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 <-- 1.064 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d3lada1) 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 d3lada1 Dihydrolipoamide dehydrogenaseFAD/​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 <-- 1.064 --> Hit
DALI alignment (Z-score: 3.9 Raw score:398.60) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLSLDCAVTITNRT-----VSRA- 54 :::::::::::::::::::::::::::::::: :::: d3lada1 1 ---------------sqkFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYkgkegKTALg 45 d1nyta1 55 ---------------------------------------------------------eeL 57 : d3lada1 46 gtclnvgcipskalldssykfheahesfklhgistgevaidvptmiarkdqivrnltggV 105 d1nyta1 58 AKLFAHTgSIQALSMD----------------elEGHEFDLIINATSSG----iSGDIP- 96 ::::::: :::::::: ::::::::::::::: ::::: d3lada1 106 ASLIKAN-GVTLFEGHgkllagkkvevtaadgssQVLDTENVILASGSKpveipRRPVTt 164 d1nyta1 97 AIPS-----------------slihPGIYCYDM---FYQKgktpflawceqrgskrnadg 136 :::: :::::::: :::: d3lada1 165 DLLAadsgvtldergfiyvddycatSVPGVYAIgdvVRGA---mlahkaseegvvvaeri 221 d1nyta1 137 lgmlVAQAahafllwhgvlpdvepvikqlqeels 170 :::: d3lada1 222 aghkAQMN-------------------------- 229 FAST alignment (Normalized score: 3.10 Raw score:612.00) d1nyta1 1 DGVGLLSDLERLSFIRPGL----RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSR--- 53 ::::::::::::::::::::::::::::: d3lada1 1 -------------------SQKFDVIVIGAGPGGYVAAIKSAQLGLKTALIE-----KYK 36 d1nyta1 54 ------------------------------------------------------------ 54 d3lada1 37 GKEGKTALGGTCLNVGCIPSKALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQ 96 d1nyta1 54 -----AEELAKLFAHTGSIQALSMDEL---------------------EGHEFDLIINAT 87 ::::::::::: ::::: ::::::::::: d3lada1 97 IVRNLTGGVASLIKAN-GVTLF-----EGHGKLLAGKKVEVTAADGSSQVLDTENVILA- 149 d1nyta1 88 SSGISGDIPAIPSSLIHPGI---------------------------------------- 107 d3lada1 150 --------------------SGSKPVEIPRRPVTTDLLAADSGVTLDERGFIYVDDYCAT 189 d1nyta1 108 ---YCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQ 164 :::: d3lada1 190 SVPGVYA----------------------------------------------------- 196 d1nyta1 165 LQEELS--------------------------------- 170 d3lada1 197 ------IGDVVRGAMLAHKASEEGVVVAERIAGHKAQMN 229 TMalign alignment (TM-score: 0.38 Raw score:64.93) d1nyta1 1 -----------DGVGLLSDLERLSFI-RPGLRILLIGA-G------GAS----------- 30 :::::::::: :: ::::::::::: : ::: d3lada1 1 SQKFDVIVIGAGPGGYVAAIK---SAQLGLKTALIEKYKGKEGKTALGGTCLNVGCIPSK 57 d1nyta1 31 --------------------------------------------R-GVLLPLLSLDCAVT 45 : :::::::::::::: d3lada1 58 ALLDSSYKFHEAHESFKLHGISTGEVAIDVPTMIARKDQIVRNLTGGVASLIKANGVTLF 117 d1nyta1 46 ITNR---------TVSRAEELAKLFAHTGSIQALSMDELEGHEF-DLIINATSSG----I 91 :::: ::::::::::::: :::::::::: : d3lada1 118 EGHGKLLAGKKVE------------------VTAADGSSQVLDTENVILASGSKPVEIPR 159 d1nyta1 92 SGDIPAIPSS-LIH---PGIYCYDMFYQKGKTPFLAW----CEQRGSKRNADG----L-- 137 :::::::::: :: ::::: ::: ::: :::::::: : d3lada1 160 RPVTTDLLAAD-SGVTL-----------DERGF-IYVDDYCATS-VPGVYAIGDVVRGAM 205 d1nyta1 138 GMLVAQA-------------AHAFLLWHGVLPDVEPVIKQLQEELS 170 ::::::: :: :: d3lada1 206 LAHKASEEGVVVAERIAGHK--------------AQ-MN------- 229 HHsearch alignment (Probability: 0.86 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTV 51 ::::::::::::::::::::::::::::::::::: d3lada1 2 QKFDVIVIGAGPGGYVAAIKSAQLGLKTALIEKYK 36