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 <-- 1.090 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1jqba2) 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 d1jqba2 Bacterial secondary 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 <-- 1.090 --> Hit
DALI alignment (Z-score: 7.4 Raw score:611.10) d1nyta1 1 -----------DGVGLLSdlerlsFIRPGLRILLIGAGGASRGVLLPLLSLDC-AVTITN 48 ::::::: ::::::::::::::::::::::::::::: :::::: d1jqba2 1 mplenavmitdMMTTGFH-gaelaDIEMGSSVVVIGIGAVGLMGIAGAKLRGAgRIIGVG 59 d1nyta1 49 rTVSRAEELAKLFahtgsIQALSM------DELEGH----EFDLIINATSSGisgDIPAi 98 :::::::::::: :::::: :::::: :::::::::::: :::: d1jqba2 60 -SRPICVEAAKFY---gaTDILNYknghieDQVMKLtngkGVDRVIMAGGGS---ETLSq 112 d1nyta1 99 psSLIHPGIYCYDM-FYQK-GKTP--flawceqrGSKRNADGlGMLVaqaAHAFLlwhgv 154 :::::::::::: :::: :::: :::::::: :::: ::::: d1jqba2 113 avKMVKPGGIISNInYHGSgDALLiprvewgcgmAHKTIKGG-LCPG-grLRAER----- 165 d1nyta1 155 lpdvepvikqlqeels 170 d1jqba2 166 -------lrdmvvynr 174 FAST alignment (Normalized score: 6.29 Raw score:1082.00) d1nyta1 1 D---------------GVGLLSDLERLS-FIRPGLRILLIGAGGASRGVLLPLLSLD-CA 43 ::::::: :::::::::::::::::::::::::::: :: d1jqba2 1 -MPLENAVMITDMMTTGFHGAEL-----ADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGR 54 d1nyta1 44 VTITNRTVSRAEELAKLFAHTGS---IQALS------MDELEGH-----EFDLIINATSS 89 :::::::::::::::: ::::: :::::: :::::::::: d1jqba2 55 IIGVGSRPICVEAAKF-------YGATDILNYKNGHIEDQVMK-LTNGKGVDRVIMAGG- 105 d1nyta1 90 GISGDIPAI-------PSSLIHPGIYCYDMFY--QKGKTPFLAWCEQRGS---------- 130 :::::::::::::::: ::::: d1jqba2 106 ---------GSETLSQAVKMVKPGGIISNINYHGSGDAL-----------LIPRVEWGCG 145 d1nyta1 131 ---KRNADGLGML---------VAQAAHAFLLWHGVLPDVEPVIKQLQEELS--- 170 :::::: :::::::: d1jqba2 146 MAHKTIKGG----LCPGGRLRAERLRDMVV----------------------YNR 174 TMalign alignment (TM-score: 0.59 Raw score:100.25) d1nyta1 1 -----------DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDC-AVTITN 48 :::::::::: ::::::::::::::::::::::::::::::: :::::: d1jqba2 1 MPLENAVMITDMMTTGFHGAE-LADIEMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVG 59 d1nyta1 49 RTVSRAEELAKLFAHTGSIQALSM--D----ELEG-H---EFDLIINATSSGISGDIP-A 97 :::::::::::: : ::::::: : :::: : :::::::::::: :: : d1jqba2 60 -SRPICVEAAKFY--G-ATDILNYKNGHIEDQVMKLTNGKGVDRVIMAGGGS----ETLS 111 d1nyta1 98 IPSSLIHPGIYCYDMFYQ---KGKTPFLAWCEQRG----S-KRNADGLGMLVAQAAHAFL 149 :::::::::::::::::: ::: ::::::: : ::::::: : : :::::: d1jqba2 112 QAVKMVKPGGIISNINYHGSG--DAL--LIPRVEWGCGMAHKTIKGGL--C-P-GGRLRA 163 d1nyta1 150 L--WHG-------VLPDVEPVIKQLQEELS 170 : : d1jqba2 164 ERL--RDMVVYNR----------------- 174 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 6 LSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG 65 :::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::: d1jqba2 17 FHGAELADIE-MGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATD 75 d1nyta1 66 SIQALSM-------DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGK 118 ::::::: ::::::::::::::::: :::::::::::::::::::::::::: d1jqba2 76 ILNYKNGHIEDQVMKLTNGKGVDRVIMAGGG---SETLSQAVKMVKPGGIISNINYHGSG 132 d1nyta1 119 T 119 : d1jqba2 133 D 133