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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.853 --> Intermediate <-- 1.280 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1gdha1) through the intermediate protein (d1nyta1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nyta1 Shikimate 5-​dehydrogenase AroENAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1gdha1 D-​glycerate dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 0.853 --> Intermediate
DALI alignment (Z-score: 3.8 Raw score:453.70) query 1 dadeevYSALVVGL--rAYVAkngfRSVLIGLSgGIDSALVAAIACDALGaqNVYGVSMp 58 :::::::: :::: :::::::: :::::::::::::::: ::::::: d1nyta1 1 -----dGVGLLSDLerlSFIR--pgLRILLIGA-GGASRGVLLPLLSLDC--AVTITNR- 49 query 59 skyssdhSKGDAAELARRTG----LNFRTVSiepmfdaymaslgltglaeenlqsrlrgt 114 ::::::::::::: ::::::: d1nyta1 50 -------TVSRAEELAKLFAhtgsIQALSMD----------------------------- 73 query 115 tlmaisNQEGH-IVLAPgnkselavGYSTLY-------gdsvgAYGPikdvyktsifrla 166 ::::: ::::: :::::: :::: d1nyta1 74 ----elEGHEFdLIINA----tssgISGDIPaipsslihpgiyCYDM------------- 112 query 167 ewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktl 226 d1nyta1 113 ------------------------------------------------------------ 113 query 227 rmvdtaeyKRRQY-------------PPGTK-------------------iSAKGFG-KD 253 ::::: ::::: :::::: :: d1nyta1 113 ------fyQKGKTpflawceqrgskrNADGLgmlvaqaahafllwhgvlpdVEPVIKqLQ 166 query 254 RRlpitnrwregh 266 :: d1nyta1 167 EE---------ls 170 FAST alignment (Normalized score: 2.78 Raw score:591.60) query 1 DADEEV-YSALVVGLRAYVAKNGF-------RSVLIGLSGGIDSALVAAIACDALGAQ-N 51 :::::::::: ::::: :::::::::::::::: : d1nyta1 1 ------DGVGLLSDLER-------LSFIRPGLRILL-IGAGGASRGVLLPLLS-----LD 41 query 52 VYGVSMPSKYSSDH--SKGDAAELARRTG----LNFRTVSIEPMFDAYMASLGLTGLAEE 105 :::::: ::::::::::: :::::: d1nyta1 42 CAVTIT--------NRTVSRAEELAKL--FAHTGSIQAL--------------------- 70 query 106 NLQSRLRGTTLMAISNQEG---HIVLAPGNK-SELAVGYSTLYGDSVGAYGPIKDVYKTS 161 ::::::: :::::: :::::::::: d1nyta1 71 ------SMDELEG------HEFDLIINA---TSSGISGDIPA------------------ 97 query 162 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 221 d1nyta1 98 ------------------------------------------------------------ 98 query 222 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 266 d1nyta1 98 ---------------------------------------------IPSSLIHPGIYCYDM 112 query 267 ---------------------------------------------------------- 267 d1nyta1 113 FYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 TMalign alignment (TM-score: 0.35 Raw score:94.08) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :: :::::::::::::: :::::::::::::::::::::::: : :::::::: d1nyta1 1 --DG-VGLLSDLERLSFIR---PGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNR-- 49 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE-PM-------------FDAYMASLGLTGL-AEE 105 ::: :::::::::::::::::::::: : : :: d1nyta1 50 -TVS-RAEELAKLFAHTGSIQALSMDEL-EGHEFDLIINATSS------------GI-SG 93 query 106 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS--V----G-AYGPIKDVY 158 : :: :::::::: : : :::::: :::::::: : : : : ::::::::: d1nyta1 94 D-IP-AIPSSLIH--P--G-IYCYDM---FYQKGKTP--F-LAWCEQRGSKRNADGLGML 140 query 159 KTSI-FRL--AEW------RNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 :::: :: : d1nyta1 141 VAQAA-HAFL--LWHGVLP----------------------------------------- 156 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 :::::::::::::: d1nyta1 157 -----------------------------------DVEPVIKQLQEELS-------- 170 HHsearch alignment (Probability: 0.04 E-value:0.17) query 7 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 66 ::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1nyta1 2 GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--SLDCAVTIT---------NRT 50 query 67 KGDAAELARRTGLNFRTVSIE 87 ::::::::::::::::::::: d1nyta1 51 VSRAEELAKLFAHTGSIQALS 71
