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 | d1jg1a_ | Protein-L-isoaspartyl O-methyltransferase | 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 <-- 1.490 --> HitDALI alignment (Z-score: 7.1 Raw score:529.30) d1nyta1 1 ------------------------------------------------------------ 1 d1jg1a_ 1 ekelyekwmrtvemlkaegiirskeveraflkyprylsvedkykkyahideplpipagqt 60 d1nyta1 1 --DGVGLLSDLErlsFIRPGLRILLIGAGgasRGVLLPLLSL-DCAVTITNRTVSRAEEL 57 :::::::::: :::::::::::::: :::::::::: ::::::::::::::::: d1jg1a_ 61 vsAPHMVAIMLE-iaNLKPGMNILEVGTG--sGWNAALISEIvKTDVYTIERIPELVEFA 117 d1nyta1 58 AKLFA--HTGSIQALSMD---eLEGHE-FDLIINATsSGISgdipaipSSLIHPGIYCYD 111 ::::: ::::::::::: ::::: :::::::: :::: :::::::::::: d1jg1a_ 118 KRNLEraGVKNVHVILGDgskgFPPKApYDVIIVTA-GAPK--ipeplIEQLKIGGKLII 174 d1nyta1 112 mFYQKG--KTPFLawceqRGSKrnadglgmlvaqaahafllwhgvlpdvepvikqlqeel 169 ::::: ::::: :::: d1jg1a_ 175 -PVGSYhlWQELL----eVRKT---------------kdgikiknhggvafvpligeygw 214 d1nyta1 170 s 170 d1jg1a_ 215 k 215 FAST alignment (Normalized score: 4.97 Raw score:950.20) d1nyta1 1 D----------------------------------------------------------- 1 d1jg1a_ 1 -EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLSVEDKYKKYAHIDEPLPIPAGQ 59 d1nyta1 2 ---GVGLLSDLERLS--FIRPGLRILLIGAGGAS-RGVLLPLLS-LDCAVTITNRTVSRA 54 :::::::::: :::::::::::::: ::::::::: ::::::::::::::: d1jg1a_ 60 TVSAPHMVAIMLE--IANLKPGMNILEVGTG---SGWNAALISEIVKTDVYTIERIPELV 114 d1nyta1 55 EELAKLFA--HTGSIQALSMDELEG-----------HEFDLIINATSSGIS-GDIPAI-- 98 :::::::: :::::::: ::::::::::: :::: d1jg1a_ 115 EFAKRNLERAGVKNVHVI-------LGDGSKGFPPKAPYDVIIVTAG----APKIP--EP 161 d1nyta1 99 PSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGS------------------KRNADGLGML 140 ::::::::::::::: ::::: d1jg1a_ 162 LIEQLKIGGKLIIPV-----------------GSYHLWQELLEVRKTKDGIKIKN----- 199 d1nyta1 141 VAQAAHAFLLWHGVLPDVEPVIKQLQEELS---------------- 170 d1jg1a_ 200 ------------------------------HGGVAFVPLIGEYGWK 215 TMalign alignment (TM-score: 0.52 Raw score:88.79) d1nyta1 1 ------------------------------------------------------------ 1 d1jg1a_ 1 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLSVEDKYKKYAHIDEPLPIPAGQT 60 d1nyta1 1 --DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSL-DCAVTITNRTVSRAEEL 57 :::::::::: :::::::::::::::: ::::::::::: ::::::::::::::::: d1jg1a_ 61 VSAPHMVAIMLE-IANLKPGMNILEVGTG--SGWNAALISEIVKTDVYTIERIPELVEFA 117 d1nyta1 58 AKLFA--HTGSIQAL-SM--DELEGHE-FDLIINATSSGISGDIPAIPSSLIHPGIYCYD 111 ::::: :::::::: :: ::::::: ::::::::: : ::::::::::::::::::: d1jg1a_ 118 KRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAG-A--PKIPEPLIEQLKIGGKLII 174 d1nyta1 112 MF------YQKGKTPFLAWCE--QRGSKRNADGLGML------------VAQAAHAFLLW 151 :: :: :: :: :: :::::::::: : d1jg1a_ 175 PVGSYHLWQE--LL-EV--RKTK--DGIKIKNHGG-VAFVPLIGEYGWK----------- 215 d1nyta1 152 HGVLPDVEPVIKQLQEELS 170 d1jg1a_ 216 ------------------- 216 HHsearch alignment (Probability: 0.54 E-value:0.00) d1nyta1 8 DLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG-- 65 ::::::: ::::::::::::::::::::::: :::::::::::::::::::::::::: d1jg1a_ 70 MLEIANL-KPGMNILEVGTGSGWNAALISEI-VKTDVYTIERIPELVEFAKRNLERAGVK 127 d1nyta1 66 SIQALSM----DELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYD 111 ::::::: ::::::::::::::::: ::::::::::::::::::: d1jg1a_ 128 NVHVILGDGSKGFPPKAPYDVIIVTAGA---PKIPEPLIEQLKIGGKLII 174