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 <-- 1.078 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1lqta1) 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 d1lqta1 Ferredoxin:NADP reductase FprAFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/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 <-- 1.078 --> Hit
DALI alignment (Z-score: 2.6 Raw score:319.90) d1nyta1 1 ---------------dgvGLLSDL------eRLSFIRPGLRILLIGAGGASRGVLLPLLS 39 :::::: ::::::::::::::::::::::::::::: d1lqta1 1 drmlnipgedlpgsiaavDFVGWYnahphfeQVSPDLSGARAVVIGNGNVALDVARILLT 60 d1nyta1 40 ---------------------LDCAVTITNRTVS-------raeelaKLFAHTG------ 65 ::::::::::::: ::::::: d1lqta1 61 dpdvlartdiadhaleslrprGIQEVVIVGRRGPlqaafttlelrelADLDGVDvvidpa 120 d1nyta1 66 ------------------------------------SIQAL--SMDE------------- 74 ::::: :::: d1lqta1 121 eldgitdedaaavgkvckqnikvlrgyadrerpghrRMVFRflTSPIeikgkrkverivl 180 d1nyta1 75 --------------------lEGHEFDLIINATSSgisgdipaipsslihpgiycydmfy 114 :::::::::::::: d1lqta1 181 grnelvsdgsgrvaakdtgerEELPAQLVVRSVGY------------------------- 215 d1nyta1 115 qkgktpflawceqrgskrnadglgmlvaqaahafllwhgvlpdvepvikqlqeels 170 d1lqta1 216 -------------------------------------------------------- 216 FAST alignment (Normalized score: 2.46 Raw score:470.60) d1nyta1 1 DGVGLLSDLERLS-----------------------------------FIRPGLRILLIG 25 :::: ::::::: d1lqta1 1 -------------DRMLNIPGEDLPGSIAAVDFVGWYNAHPHFEQVSPDLSG-ARAVVIG 46 d1nyta1 26 AGGASRGVLLPLLSLD-------------------------CAVTITNRTVSRAE----- 55 :::::::::::: ::::::::: d1lqta1 47 NGNVALDVARIL----LTDPDVLARTDIADHALESLRPRGIQEVVIVGRR-----GPLQA 97 d1nyta1 56 ----ELAKLFAHTG---------------------------------------------- 65 ::::::::: d1lqta1 98 AFTTLELRELADL-DGVDVVIDPAELDGITDEDAAAVGKVCKQNIKVLRGYADRERPGHR 156 d1nyta1 66 SIQALSMDEL----------------------------------------EGHEFDLIIN 85 ::::: :::::::::: d1lqta1 157 RMVFR-----FLTSPIEIKGKRKVERIVLGRNELVSDGSGRVAAKDTGEREELPAQLVVR 211 d1nyta1 86 ATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAA 145 : d1lqta1 212 S----------------------------------------------------------- 212 d1nyta1 146 HAFLLWHGVLPDVEPVIKQLQEELS--- 170 d1lqta1 213 -------------------------VGY 215 TMalign alignment (TM-score: 0.40 Raw score:67.24) d1nyta1 1 -----------------D-GVGLLSD---LERLSFIRPGLRILLIGAGGASRGVLLPLLS 39 : ::::::: ::::::::::::::::::::::::::::::: d1lqta1 1 DRMLNIPGEDLPGSIAAVDFVGWYNAHPHFEQVSPDLSGARAVVIGNGNVALDVARILLT 60 d1nyta1 40 -----------------L--D-C-AVTITNRTVS--RAE-E-LAKLFA-H--TG------ 65 : : : :::::::::: ::: : :::::: : :: d1lqta1 61 DPDVLARTDIADHALESLRPRGIQEVVIVGRRGPLQAAFTTLELRELADLDGVDVVIDPA 120 d1nyta1 66 ------------------------------------SIQALS-M---------------- 72 :::::: : d1lqta1 121 ELDGITDEDAAAVGKVCKQNIKVLRGYADRERPGHRRMVFRFLTSPIEIKGKRKVERIVL 180 d1nyta1 73 DE------------------LEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFY 114 :: :::::::::::::: : d1lqta1 181 GRNELVSDGSGRVAAKDTGEREELPAQLVVRSVG------------------------Y- 215 d1nyta1 115 QKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 d1lqta1 216 -------------------------------------------------------- 216 HHsearch alignment (Probability: 0.88 E-value:0.00) d1nyta1 11 RLSFIRPGLRILLIGAGGASRGVLLPLLS--------------------LDC-AVTITNR 49 ::::::::::::::::::::::::::::: ::: ::::::: d1lqta1 32 QVSPDLSGARAVVIGNGNVALDVARILLTDPDVLARTDIADHALESLRPRGIQEVVIVGR 91 d1nyta1 50 TV 51 :: d1lqta1 92 RG 93