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 | d1ej0a_ | RNA methyltransferase FtsJ | 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 <-- 1.374 --> HitDALI alignment (Z-score: 7.9 Raw score:638.30) d1nyta1 1 -----DGVGLLSDLERLSFIRPGLRILLIGAGGasRGVLLPLLSLD---CAVTITNrTVS 52 :::::::::::::::::::::::::::: ::::::::::: ::::::: ::: d1ej0a_ 1 glrsrAWFKLDEIQQSDKLFKPGMTVVDLGAAP--GGWSQYVVTQIggkGRIIACD-LLP 57 d1nyta1 53 RaeelaKLFAhtgSIQAL--------SMDELE----GHEFDLIINATSS----------g 90 : :::: ::::: :::::: ::::::::::::: d1ej0a_ 58 M-----DPIV---GVDFLqgdfrdelVMKALLervgDSKVQVVMSDMAPnmsgtpavdip 109 d1nyta1 91 ISGD--IPAIP--SSLIHPGIYCYDMFYQK--GKTPfLAWCEQrGSKRNADGLgmLVAQA 144 :::: ::::: ::::::::::::::::: :::: :::::: ::::::::: ::::: d1ej0a_ 110 RAMYlvELALEmcRDVLAPGGSFVVKVFQGegFDEY-LREIRS-LFTKVKVRK--PDSSR 165 d1nyta1 145 Ahafllwhgvlpdvepvikqlqeels 170 : d1ej0a_ 166 A-----------rsrevyivatgrkp 180 FAST alignment (Normalized score: 6.32 Raw score:1105.00) d1nyta1 1 DG---VGLLSDLER----LSFIRPGLRILLIGAGGAS-RGVLLPLLS---LDCAVTITNR 49 ::::::::: :::::::::::::::: ::::::::: :::::::::: d1ej0a_ 1 --GLRSRAWFKLDEIQQSDKLFKPGMTVVDLGAA---PGGWSQYVVTQIGGKGRIIACDL 55 d1nyta1 50 TVSRAEELAKLFA----HTGSIQAL--------SMDE----LEGHEFDLIINATSSGISG 93 :::::::: :::: ::::::::::::: d1ej0a_ 56 -------------LPMDPIVGVDFLQGDFRDELVMKALLERVGDSKVQVVMSDM------ 96 d1nyta1 94 DIPAI-------------------------PSSLIHPGIYCYDMFYQKGK---TPFLAWC 125 :::::::::::::::::: ::::::: d1ej0a_ 97 -----APNMSGTPAVDIPRAMYLVELALEMCRDVLAPGGSFVVKVFQG--EGFDEYLREI 149 d1nyta1 126 EQRGSKRNADGLGM-LVAQAAHAFLLWHGVLPDVEPVIKQLQEELS-------------- 170 :: :::::::: :::: d1ej0a_ 150 RS-LFTKVKVR---KPDSS---------------------------RARSREVYIVATGR 178 d1nyta1 171 -- 171 d1ej0a_ 179 KP 180 TMalign alignment (TM-score: 0.59 Raw score:100.59) d1nyta1 1 -----DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNRTVS 52 :::::::::::::::::::::::::::: :::::::::: : ::::::: : d1ej0a_ 1 GLRSRAWFKLDEIQQSDKLFKPGMTVVDLGAAP--GGWSQYVVTQIGGKGRIIACD-L-- 55 d1nyta1 53 RAEELAKLFAHTGSIQAL--------SMDE-LE--GH-EFDLIINATSS--------GIS 92 : :: ::: :::::: :::: :: :: ::::::::::: ::: d1ej0a_ 56 L--PM--DPI--VGVDFLQGDFRDELVMKALLERVGDSKVQVVMSDMAPNMSGTPAVDIP 109 d1nyta1 93 --GD--IPA-IP-SSLIHPGIYCYDMFYQK--GKTPFLAWCEQRGSKRNADGLGMLVAQA 144 :: ::: :: ::::::::::::::::: :::: :::::: ::::::::: : :::: d1ej0a_ 110 RAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEY-LREIRS-LFTKVKVRK-P-DSSR 165 d1nyta1 145 A----HAFLLWHGVLPDVEPVI---------KQLQEELS 170 : : d1ej0a_ 166 ARSRE----------------VYIVATGRKP-------- 180 HHsearch alignment (Probability: 0.14 E-value:0.04) d1nyta1 5 LLSDLERLSFIRPGLRILLIGA--GGASRGVLLPL 37 :::::::::::::::::::::: ::::::::::: d1ej0a_ 10 LDEIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQI 44