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 <-- 1.840 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1dxya1) 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 d1dxya1 D-​2-​hydroxyisocaproate 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 <-- 1.840 --> Hit
DALI alignment (Z-score: 8.7 Raw score:723.80) d1nyta1 1 ----DGVGLLSDLERLS-----------------------fiRPGLRILLIGAGGASRGV 33 ::::::::::::: :::::::::::::::::: d1dxya1 1 spaaIAEFALTDTLYLLrnmgkvqaqlqagdyekagtfigkeLGQQTVGVMGTGHIGQVA 60 d1nyta1 34 LLPLLSLDCAVTITNRtvsRAEElaKLFAhtgSIQALSMDELegHEFDLIINATSsGISG 93 :::::::::::::::: :::: :::: :::::::::: ::::::::::: :::: d1dxya1 61 IKLFKGFGAKVIAYDP---YPMK--GDHP---DFDYVSLEDL-fKQSDVIDLHVP-GIEQ 110 d1nyta1 94 -DIPA--iPSSLIHPGIYCYDMFYqkgkTPFLAW-cEQRG-----SKRNADG-------- 136 :::: :::::::::::::::: :::::: :::: ::::::: d1dxya1 111 nTHIIneaAFNLMKPGAIVINTAR----PNLIDTqaMLSNlksgkLAGVGIDtyeyeted 166 d1nyta1 137 ----------------------------LGMLVaqaahafllwhgvlpdvepvikqlqee 168 ::::: d1dxya1 167 llnlakhgsfkdplwdellgmpnvvlspHIAYY--------------------------- 199 d1nyta1 169 ls 170 d1dxya1 200 -- 200 FAST alignment (Normalized score: 7.26 Raw score:1336.00) d1nyta1 1 D-----GVGLLSDLERLSFI---------------------------RPGLRILLIGAGG 28 :::::::::: ::::::::::::: d1dxya1 1 -SPAAIAEFALTDTLY----LLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVMGTGH 55 d1nyta1 29 ASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFA----HTGSIQALSMDELEGHEFDLII 84 :::::::::::::::::::::: ::::::::::::::: :::::: d1dxya1 56 IGQVAIKLFKGFGAKVIAYDPY------------PMKGDHPDFDYVSLEDLFK-QSDVID 102 d1nyta1 85 NATSSGISGDIP--------AIPSSL---IHPGIYCYDMFYQKGKTP-----FLAWCEQR 128 ::: :::::: ::::::::::: ::::::: d1dxya1 103 LHV---------PGIEQNTHIINEAAFNLMKPGAIVINTA-------RPNLIDTQAMLS- 145 d1nyta1 129 -----GSKRNADG--------------------------------------LGMLVAQAA 145 :::::: :::: d1dxya1 146 NLKSGKLAGVG--IDTYEYETEDLLNLAKHGSFKDPLWDELLGMPNVVLSPHIAY----- 198 d1nyta1 146 HAFLLWHGVLPDVEPVIKQLQEELS- 170 d1dxya1 199 -------------------------Y 199 TMalign alignment (TM-score: 0.60 Raw score:101.23) d1nyta1 1 --D--GVGLLSDLERLSF-----------------------IRPGLRILLIGAGGASRGV 33 : ::::::::::::: ::::::::::::::::::: d1dxya1 1 SPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVMGTGHIGQVA 60 d1nyta1 34 LLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGIS- 92 ::::::::::::::::: :: :: :: : : ::::::: ::::::::::::::: :: d1dxya1 61 IKLFKGFGAKVIAYDPY-PM--KG-DH-P-D--FDYVSLE-DLFKQSDVIDLHVPG-IEQ 110 d1nyta1 93 GDIPAI-PS-SLIHPGIYCYDMFYQKGKTPFLA-WCEQR----GSKRNADG--------- 136 :::::: :: ::::::::::::::: ::::: ::::: :::::::: d1dxya1 111 NTHIINEAAFNLMKPGAIVINTARP---NLIDTQAMLSNLKSGKLAGVGIDTYEYETEDL 167 d1nyta1 137 ------------------------LGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 :::::::: d1dxya1 168 LNLAKHGSFKDPLWDELLGMPNVVLSPHIAYY-------------------------- 199 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 :::::::::::::::::::::::::::::::::::::::::::::: :::::: d1dxya1 40 GKELGQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPD--------FDYVSL 91 d1nyta1 73 DELEGHEFDLIINATSSGIS--GDIPAIPSSLIHPGIYCYDMFYQK--GKTPFLAWCEQR 128 :: ::::::::::::::::: :::::::::::::::::::::::: :::::: ::::: d1dxya1 92 ED-LFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAML-SNLKS 149 d1nyta1 129 GSKRNADGLGMLVAQ 143 ::: ::::::::::: d1dxya1 150 GKL-AGVGIDTYEYE 163