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 | d1kpga_ | CmaA1 | 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 <-- 1.325 --> HitDALI alignment (Z-score: 5.9 Raw score:624.30) d1nyta1 1 ----------------------------------------------DGVGLLSDLErlSF 14 :::::::::: :: d1kpga_ 1 delkphfanvqahydlsddffrlfldptqtyscayferddmtlqeaQIAKIDLALG--KL 58 d1nyta1 15 IRP-GLRILLIGAGgasRGVLLPLLS-LDCAVTITNRTVSRAEELAKLF--AHTG-SIQA 69 ::: :::::::::: ::::::::: :::::::::::::::::::::: :::: :::: d1kpga_ 59 GLQpGMTLLDVGCG--wGATMMRAVEkYDVNVVGLTLSKNQANHVQQLVanSENLrSKRV 116 d1nyta1 70 LSM--DELEgHEFDLIINA-TSSG-ISGDIpaipSSLIH---PGIYCYDMFYQK------ 116 ::: :::: ::::::::: :::: ::::: ::::: :::::::::::: d1kpga_ 117 LLAgwEQFD-EPVDRIVSIgAFEHfGHERYdaffSLAHRllpADGVMLLHTITGlhpkei 175 d1nyta1 117 ------------------------------GKTPflAWCEQRGSKR-------------- 132 :::: :::::::::: d1kpga_ 176 herglpmsftfarflkfivteifpggrlpsIPMV-qECASANGFTVtrvqslqphyaktl 234 d1nyta1 133 -----nadglgmlvaqaahafllwhgvlpdvepvikqlqEELS-------- 170 :::: d1kpga_ 235 dlwsaalqankgqaialqseevyerymkyltgcaemfriGYIDvnqftcqk 285 FAST alignment (Normalized score: 5.40 Raw score:1188.00) d1nyta1 1 D-------------------------------------------GVGLLSDLERLS---- 13 :::::::::: d1kpga_ 1 -DELKPHFANVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDL--ALGK 57 d1nyta1 14 -FIRPGLRILLIGAGGAS-RGVLLPLL-SLDCAVTITNRTVSRAEELAKLF--AHTG-SI 67 :::::::::::::: :::::::: ::::::::::::::::::::::: :::: :: d1kpga_ 58 LGLQPGMTLLDVGCG---WGATMMRAVEKYDVNVVGLTLSKNQANHVQQLVANSENLRSK 114 d1nyta1 68 QAL--SMDELEGHEFDLIINATSSGISGDIPAI-------------PSSLIHPGIYCYDM 112 ::: ::::: ::::::::: ::::: ::::::::::::: d1kpga_ 115 RVLLAGWEQF-DEPVDRIVS-IGAFE-------HFGHERYDAFFSLAHRLLPADGVMLL- 164 d1nyta1 113 FYQKGK------------------------------------------TPFLAWCEQRGS 130 :::::::::::: d1kpga_ 165 ------HTITGLHPKEIHERGLPMSFTFARFLKFIVTEIFPGGRLPSIPMVQECASANGF 218 d1nyta1 131 KRNADGL------GMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS-------------- 170 :::::::::::::: d1kpga_ 219 -------TVTRVQSLQPHYAKTLDLWS-------------------AALQANKGQAIALQ 252 d1nyta1 171 --------------------------------- 171 d1kpga_ 253 SEEVYERYMKYLTGCAEMFRIGYIDVNQFTCQK 285 TMalign alignment (TM-score: 0.58 Raw score:99.07) d1nyta1 1 ----------------------------------------------DGVGLLSDLERLSF 14 :::::::::: ::: d1kpga_ 1 DELKPHFANVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALG-KLG 59 d1nyta1 15 IRPGLRILLIGAGGASRGVLLPLLS-LDCAVTITNRTVSRAEELAKLFA-H-T-GSIQAL 70 ::::::::::::: :::::::::: ::::::::::::::::::::::: : : :::::: d1kpga_ 60 LQPGMTLLDVGCG--WGATMMRAVEKYDVNVVGLTLSKNQANHVQQLVANSENLRSKRVL 117 d1nyta1 71 -SM-DELEGHEFDLIINATSSGISGD-IP-AIPSSLIH---PGIYCYDMFYQ-------- 115 :: :::: ::::::::::::::::: :: :::::::: ::::::::::: d1kpga_ 118 LAGWEQFD-EPVDRIVSIGAFEHFGHERYDAFFSLAHRLLPADGVMLLHTITGLHPKEIH 176 d1nyta1 116 ----------------------------KGKTPFLAWCEQRGSKRNADGLGMLV--AQA- 144 ::::: :::::::::::::::::::: : d1kpga_ 177 ERGLPMSFTFARFLKFIVTEIFPGGRLPSIPMV-QECASANGFTVTRVQSLQPHYA--KT 233 d1nyta1 145 --------------------------------------------AHAFLLWHGVLPDVEP 160 d1kpga_ 234 LDLWSAALQANKGQAIALQSEEVYERYMKYLTGCAEMFRIGYID---------------- 277 d1nyta1 161 VIKQLQ------EELS 170 :: d1kpga_ 278 ----VNQFTCQK---- 285 HHsearch alignment (Probability: 0.72 E-value:0.00) d1nyta1 8 DLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG-- 65 :::::: ::::::::::::::::: ::::::::::::::::::::::::::::::::: d1kpga_ 54 ALGKLG-LQPGMTLLDVGCGWGAT-MMRAVEKYDVNVVGLTLSKNQANHVQQLVANSENL 111 d1nyta1 66 -SIQALSMD-ELEGHEFDLIINAT 87 :::::::: :::::::::::::: d1kpga_ 112 RSKRVLLAGWEQFDEPVDRIVSIG 135