SLPYLKQIVDSVKLTHPNLPLI-LYASGS------GGLLERLPLTG-VDVVSLDWTV 267 : ::::::::::::::::: :::::: ::::::::::: :::::::::: d1odza_ 193 F----RYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYG 245