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 <-- 2.023 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1b16a_) 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 d1b16a_ Drosophila alcohol 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 <-- 2.023 --> Hit
DALI alignment (Z-score: 7.4 Raw score:695.20) d1nyta1 1 dgvgllsdlerlsFIRPGLRILLIG-AGGASRGVLLPLLSLDC-AVTITNRTVSraEELA 58 :::::::::::: ::::::::::::::::: :::::::::: :::: d1b16a_ 1 -------------MDLTNKNVIFVAaLGGIGLDTSRELVKRNLkNFVILDRVEN--PTAL 45 d1nyta1 59 KLFAHTG---SIQALSM----------dELEGH-----EFDLIINATS------------ 88 ::::::: ::::::: ::::: :::::::::: d1b16a_ 46 AELKAINpkvNITFHTYdvtvpvaeskkLLKKIfdqlkTVDILINGAGilddhqiertia 105 d1nyta1 89 SGISgDIPAI---PSSLIH-----PGIYCYDMFY----------------QKGKTpfLAW 124 :::: ::::: :::::: :::::::::: ::::: ::: d1b16a_ 106 INFT-GLVNTttaILDFWDkrkggPGGIIANICSvtgfnaihqvpvysasKAAVVsfTNS 164 d1nyta1 125 CE----QRGSkRNADG-------------------------------------------- 136 :: :::: ::::: d1b16a_ 165 LAklapITGV-TAYSInpgitrtplvhtfnswldveprvaelllshptqtseqcgqnfvk 223 d1nyta1 137 ---------LGMLvaqAAHAfllwhgvlpdvepvIKQL---qeels 170 :::: :::: :::: d1b16a_ 224 aieankngaIWKL---DLGT------------leAIEWtkhwdshi 254 FAST alignment (Normalized score: 4.93 Raw score:1026.00) d1nyta1 1 DGVGLLSDLERLSFI--RPGLRILLI-GAGGASRGVLLPLLSLD-CAVTITNRTVSR-AE 55 ::::::::: ::::::::::::::::: ::::::::: :: d1b16a_ 1 ---------------MDLTNKNVIFVAALGGIGLDTSRELVKRNLKNFVILDRV---ENP 42 d1nyta1 56 ELAKLFAHT----GSIQALS-----------MDELEG-----HEFDLIINATSSGISGDI 95 :::::::: :::::: :::::: ::::::::: d1b16a_ 43 TALAELKA-INPKVNITFH-TYDVTVPVAESKKLLKKIFDQLKTVDILING--------- 91 d1nyta1 96 PAI--------------------------PSSLIHP--------GIYCYDMFYQKGK--- 118 :::: ::::::: d1b16a_ 92 ---AGILDDHQIERTIAINFTGLVNTTTAILDF---WDKRKGGPGGIIANI------CSV 139 d1nyta1 119 -----------------------TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVL 155 ::::::::::: :::::: :::: d1b16a_ 140 TGFNAIHQVPVYSASKAAVVSFTNSLAKLAPITG-VTAYSI-----NPGI---------- 183 d1nyta1 156 PDVEPVIKQLQEELS--------------------------------------------- 170 d1b16a_ 184 ---------------TRTPLVHTFNSWLDVEPRVAELLLSHPTQTSEQCGQNFVKAIEAN 228 d1nyta1 171 -------------------------- 171 d1b16a_ 229 KNGAIWKLDLGTLEAIEWTKHWDSHI 254 TMalign alignment (TM-score: 0.62 Raw score:104.86) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDC-AVTITNRTVSRAEELA 58 : ::::::::::: ::::::::::::::::: :::::: :::: :::: d1b16a_ 1 ------------M-DLTNKNVIFVAALGGIGLDTSRELVKRNLKNFVILD-RVEN-PTAL 45 d1nyta1 59 KLFAH-TG-S-IQALSM----------DELEG-H----EFDLIINATSS-------GIS- 92 ::::: :: : :::::: ::::: : ::::::::::: ::: d1b16a_ 46 AELKAINPKVNITFHTYDVTVPVAESKKLLKKIFDQLKTVDILINGAGILDDHQIERTIA 105 d1nyta1 93 --GDIP-AI--PS-SLIHP-----GIYCYDMFY-----------------Q--KGKTPFL 122 :::: :: :: ::::: ::::::::: : ::::::: d1b16a_ 106 INFTGLVNTTTAILDFWDKRKGGPGGIIANICSVTGFNAIHQVPVYSASKAAVVSFTNSL 165 d1nyta1 123 A-WCE-QRGSKRNADGL---------------------------------------GM-- 139 : :: :::::::::: :: d1b16a_ 166 AK-LAP-ITGVTAYSINPGITRTPLVHTFNSWLDVEPRVAELLLSHPTQTSEQCGQNFVK 223 d1nyta1 140 ----------LVAQAAHAFLLWHGVLPDVEPVIKQLQEELS----- 170 ::::::: :: : :::::: d1b16a_ 224 AIEANKNGAIWKLDLGT----------LE---A--IEWTKHWDSHI 254 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 15 IRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGS--IQALS 71 ::::::::::: ::::::::::::::::::::::::::::::::::::::::: ::::: d1b16a_ 2 DLTNKNVIFVAALGGIGLDTSRELVKRNLKNFVILDRVENPTALAELKAINPKVNITFHT 61 d1nyta1 72 M---------------DELEGHEFDLIINATSSG 90 : :::::::::::::::::: d1b16a_ 62 YDVTVPVAESKKLLKKIFDQLKTVDILINGAGIL 95