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 <-- 0.775 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1o89a2) 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 d1o89a2 Hypothetical protein YhdHNAD(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 <-- 0.775 --> Hit
DALI alignment (Z-score: 7.9 Raw score:608.80) d1nyta1 1 --------------DGVGLLSDLErLSFIRPG-LRILLIG-AGGASRGVLLPLLSLDCAV 44 :::::::::: ::::::: ::::::: ::::::::::::::::::: d1o89a2 1 ldarkamiigtagfTAMLCVMALE-DAGVRPQdGEIVVTGaSGGVGSTAVALLHKLGYQV 59 d1nyta1 45 TITNRTVSRAEELAKLFahtgsIQALSMDEL------eGHEFDLIINATSSgisgdIPAI 98 ::::::::::::::::: ::::::::: ::::::::::::: :::: d1o89a2 60 VAVSGRESTHEYLKSLG----aSRVLPRDEFaesrpleKQVWAGAIDTVGD-----KVLA 110 d1nyta1 99 P-sSLIHPGIYCYDMF-yqkgktpflAWCEQRGSKRNADGlgMLVAqaahafllwhgvlp 156 : ::::::::::::: :::::::::::::: :::: d1o89a2 111 KvlAQMNYGGCVAACGlaggftlpttVMPFILRNVRLQGV--DSVM-------------- 154 d1nyta1 157 dVEPVIKQ----------lqeels 170 ::::::: d1o89a2 155 -TPPERRAqawqrlvadlpesfyt 177 FAST alignment (Normalized score: 6.01 Raw score:1042.00) d1nyta1 1 D---------------GVGLLSDLERLSFIRPG-LRILLI-GAGGASRGVLLPLLSLDCA 43 :::::::::::: :::: :::::: ::::::::::::::::::: d1o89a2 1 -LDARKAMIIGTAGFTAMLCVMALEDAG-VRPQDGEIVVTGASGGVGSTAVALLHKLGYQ 58 d1nyta1 44 VTITNRTVSRAEELAKLFAHTGS---IQALSMDELEGH---------EFDLIINATSSGI 91 :::::::::::::::: ::::::::: :::::::: d1o89a2 59 VVAVSGRESTHEYLKS-------LGASRVLPRDEF---AESRPLEKQVWAGAIDT----- 103 d1nyta1 92 SGDIPAIPSS-----------LIHPGIYCYDMFYQKGKTPFL------------AWCEQR 128 :::::::::: :::: d1o89a2 104 ----------VGDKVLAKVLAQMNYGGCVAA-----------CGLAGGFTLPTTVMPF-- 140 d1nyta1 129 GS----KRNADG-----------LGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS--- 170 ::::: :::::::: d1o89a2 141 --ILRNVRLQG-VDSVMTPPERRAQAWQRLV--------------------------ADL 171 d1nyta1 171 ------ 171 d1o89a2 172 PESFYT 177 TMalign alignment (TM-score: 0.58 Raw score:98.09) d1nyta1 1 -------------D-GVGLLSDLERLSFIRPG-LRILLIG-AGGASRGVLLPLLSLDCAV 44 : ::::::::: ::::::: ::::::: ::::::::::::::::::: d1o89a2 1 LDARKAMIIGTAGFTAMLCVMALE-DAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQV 59 d1nyta1 45 TITNRTVSRAEELAKLFAHTGSIQALSM-DEL-----EGHEFDLIINATSSGISGDIP-A 97 :::: :::::::::::: : ::::::: ::: :::::::::::: : ::: : d1o89a2 60 VAVS-GRESTHEYLKSL--G-ASRVLPRDEFAESRPLEKQVWAGAIDTV--G---DKVLA 110 d1nyta1 98 IPSSLIHPGIYCYDMFY---QKGKTPFLAWCEQRGS----KRNADGLGMLVAQ-AAHAFL 149 ::::::::::::::::: ::: :: ::::: ::::::::::::: :::::: d1o89a2 111 KVLAQMNYGGCVAACGLAGG----FTL-PT-TVMPFILRNVRLQGVDSVMTPPERRAQAW 164 d1nyta1 150 L------------WHGVLPDVEPVIKQLQEELS 170 : d1o89a2 165 QRLVADLPESFYT-------------------- 177 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 6 LSDLERLSFIRPGLRILLIGA-GGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHT 64 ::::::::::::::::::::: ::::::::::::::::::::::::::::::: :::::: d1o89a2 20 VMALEDAGVRPQDGEIVVTGASGGVGSTAVALLHKLGYQVVAVSGRESTHEYL-KSLGAS 78 d1nyta1 65 GSIQALSMDE---LEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDM 112 :::::::::: :::::::::::::: :::::::::::::::::::: d1o89a2 79 RVLPRDEFAESRPLEKQVWAGAIDTVG----DKVLAKVLAQMNYGGCVAAC 125