Intermediate <-- 1.280 --> Hit
DALI alignment (Z-score: 9.3 Raw score:709.70) d1nyta1 1 ----DGVGLLSDLERLS-------------------------fiRPGLRILLIGAGGASR 31 ::::::::::::: :::::::::::::::: d1gdha1 1 vtvaTAEIAMLLLLGSArragegekmirtrswpgweplelvgekLDNKTLGIYGFGSIGQ 60 d1nyta1 32 GVLLPLLSLDCAVTITNRTvsRAEE-LAKLFAhtgsIQALSMDELegHEFDLIINATSSg 90 ::::::::::::::::::: :::: :::::: ::::::::: :::::::::::: d1gdha1 61 ALAKRAQGFDMDIDYFDTH--RASSsDEASYQ----ATFHDSLDSllSVSQFFSLNAPS- 113 d1nyta1 91 ISGDI---paiPSSLIHPGIYCYDMFYqkgkTPFLAW-cEQRG-----SKRNADGL---- 137 ::::: :::::::::::::::: :::::: :::: :::::::: d1gdha1 114 TPETRyffnkaTIKSLPQGAIVVNTAR----GDLVDNelVVAAleagrLAYAGFDVfage 169 d1nyta1 138 ---------------gmLVAQAahafllwhgvlpdvepvikqlqeels 170 ::::: d1gdha1 170 pninegyydlpntflfpHIGSA-------------------------- 191 FAST alignment (Normalized score: 7.12 Raw score:1283.00) d1nyta1 1 D-----GVGLLSDLERLSFI-----------------------------RPGLRILLIGA 26 :::::::::: ::::::::::: d1gdha1 1 -VTVATAEIAMLLLLG----SARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGF 55 d1nyta1 27 GGASRGVLLPLLSLDCAVTITNRTVSR--AEELAKLFAHTG-SIQAL-SMDELEGH---E 79 :::::::::::::::::::::::: ::::::: ::::: :::: : d1gdha1 56 GSIGQALAKRAQGFDMDIDYFDTH---RASSSDEAS-----YQATFHDSLDS----LLSV 103 d1nyta1 80 FDLIINATSSGISGDIP--------AIPSSL---IHPGIYCYDMFYQKGKTP------FL 122 :::::::: :::::: :::::::::: :: d1gdha1 104 SQFFSLNA---------PSTPETRYFFNKATIKSLPQGAIVVNT--------ARGDLVDN 146 d1nyta1 123 AWCEQR-----GSKRNADG------------------------LGMLVAQAAHAFLLWHG 153 ::::: :::::: :::: d1gdha1 147 ELVVA-ALEAGRLAYAG--FDVFAGEPNINEGYYDLPNTFLFPHIGS------------- 190 d1nyta1 154 VLPDVEPVIKQLQEELS- 170 d1gdha1 191 -----------------A 191 TMalign alignment (TM-score: 0.60 Raw score:102.61) d1nyta1 1 ----DGVGLLSDLERLSF-------------------------IRPGLRILLIGAGGASR 31 :::::::::::::: ::::::::::::::::: d1gdha1 1 VTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQ 60 d1nyta1 32 GVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGI 91 ::::::::::::::::: : : :::::::::: :::::::::::::::::::::::::: d1gdha1 61 ALAKRAQGFDMDIDYFD-T--H-RASSSDEASY-QATFHDSLDSLLSVSQFFSLNAPSTP 115 d1nyta1 92 -SGDIPA-IPSSLIHPGIYCYDMFYQKGKTPFLA-WCEQR----GSKRNADGL------- 137 :::::: :::::::::::::::::: ::::: ::::: ::::::::: d1gdha1 116 ETRYFFNKATIKSLPQGAIVVNTARG---DLVDNELVVAALEAGRLAYAGFDVFAGEPNI 172 d1nyta1 138 ------------GMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 ::::::: d1gdha1 173 NEGYYDLPNTFLFPHIGSA-------------------------- 191 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 :::::::::::::::::::::::::::::::::::::::::::::::: :::::::: d1gdha1 42 GEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASSSDEASY----QATFHDSL 97 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAIP---SSLIHPGIYCYDMF 113 :: :::::::::::::::: ::::::: :::::::::::::: d1gdha1 98 DS-LLSVSQFFSLNAPSTP-ETRYFFNKATIKSLPQGAIVVNTA 139