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 | d1t43a_ | N5-glutamine methyltransferase, HemK | 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 <-- 1.961 --> HitDALI alignment (Z-score: 6.9 Raw score:594.10) d1nyta1 1 ------------------------------------------------------------ 1 d1t43a_ 1 eyqhwlreaisqlqasesprrdaeillehvtgrgrtfilafgetqltdeqcqqldalltr 60 d1nyta1 1 --------------------------------DGVGLLSDLErlSFIR-pGLRILLIGAG 27 :::::::::: :::: :::::::::: d1t43a_ 61 rrdgepiahltgvrefwslplfvspatliprpDTECLVEQAL--ARLPeqPCRILDLGTG 118 d1nyta1 28 gasRGVLLPLLSLD--CAVTITNRTVSRAEELAKLFA--HTGSIQALS---MDELEGHEF 80 ::::::::::: ::::::::::::::::::::: ::::::::: ::::::::: d1t43a_ 119 --tGAIALALASERpdCEIIAVDRMPDAVSLAQRNAQhlAIKNIHILQsdwFSALAGQQF 176 d1nyta1 81 DLIINATsSGIS-------------------------GDIP----aIPSSLIHPGIYCYD 111 ::::::: :::: :::: :::::::::::::: d1t43a_ 177 AMIVSNP-PYIDeqdphlqqgdvrfepltalvaadsgMADIvhiieQSRNALVSGGFLLL 235 d1nyta1 112 MFY--QKGKTpflAWCEQRGsKRNAdgLGMLVaqaahafllwhgvlpdvepvikqlqeel 169 ::: ::::: ::::::: :::: ::::: d1t43a_ 236 EHGwqQGEAV-rqAFILAGY-HDVE--TCRDY------------------gdnervtlgr 273 d1nyta1 170 s 170 d1t43a_ 274 y 274 FAST alignment (Normalized score: 4.27 Raw score:921.40) d1nyta1 1 D----------------------------------------------------------- 1 d1t43a_ 1 -EYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLT 59 d1nyta1 2 ----------------------------------GVGLLSDLERLSFIRPG------LRI 21 :::::::::: ::: d1t43a_ 60 RRRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQALA-------RLPEQPCRI 112 d1nyta1 22 LLIGAGGAS-RGVLLPLLS--LDCAVTITNR---TVSRAEELAKLFA-HTGSIQALS--- 71 :::::: ::::::::: :::::::::: ::::::::::: :::::::: d1t43a_ 113 LDLGTG---TGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQH--LAIKNIHIL-QSD 166 d1nyta1 72 -MDELEGHEFDLIINATSSGISGDIPAIPSSLI--------------------------- 103 :::::::::::::::: d1t43a_ 167 WFSALAGQQFAMIVSNP----------------PYIDEQDPHLQQGDVRFEPLTALVAAD 210 d1nyta1 104 -----------------HPGIYCYDMFYQKGK---TPFLAWCEQRGSK-RNADGLGMLVA 142 :::::::::::: ::::::::: ::: ::::: d1t43a_ 211 SGMADIVHIIEQSRNALVSGGFLLLEHGW---QQGEAVRQAFIL-AGYHDVETC------ 260 d1nyta1 143 QAAHAFLLWHGVLPDVEPVIKQLQEELS-------------- 170 d1t43a_ 261 ----------------------------RDYGDNERVTLGRY 274 TMalign alignment (TM-score: 0.61 Raw score:103.09) d1nyta1 1 ------------------------------------------------------------ 1 d1t43a_ 1 EYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTR 60 d1nyta1 1 ---------------DGV----------------G-LLSDLERLSFIR-PGLRILLIGAG 27 ::: : :::::: :::: ::::::::::: d1t43a_ 61 RRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQAL--ARLPEQPCRILDLGTG 118 d1nyta1 28 GASRGVLLPLL-SLD-CAVTITNRTVSRAEELAKLFA--HTGSIQAL-S-M-DELEGHEF 80 ::::::::: ::: ::::::::::::::::::::: :::::::: : : :::::::: d1t43a_ 119 --TGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQF 176 d1nyta1 81 DLIINATSSGI------------------------SGDIP-AI--PS-SLIHPGIYCYDM 112 ::::::::::: ::::: :: :: :::::::::::: d1t43a_ 177 AMIVSNPPYIDEQDPHLQQGDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLE 236 d1nyta1 113 F-Y-QKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQ---- 166 : : :::::: :: ::::::::::::: :: : : :: d1t43a_ 237 HGWQQGEAVR-QA-FILAGYHDVETCR--DY--G----------------D---NERVTL 271 d1nyta1 167 ---EELS 170 d1t43a_ 272 GRY---- 274 HHsearch alignment (Probability: 0.29 E-value:0.00) d1nyta1 15 IRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHT--GSIQALSM 72 :::::::::::::::::::::::::::::::::::::::::::::::::: :::::::: d1t43a_ 106 PEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQS 165 d1nyta1 73 D---ELEGHEFDLIINA 86 : ::::::::::::: d1t43a_ 166 DWFSALAGQQFAMIVSN 182