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 <-- 0.813 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1chua2) 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 d1chua2 L-​aspartate oxidaseFAD/​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 <-- 0.813 --> Hit
DALI alignment (Z-score: 4.4 Raw score:380.20) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLSlDCAVTITNRTVSR------- 53 ::::::::::::::::::::: ::::::::::::: d1chua2 1 -----------ntlpehsCDVLIIGSGAAGLSLALRLAD-QHQVIVLSKGPVTefdetds 48 d1nyta1 54 ----------------------------------------aeeLAKLFAHTGSIQALSMD 73 ::::::::::::::::: d1chua2 49 idshvedtliagagicdrhavefvasnarscvqwlidqgvlttLVSKALNHPNIRVLERT 108 d1nyta1 74 ------------------------------elEGHEFDLIINATSSGIS----------- 92 ::::::::::::::::: d1chua2 109 navdlivsdkiglpgtrrvvgawvwnrnketvETCHAKAVVLATGGASKvyqyttnpdis 168 d1nyta1 93 GDIP-----------------aipsslihpgIYCYDM---FYQKGktpflawceqrgskr 132 :::: :::::: ::::: d1chua2 169 SGDGiamawragcrvancggvmvddhgrtdvEGLYAIgevSYTGL-------------hg 215 d1nyta1 133 nadglgmLVAQaahafllwhgvlpdvepvikqlqeels 170 :::: d1chua2 216 anrmasnSLLE--clvygwsaaeditrrmhdistlppw 251 FAST alignment (Normalized score: 3.03 Raw score:625.50) d1nyta1 1 DGVGLLSDLERLSFIRPGL--------RILLIGAGGASRGVLLPLLSLDCAVTITNRTVS 52 :::::::::::::::::::: ::::::::: d1chua2 1 -------------------NTLPEHSCDVLIIGSGAAGLSLALRLAD-QHQVIVLSK--- 37 d1nyta1 53 RAE-----------------------------------------------------ELAK 59 :::: d1chua2 38 ---GPVTEFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLTTLVS 94 d1nyta1 60 LFAHTGSIQALSMDEL-----------------------------------EGHEFDLII 84 ::::::::::: ::::::::: d1chua2 95 KALNHPNIRVL-----ERTNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVV 149 d1nyta1 85 NATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGK-----------------TPFLAWCEQ 127 ::: ::::::::: d1chua2 150 LAT-------------------------------GGASKVYQYTTNPDISSGDGIAMAWR 178 d1nyta1 128 RGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS----------------- 170 ::: d1chua2 179 AGC----------------------------------------RVANCGGVMVDDHGRTD 198 d1nyta1 171 ----------------------------------------------------- 171 d1chua2 199 VEGLYAIGEVSYTGLHGANRMASNSLLECLVYGWSAAEDITRRMHDISTLPPW 251 TMalign alignment (TM-score: 0.35 Raw score:58.97) d1nyta1 1 --------------DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLL----------- 35 :::::::::: ::::::::::: :::::: d1chua2 1 NTLPEHSCDVLIIGSGAAGLSLAL--RLADQHQVIVL------SKGPVTEFDETDSIDSH 52 d1nyta1 36 ----------------------------------------P-LLS-LD-CAVT--ITNRT 50 : ::: :: :::: ::::: d1chua2 53 VEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLTTLVSKALNHPNIRVLERTNAVD 112 d1nyta1 51 -------------------VSRAEELAKLFAHTGSIQALSMDELEGHEFDLIIN-A---- 86 :::: : :::: :: :::::::: : d1chua2 113 LIVSDKIGLPGTRRVVGAW--VWNR--N--------KETV--ET--CHAKAVVLATGGAS 156 d1nyta1 87 ---------------TSSGISGDIP-------AIPSSLIHPGIYCYDMFYQKGK--TPFL 122 ::::: :::: :::::: :: d1chua2 157 KVYQYTTNPDISSGDGIAMA-WRAGCRVANCG----------------GVMVDDHG--RT 197 d1nyta1 123 AWCEQRGSKRNADGLGML---V-------AQAAHAFLLWHGVLPDVE-PVIK--QLQ--- 166 :: : : :::::::: : :::: :: ::: : d1chua2 198 DV-E---G--LYAIGEVSYTGLHGANRMASNSL------------LEC-LVYGW--SAAE 236 d1nyta1 167 ---------------EELS 170 d1chua2 237 DITRRMHDISTLPPW---- 251 HHsearch alignment (Probability: 0.80 E-value:0.00) d1nyta1 16 RPGLRILLIGAGGASRGVLLPLLSLDCAVTIT 47 :::::::::::::::::::::::::::::::: d1chua2 5 EHSCDVLIIGSGAAGLSLALRLADQHQVIVLS 36