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 | d1vbfa_ | 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 <-- 1.351 --> HitDALI alignment (Z-score: 5.8 Raw score:472.00) d1nyta1 1 -----------------------------------------------------dgvglls 7 d1vbfa_ 1 asekeeilrkiktqelaeafnkvdrslflpenlkdyayahthealpilpginttalnlgi 60 d1nyta1 8 dlerlsFIRPGLRILLIGAGGasRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSI 67 ::::::::::::::: ::::::::::::::::::::::::::::::::::::: d1vbfa_ 61 fmldelDLHKGQKVLEIGTGI--GYYTALIAEIVDKVVSVEINEKMYNYASKLLSYYNNI 118 d1nyta1 68 QALSMD---eLEGH-EFDLIINATsSGISgdipaipSSLIHPGIYCYDmFYQK--GKTPF 121 :::::: :::: ::::::::: :::: :::::::::::: :::: ::::: d1vbfa_ 119 KLILGDgtlgYEEEkPYDRVVVWA-TAPT--llckpYEQLKEGGIMIL-PIGVgrVQKLY 174 d1nyta1 122 LawceqrGSKR------nadglgmlvaqaahafllwhgvlpdvepvikqlqeels 170 : :::: d1vbfa_ 175 K-----vIKKGnspslenlgevmfgrigglygfyddyddiefrvnklerqiksil 224 FAST alignment (Normalized score: 4.80 Raw score:936.00) d1nyta1 1 D----------------------------------------------------------G 2 : d1vbfa_ 1 -ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLG 59 d1nyta1 3 VGLLSDLERLS-FIRPGLRILLIGAGGAS-RGVLLPLLSLD--CAVTITNRTVSRAEELA 58 :::::: :::::::::::::: ::::::::: ::::::::::::::::: d1vbfa_ 60 IFMLDE-----LDLHKGQKVLEIGTG---IGYYTALIAE--IVDKVVSVEINEKMYNYAS 109 d1nyta1 59 KLFAHTGSIQALSMDELEG-----------HEFDLIINATSSGISGDIPAI-------PS 100 :::::::::::: ::::::::::: :: d1vbfa_ 110 KLLSYYNNIKLI-------LGDGTLGYEEEKPYDRVVVWAT----------APTLLCKPY 152 d1nyta1 101 SLIHPGIYCYDMFYQKGKTPFLAWCEQRGSK--------------------RNADGLGML 140 ::::::::::: :::: d1vbfa_ 153 EQLKEGGIMIL--------------------PIGVGRVQKLYKVIKKGNSPSLEN----- 187 d1nyta1 141 VAQAAHAFLLWHGVLPDVEPVIKQLQEELS------------------------------ 170 d1vbfa_ 188 ------------------------------LGEVMFGRIGGLYGFYDDYDDIEFRVNKLE 217 d1nyta1 171 ------- 171 d1vbfa_ 218 RQIKSIL 224 TMalign alignment (TM-score: 0.53 Raw score:89.74) d1nyta1 1 ------------------------------------------------------DGVGLL 6 :::::: d1vbfa_ 1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYAHTHEALPILPGINTTALNLGI 60 d1nyta1 7 SDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEE-LAKLFAHTG 65 :::: ::::::::::::::::: :::::::::::::::::: ::::::: ::::::::: d1vbfa_ 61 FMLD-ELDLHKGQKVLEIGTGI--GYYTALIAEIVDKVVSVE-INEKMYNYASKLLSYYN 116 d1nyta1 66 SIQAL-S-M-DELEGH-EFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMF-----YQK 116 ::::: : : :::::: ::::::::: :: ::::::::::::::::::::: :: d1vbfa_ 117 NIKLILGDGTLGYEEEKPYDRVVVWA-TA--PTLLCKPYEQLKEGGIMILPIGVGRVQK- 172 d1nyta1 117 GKTPFLAWCEQRGSKRNADGLGML--------------------------------VAQA 144 :: ::: ::::::: :::::::: d1vbfa_ 173 -LY-KVI-KKGNSPS-LENLGEVMFGRIGGLYGFYDDYDDIEFRVNKLERQIKSIL---- 224 d1nyta1 145 AHAFLLWHGVLPDVEPVIKQLQEELS 170 d1vbfa_ 225 -------------------------- 225 HHsearch alignment (Probability: 0.90 E-value:0.00) d1nyta1 8 DLERLSFIRPGLRILLIGAG-GASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGS 66 :::::::: ::::::::::: :::::::: :::::::::::::::::::::::::::: d1vbfa_ 62 MLDELDLH-KGQKVLEIGTGIGYYTALIA---EIVDKVVSVEINEKMYNYASKLLSYYNN 117 d1nyta1 67 IQALSMD----ELEGHEFDLIINATSSGISGDIPAIPSSLIHP-GIYCYDMFYQK 116 ::::::: :::::::::::::::: ::::::::::::: ::::::::::: d1vbfa_ 118 IKLILGDGTLGYEEEKPYDRVVVWATA---PTLLCKPYEQLKEGGIMILPIGVGR 169