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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1nyta1 | Shikimate 5-dehydrogenase AroE | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1m6ya2 | TM0872, methyltransferase domain | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | α/β |
Query <-- 0.853 --> IntermediateDALI 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 <-- 0.854 --> HitDALI alignment (Z-score: 7.7 Raw score:664.30) d1nyta1 1 -------DGVGLlSDLErLSFIRP-GLRILLIGAGgasRGVLLPLLSLD--CAVTITNRT 50 ::::: :::: :::::: :::::::::: ::::::::::: ::::::::: d1m6ya2 1 rkysqrhIPVMV-REVI-EFLKPEdEKIILDCTVG--eGGHSRAILEHCpgCRIIGIDVD 56 d1nyta1 51 VSRAEELAKLFAHT-GSIQALSM--DELEG-------HEFDLIINATS---------sgI 91 :::::::::::::: :::::::: ::::: ::::::::::: : d1m6ya2 57 SEVLRIAEEKLKEFsDRVSLFKVsyREADFllktlgiEKVDGILMDLGvstyqlkgenrE 116 d1nyta1 92 SGDIpaipSSLIH---PGIYCYDMFYQKGKT-PFLAWCEQR-GSKRNadgLGMLVaqAAH 146 :::: ::::: ::::::::::::::: ::::::::: ::::: ::::: ::: d1m6ya2 117 LENLkeflKKAEDllnPGGRIVVISFHSLEDrIVKETFRNSkKLRILtekPVRPS--EEE 174 d1nyta1 147 AFLlwhgvlpdvepvikqlqeels 170 ::: d1m6ya2 175 IRE------nprarsgrlraaeri 192 FAST alignment (Normalized score: 6.28 Raw score:1135.00) d1nyta1 1 D-----------GVGLLSDLERLS-FIRPGLRILLIGAGGAS-RGVLLPLLS--LDCAVT 45 ::::::: :::::::::::::: ::::::::: :::::: d1m6ya2 1 -RKYSQRHIPVMVREVIEF-----LKPEDEKIILDCTVG---EGGHSRAILEHCPGCRII 51 d1nyta1 46 ITNRTVSRAEELAKLFAH-TGSIQAL--SMDELEG-------HEFDLIINATSSGISGDI 95 :::::::::::::::::: ::::::: ::::::: ::::::::: d1m6ya2 52 GIDVDSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILMD--------- 102 d1nyta1 96 PAI------------------------PSSLIHPGIYCYDMFYQKGK---TPFLAWCEQR 128 :::::::::::::::::: :::::::::: d1m6ya2 103 ---LGVSTYQLKGENRELENLKEFLKKAEDLLNPGGRIVVISFHS--LEDRIVKETFRNS 157 d1nyta1 129 GSKRNADGLGMLVA-------------QAAHAFLLWHGVLPDVEPVIKQLQEELS----- 170 ::::::: d1m6ya2 158 --------------KKLRILTEKPVRPSEEEIRE---------------------NPRAR 182 d1nyta1 171 ---------- 171 d1m6ya2 183 SGRLRAAERI 192 TMalign alignment (TM-score: 0.59 Raw score:100.82) d1nyta1 1 -------DGVGLLSDLERLSFIRPG-LRILLIGAGGASRGVLLPLLSLD--CAVTITNRT 50 ::::: :::::: ::::: ::::::::: :::::::::::: ::::::: : d1m6ya2 1 RKYSQRHIPVMV-REVIEF-LKPEDEKIILDCTVG--EGGHSRAILEHCPGCRIIGID-V 55 d1nyta1 51 VSRAEELAKL-FAHT-GSIQAL-S----M-DELE---GHEFDLIINATS---------SG 90 :::::::::: :::: :::::: : : :::: :::::::::::: :: d1m6ya2 56 DSEVLRIAEEKLKEFSDRVSLFKVSYREADFLLKTLGIEKVDGILMDLGVSTYQLKGENR 115 d1nyta1 91 ISGDI-PAIPS--SLIHPGIYCYDMFY-QKGKTPFLAWC-EQRGSKRNADGLGMLVAQAA 145 ::::: ::::: :::::::::::::: ::::::::::: ::::::::::::: ::: :: d1m6ya2 116 ELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPV-RPS-EE 173 d1nyta1 146 HAFLLW------HGVLPDVEPVIKQLQ------EELS 170 ::: :: :: d1m6ya2 174 EIR-ENPRARSG-------------RLRAAERI---- 192 HHsearch alignment (Probability: 0.24 E-value:0.03) d1nyta1 17 PGLRILL--IGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFA 62 ::::::: :::::::::::::: ::::::::::::::::::::::: d1m6ya2 23 DEKIILDCTVGEGGHSRAILEHC--PGCRIIGIDVDSEVLRIAEEKLK 68