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 <-- 1.131 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1js1x2) 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 d1js1x2 Transcarbamylase-​like proteinAspartate/​ornithine carbamoyltransferaseATC-​likeα/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 <-- 1.131 --> Hit
DALI alignment (Z-score: 7.4 Raw score:583.40) d1nyta1 1 dgvgllsdlerlsfiRPGLRILLIG-------aGGASRGVLLPLLSLDCAVTITNrTVSR 53 :::::::::: :::::::::::::::::::::: :::: d1js1x2 1 ---------------TARPKVVMTWaphprplpQAVPNSFAEWMNATDYEFVITH-PEGY 44 d1nyta1 54 aeELAKLFAHTgsIQALSmdELEG--HEFDLIINAT----------ssgisgDIPAIPSS 101 ::::::::: ::::: :::: :::::::::: :::::::: d1js1x2 45 --ELDPKFVGN--ARVEY--DQMKafEGADFIYAKNwaaytgdnygqilstdRNWTVGDR 98 d1nyta1 102 LIH--pGIYCYDMFYqkGKTP--FLAWCEQrgSKRNAD--GLGMLVAQAAHAFLLWHGVl 155 ::: ::::::::: :::: ::::::: :::::: ::::::::::::::::::: d1js1x2 99 QMAvtnNAYFMHCLP--VRRNmiVTDDVIE--SPQSIVipEAANREISATVVLKRLLEN- 153 d1nyta1 156 pdvepvikqlqeels 170 d1js1x2 154 -------lphhhhhh 161 FAST alignment (Normalized score: 4.36 Raw score:721.20) d1nyta1 1 DGVGLLSDLERLSFIR-PGLRILLIGA----------GGASRGVLLPLLSLDCAVTITNR 49 ::::::: :::::::::::::::::::::: d1js1x2 1 ----------------TARPKVVM---TWAPHPRPLPQAVPNSFAEWMNATDYEFVITH- 40 d1nyta1 50 TVSR------AEELAKLFAHTG--SIQALSMDELEG-------HEFDLIINATSSGISGD 94 :::: ::::: :::::::: d1js1x2 41 ----PEGYELDPKF--------VGNARVE-------YDQMKAFEGADFIYA--------- 72 d1nyta1 95 IP---------------------AIPSSLIHP-----GIYCYDMFYQKGKTPFLAWCEQR 128 :::::: ::::::: d1js1x2 73 --KNWAAYTGDNYGQILSTDRNWTVGDRQ---MAVTNNAYFMHC---------------- 111 d1nyta1 129 G---------------SKRNA-------DGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQ 166 :::: ::::::::::::::: d1js1x2 112 -LPVRRNMIVTDDVIESPQS-IVIPEAANREISATVVLKRLLE----------------- 152 d1nyta1 167 EELS--------- 170 d1js1x2 153 ----NLPHHHHHH 161 TMalign alignment (TM-score: 0.54 Raw score:91.05) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-------AGGASRGVLLPLLSLDCAVTITNRTVSR 53 :::::::::: :::::::::::::::::::::::: ::: d1js1x2 1 ---------------TARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYEFVITHP-EGY 44 d1nyta1 54 AEELAKLFAHTGSIQALSMDELEGH-E-FDLIINATSS-------------GISGDIPAI 98 ::::::::: ::::: ::::: : :::::::::: ::::: d1js1x2 45 ELDPKFVGN----ARVEY--DQMKAFEGADFIYAKNWAAYTGDNYGQILST----DRNWT 94 d1nyta1 99 PS-SLIH--PGIYCYDMFYQKGKTP---FLAWCEQRGSKRNAD--GLGMLVAQAAHAFLL 150 :: :::: ::::::::::: :: ::::::: :::::: ::::::::::::::: d1js1x2 95 VGDRQMAVTNNAYFMHCLPV---RRNMIVTDDVIE--SPQSIVIPEAANREISATVVLKR 149 d1nyta1 151 WHGV--------LPDVEPVIKQLQEELS 170 :::: d1js1x2 150 LLENLPHHHHHH---------------- 161 HHsearch alignment (Probability: 0.36 E-value:0.00) d1nyta1 27 GGASRGVLLPLLSLDCAVTITNRTV-SRAEELAKLFAHTGSIQALSMDELEGHEFDLIIN 85 ::::::::::::::::::::::::: :::::::::: :::::::::::::::::: d1js1x2 19 QAVPNSFAEWMNATDYEFVITHPEGYELDPKFVGNA------RVEYDQMKAFEGADFIYA 72 d1nyta1 86 ATSSGISGDI 95 :::::::::: d1js1x2 73 KNWAAYTGDN 82