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 <-- 1.915 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1psda1) 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 d1psda1 Phosphoglycerate 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 <-- 1.915 --> Hit
DALI alignment (Z-score: 8.6 Raw score:702.40) d1nyta1 1 ----DGVGLLSDLERLS----------------------fiRPGLRILLIGAGGASRGVL 34 ::::::::::::: ::::::::::::::::::: d1psda1 1 ntrsVAELVIGELLLLLrgvpeanakahrgvwnklaagsfeARGKKLGIIGYGHIGTQLG 60 d1nyta1 35 LPLLSLDCAVTITNRTVsraEELAklfahtGSIQALSmdELEG--HEFDLIINATSsGIS 92 ::::::::::::::::: :::: ::::::: :::: ::::::::::: ::: d1psda1 61 ILAESLGMYVYFYDIEN---KLPL------GNATQVQ--HLSDllNMSDVVSLHVP-ENP 108 d1nyta1 93 G-DIPA--iPSSLIHPGIYCYDMFYqkgkTPFLAW-cEQRG-----SKRNADGL------ 137 : :::: :::::::::::::::: :::::: :::: :::::::: d1psda1 109 StKNMMgakEISLMKPGSLLINASR----GTVVDIpaLCDAlaskhLAGAAIDVfptepa 164 d1nyta1 138 ------------------gmLVAQaahafllwhgvlpdvepvikqlqeels 170 :::: d1psda1 165 tnsdpftsplcefdnvlltpHIGG--------------------------- 188 FAST alignment (Normalized score: 6.79 Raw score:1214.00) d1nyta1 1 D-----GVGLLSDLERLSFI--------------------------RPGLRILLIGAGGA 29 :::::::::: :::::::::::::: d1psda1 1 -NTRSVAELVIGELLL----LLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHI 55 d1nyta1 30 SRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG------SIQAL-SMDELEGH---E 79 ::::::::::::::::::::: ::::: :::: : d1psda1 56 GTQLGILAESLGMYVYFYDIE---------------NKLPLGNATQVQHLSD----LLNM 96 d1nyta1 80 FDLIINATSSGISGDIP----AIPSSL---IHPGIYCYDMFYQKGKTP-----FLAWCEQ 127 :::::::: :::: :::::: ::::::::::: ::::::: d1psda1 97 SDVVSLHV--PENP---STKNMMGAKEISLMKPGSLLINAS-------RGTVVDIPALCD 144 d1nyta1 128 R-----GSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------------ 170 :::::: d1psda1 145 -ALASKHLAGAA------------------------------------IDVFPTEPATNS 167 d1nyta1 171 --------------------- 171 d1psda1 168 DPFTSPLCEFDNVLLTPHIGG 188 TMalign alignment (TM-score: 0.59 Raw score:99.46) d1nyta1 1 --D--GVGLLSDLERLSF----------------------IRPGLRILLIGAGGASRGVL 34 : ::::::::::::: :::::::::::::::::::: d1psda1 1 NTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLG 60 d1nyta1 35 LPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSSGI-SG 93 :::::::::::::::: :: : : ::: ::::::::::::::::::::::::: :: d1psda1 61 ILAESLGMYVYFYDIE-NK--L-P-LGN----ATQVQHLSDLLNMSDVVSLHVPENPSTK 111 d1nyta1 94 DIPA-IPS-SLIHPGIYCYDMFYQKGKTPFLA-WCEQR----GSKRNADGL-------GM 139 :::: :: ::::::::::::::: ::::: ::::: ::::::::: d1psda1 112 NMMGA-KEISLMKPGSLLINASRG---TVVDIPALCDALASKHLAGAAIDVFPTEPAT-- 165 d1nyta1 140 LVAQAAHAFLLWHGVLPDVEPVIKQL-QEELS---------------- 170 :: :::: d1psda1 166 ------------------------NSD-PFTSPLCEFDNVLLTPHIGG 188 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 11 RLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQAL 70 ::::::::::::::::::::::::::::::::::::::::::::::::: ::: d1psda1 37 AGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNAT--------QVQ 88 d1nyta1 71 SMDELEGHEFDLIINATSSGISGDIPAIP---SSLIHPGIYCYDMFYQKG--KTPFLAWC 125 :::: ::::::::::::::: :::::::: :::::::::::::::::: :::::::: d1psda1 89 HLSD-LLNMSDVVSLHVPEN-PSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDAL 146 d1nyta1 126 EQRGSKRNADGLGMLVA 142 ::::: :::::::::: d1psda1 147 -ASKHL-AGAAIDVFPT 161