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 <-- 1.549 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1xi3a_) 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 d1xi3a_ Thiamin phosphate synthaseThiamin phosphate synthaseTIM 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 <-- 1.549 --> Hit
DALI alignment (Z-score: 11.3 Raw score:1182.40) d1j93a_ 1 tqplllDAVRgkeverpPVWLMrQAGRYMksyqllcekyplfrdrsenvdLVVEISLQPW 60 :::: ::::: :::::: :::::::::: d1xi3a_ 1 ------NLRN-----klKLYVI-TDRRLK---------------------PEVESVREAL 27 d1j93a_ 61 KvFRPDGVILFSdILTPlsgmnipfdiikgkgpvifdplrtaadvekvrefipeksVPYV 120 : :::::::::: :::: :::: d1xi3a_ 28 E-GGATAIQMRI-KNAP---------------------------------------TREM 46 d1j93a_ 121 GEALTILRKEVN-NQAAVLGFVgapftlasyvveggssknftkikrlafaepkvlhallq 179 :::::::::::: ::::::::: d1xi3a_ 47 YEIGKTLRQLTReYDALFFVDD-------------------------------------- 68 d1j93a_ 180 kfatsmakYIRYQADSGAQAVQIFDswatelspvdfeefslpylkqIVDSVKLTHPNLPL 239 ::::::::::::::::: :::::::::::::: d1xi3a_ 69 --------RVDVALAVDADGVQLGP------------------edmPIEVAKEIAPNLII 102 d1j93a_ 240 ILYASgSGGLLERLPLTGVDVVSLD--------WTVD--MADGRRRLgpNVAIQGNVDPg 289 ::::: ::::::::::::::::::: :::: :::::::: :::::::::: d1xi3a_ 103 GASVY-SLEEALEAEKKGADYLGAGsvfptdarVIGLegLRKIVESV--KIPVVAIGGI- 158 d1j93a_ 290 vlfgskefITNRINDTVKKAgkgkHILN-lghgikvgtpeENFAHFFEIAKGLRY 343 :::::::::::: :::: ::::::::::::::: d1xi3a_ 159 --------NKDNAREVLKTG---vDGIAvisavmgaedvrKATEELRKIVEEVLG 202 FAST alignment (Normalized score: 7.11 Raw score:1871.00) d1j93a_ 1 TQPLLLDAVRGKEVERP------PVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVD--LV 52 :::: ::::: :: d1xi3a_ 1 -----------------NLRNKLKLYV-ITDRR-----------------------LKPE 19 d1j93a_ 53 VEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFI 112 ::::::::: ::::::::: d1xi3a_ 20 VESVREALE-GGATAIQMR----------------------------------------- 37 d1j93a_ 113 PEK----SVPYVGEALTILRKEVNN----QAAVLGFVGAPFTLASYVVEGGSSKNFTKIK 164 ::::::::::::::: :::::: d1xi3a_ 38 ---IKNAPTREMYEIGKTLRQL---TREYDALFFV------------------------- 66 d1j93a_ 165 RLAFAEPKVLHALLQKFATS--MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPY 222 ::::::: :::::::: d1xi3a_ 67 --------------------DDRVDVALA---VDADGVQL-------------------- 83 d1j93a_ 223 LKQ-----IVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTV---------- 267 ::::::::::::::::::: :::::::::::::::::: d1xi3a_ 84 ---GPEDMPIEVAKEIAPNLIIGASVY-SLEEALEAEKKGADYLGA----GSVFPTDARV 135 d1j93a_ 268 ----DMADGRRRLGPNVAIQGNVDPGVLFGSKEF------ITNRINDTVKKAGKGKHILN 317 :::::::: ::::: :::::::::: d1xi3a_ 136 IGLEGLRKIVES--VKIPV---------------VAIGGINKDNAREVLK---------- 168 d1j93a_ 318 LGHGIKVGT-----------------PEENFAHFFEIAKGLRY--- 343 :::::::::::::: d1xi3a_ 169 ---------TGVDGIAVISAVMGAEDVRKATEELRKIVEE---VLG 202 TMalign alignment (TM-score: 0.38 Raw score:129.89) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : : :::: d1xi3a_ 1 ------N-L-------RNKL---------------------------------------- 6 d1j93a_ 61 KVFRPDGVILFSDI-LTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 ::::::::: ::: : : d1xi3a_ 7 -----KLYVITDRRLKPE---------------------------------------V-E 21 d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 :::::::: : :::::::: : :: :: d1xi3a_ 22 SVREALEG---G----ATAIQMRI--K---NA-------------------------PT- 43 d1j93a_ 180 KFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPL 239 ::::::::::::::::::::::::: :: ::::: ::: :: d1xi3a_ 44 REMYEIGKTLRQLTREYDALFFVDD--------------RV-DVALA--VDA------DG 80 d1j93a_ 240 ILYASGSGGLLERLPL-T-GVDVVSLDWT-VDMADGRRRLGPNVAIQGNVDP------GV 290 ::::::::::::::: : :::::::::: ::::::::: : ::::::::: :: d1xi3a_ 81 -VQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKK-G--ADYLGAGSVFPTDARVI 136 d1j93a_ 291 LFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGT-PEENFAHFFEIAKG--------- 340 : :: :::::::::: :::::: ::: : :: :::::::::: d1xi3a_ 137 G------LE-GLRKIVESVK--IPVVAI--GGI--NK-DN-AREVLKTGVDGIAVISAVM 181 d1j93a_ 341 ------------------LR-Y 343 :: d1xi3a_ 182 GAEDVRKATEELRKIVEEVLG- 202 HHsearch alignment (Probability: 0.93 E-value:0.00) d1j93a_ 187 KYIRYQADSGAQAVQIFD 204 :::::::::::::::::: d1xi3a_ 21 ESVREALEGGATAIQMRI 38