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 <-- 0.657 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1fp1d2) 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 d1fp1d2 Chalcone O-​methyltransferaseS-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/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 <-- 0.657 --> Hit
DALI alignment (Z-score: 6.8 Raw score:525.50) d1nyta1 1 -----------------------------------------------------dGVGLLS 7 :::::: d1fp1d2 1 rgylasfttflcypallqvwmnfkeavvdedfmgkdkkmnqifnksmvdvcateMKRMLE 60 d1nyta1 8 DLErlsFIRPGLRILLIGAGgasrGVLLPLLSL--DCAVTITNrTVSRAEELaKLFAhtg 65 ::: :::::::::::::: ::::::::: :::::::: :::::::: :::: d1fp1d2 61 IYT---GFEGISTLVDVGGG--sgRNLELIISKypLIKGINFD-LPQVIENA-PPLS--- 110 d1nyta1 66 SIQALSMD-elEGHEFDLIINATSSGISGD--ipAIPSSLIH---PGIYCYDMFYQK--- 116 :::::::: ::::::::::::::::::: :::::::: :::::::::::: d1fp1d2 111 GIEHVGGDmfaSVPQGDAMILKAVCHNWSDekciEFLSNCHKalsPNGKVIIVEFILpee 170 d1nyta1 117 --------------------------GKTPFLAWCEQRGSKRNADgLGMLVaqaahafll 150 ::::::::::::::::::: ::::: d1fp1d2 171 pntseesklvstldnlmfitvggrerTEKQYEKLSKLSGFSKFQV-ACRAF--------- 220 d1nyta1 151 whgvlpdvepvikqlqeels 170 d1fp1d2 221 ----------nslgvmefyk 230 FAST alignment (Normalized score: 4.28 Raw score:846.90) d1nyta1 1 D------------------------------------------------------GVGLL 6 ::::: d1fp1d2 1 -RGYLASFTTFLCYPALLQVWMNFKEAVVDEDFMGKDKKMNQIFNKSMVDVCATEMKRML 59 d1nyta1 7 SDLERLSFIRPG--LRILLIGA----GGASRGVLLPLLS-LDCAVTITNRTVSRAEELAK 59 : :::::: :::::: :::::::::: ::::::::: ::::::: d1fp1d2 60 E---IYTGFE--GISTLVDV--GGGSGRNLELIISK---YPLIKGINFD-LPQVIEN--- 105 d1nyta1 60 LF-AHTGSIQALSMDELE-------GHEFDLIINATSSGISGDIPAI------------- 98 ::::::::: ::::::::: ::::: d1fp1d2 106 --APPLSGIEHV------GGDMFASVPQGDAMIL-KAVCH-------NWSDEKCIEFLSN 149 d1nyta1 99 PSSLIHPGIYCYDMFYQKGK-----------------------------------TPFLA 123 :::::::::::::: ::::: d1fp1d2 150 CHKALSPNGKVIIV------EFILPEEPNTSEESKLVSTLDNLMFITVGGRERTEKQYEK 203 d1nyta1 124 WCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------------- 170 ::::::::::: d1fp1d2 204 LSKLSGFSKFQ------------------------------------VACRAFNSLGVME 227 d1nyta1 171 --- 171 d1fp1d2 228 FYK 230 TMalign alignment (TM-score: 0.57 Raw score:97.70) d1nyta1 1 -----------------------------------------------------DGVGLLS 7 ::::::: d1fp1d2 1 RGYLASFTTFLCYPALLQVWMNFKEAVVDEDFMGKDKKMNQIFNKSMVDVCATEMKRMLE 60 d1nyta1 8 DLERLSFIRPGLRILLIGAGGASRGVLLPLLS-LD-CAVTITNRTVSRAEELAKLFAHTG 65 ::: ::::::::::::::: :: ::::::: :: ::::::: :::::::: : :::: d1fp1d2 61 IYT---GFEGISTLVDVGGGS-GR-NLELIISKYPLIKGINFD-LPQVIENA--P-PLSG 111 d1nyta1 66 SIQALS-M-DELEGHEFDLIINATSSGISGD--I-PAI-P-SSLIHPGIYCYDMF-YQ-- 115 :::::: : :::: : ::::::::::::::: : ::: : :::::::::::::: :: d1fp1d2 112 IEHVGGDMFASVP-Q-GDAMILKAVCHNWSDEKCIEFLSNCHKALSPNGKVIIVEFILPE 169 d1nyta1 116 ---------------------------KGKTPFLAWCEQ-RGSKRNADGLGMLVAQAAHA 147 ::::: :::::: :::::::: :: :: d1fp1d2 170 EPNTSEESKLVSTLDNLMFITVGGRERTEKQY-EKLSKLSGFSKFQVA-CR-AF------ 220 d1nyta1 148 FLLWHGVLPDVEPVI-KQL------QEELS 170 :: : d1fp1d2 221 -------------NSL--GVMEFYK----- 230 HHsearch alignment (Probability: 0.18 E-value:0.04) d1nyta1 16 RPG-LRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDE 74 ::: :::::::::::::::::::::::::::::::::: : :::::::::::::::: d1fp1d2 65 FEGISTLVDVGGGSGRNLELIISKYPLIKGINFDLPQV--I---ENAPPLSGIEHVGGDM 119 d1nyta1 75 L-EGHEFDLIINATSSGIS 92 : ::::::::::::::::: d1fp1d2 120 FASVPQGDAMILKAVCHNW 138