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 <-- 1.408 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1i1na_) 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 d1i1na_ Protein-​L-​isoaspartyl 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 <-- 1.408 --> Hit
DALI alignment (Z-score: 6.0 Raw score:504.50) d1nyta1 1 ------------------------------------------------------------ 1 d1i1na_ 1 wksggashselihnlrkngiiktdkvfevmlatdrshyakcnpymdspqsigfqatisap 60 d1nyta1 1 -DGVGLLSDLErlSFIRPGLRILLIGAGgasRGVLLPLLSLD---CAVTITNRTVSRAEE 56 :::::::::: ::::::::::::::: ::::::::::: ::::::::::::::: d1i1na_ 61 hMHAYALELLF--DQLHEGAKALDVGSG--sGILTACFARMVgctGKVIGIDHIKELVDD 116 d1nyta1 57 LAKLF----AHTG---SIQALSMD---eLEGHE-FDLIINATSSgisGDIPaipSSLIHP 105 ::::: :::: :::::::: ::::: :::::::::: :::: :::::: d1i1na_ 117 SVNNVrkddPTLLssgRVQLVVGDgrmgYAEEApYDAIHVGAAA---PVVPqalIDQLKP 173 d1nyta1 106 GIYCYDmFYQK---GKTPFL-awceqRGSKrnadglgmlvaqaahafllwhgvlpdvepv 161 :::::: :::: :::::: :::: d1i1na_ 174 GGRLIL-PVGPaggNQMLEQydklqdGSIK-----------------mkplmgviyvplt 215 d1nyta1 162 ikqlqeels 170 d1i1na_ 216 dkekqwsrw 224 FAST alignment (Normalized score: 5.07 Raw score:989.60) d1nyta1 1 D----------------------------------------------------------- 1 d1i1na_ 1 -WKSGGASHSELIHNLRKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISA 59 d1nyta1 2 ---GVGLLSDLER-LSFIRPGLRILLIGAGGAS-RGVLLPLLS---LDCAVTITNRTVSR 53 ::::::: :::::::::::::::: ::::::::: :::::::::::::: d1i1na_ 60 PHMHAYALEL---LFDQLHEGAKALDVGSG---SGILTACFARMVGCTGKVIGIDHIKEL 113 d1nyta1 54 AEELAKL-------FAHTGSIQALSMDELEG-----------HEFDLIINATSSGIS-GD 94 ::::::: :::::::::: ::::::::::: :: d1i1na_ 114 VDDSVNNVRKDDPTLLSSGRVQLV-------VGDGRMGYAEEAPYDAIHVGAA----APV 162 d1nyta1 95 IPAI--PSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGS---------------------K 131 :: ::::::::::::: : d1i1na_ 163 VP--QALIDQLKPGGRLIL-------------------PVGPAGGNQMLEQYDKLQDGSI 201 d1nyta1 132 RNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------------------- 170 :::: d1i1na_ 202 KMKP-----------------------------------LMGVIYVPLTDKEKQWSRW 224 TMalign alignment (TM-score: 0.53 Raw score:89.86) d1nyta1 1 ------------------------------------------------------------ 1 d1i1na_ 1 WKSGGASHSELIHNLRKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAP 60 d1nyta1 1 D-GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNRTVSRAEE 56 : ::::::::: :::::::::::::::: :: :::::::: : ::::::::::::::: d1i1na_ 61 HMHAYALELLF--DQLHEGAKALDVGSGS-GI-LTACFARMVGCTGKVIGIDHIKELVDD 116 d1nyta1 57 LAKLFA---H-TG---SIQAL-SM--DELEGHE-FDLIINATSSGISGDIPAIPSSLIHP 105 :::::: : :: ::::: :: ::::::: ::::::::: : ::::::::::::: d1i1na_ 117 SVNNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDAIHVGAA-A--PVVPQALIDQLKP 173 d1nyta1 106 GIYCYDMF------YQKGKTPFLAWCE--QRGSKRNADGLGML---------------VA 142 :::::::: :: :: ::: :: :::::::::: : d1i1na_ 174 GGRLILPVGPAGGNQM--LE-QYD-KLQD--GSIKMKPLMG-VIYVPLTDKEKQWSRW-- 224 d1nyta1 143 QAAHAFLLWHGVLPDVEPVIKQLQEELS 170 d1i1na_ 225 ---------------------------- 225 HHsearch alignment (Probability: 0.82 E-value:0.00) d1nyta1 16 RPGLRILLIGAGGAS-RGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHT-------GSI 67 ::::::::::::::: :::::::::::::::::::::::::::::::::: ::: d1i1na_ 75 HEGAKALDVGSGSGILTACFARMVGCTGKVIGIDHIKELVDDSVNNVRKDDPTLLSSGRV 134 d1nyta1 68 QALSM----DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCY 110 ::::: ::::::::::::::::: :::::::::::::::::: d1i1na_ 135 QLVVGDGRMGYAEEAPYDAIHVGAAA---PVVPQALIDQLKPGGRLI 178