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 | d1kyha_ | Hypothetical protein YxkO | Ribokinase-like | Ribokinase-like | 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 <-- 0.950 --> HitDALI alignment (Z-score: 5.4 Raw score:561.20) d1nyta1 1 -dgvgllsdlerlsfirPGLRILLIGA----GGASRGVLLPLLSLDC-AVTITNrTVSRA 54 :::::::::: :::::::::::::::: :::::: ::::: d1kyha_ 1 nvpfwteehvratlperTYGTALLLAGsddmPGAALLAGLGAMRSGLgKLVIGT-SENVI 59 d1nyta1 55 EELAKLFAhtgSIQALSM------delEGHEFDLIIN-ATSSgISGDI---paipSSLIh 104 :::::::: ::::::: :::::::::: :::: ::::: :::: d1kyha_ 60 PLIVPVLP---EATYWRDgwkkaadaqLEETYRAIAIgPGLP-QTESVqqavdhvLTAD- 114 d1nyta1 105 pgIYCYDMF--YQKGKtpflawcEQRGSkRNADGLG------------------------ 138 ::::::: ::::: ::::: ::::::: d1kyha_ 115 --CPVILDAgaLAKRT------yPKREG-PVILTPHpgeffrmtgvpvnelqkkraeyak 165 d1nyta1 139 ----------MLVA--------------qaaHAFL------------------------- 149 :::: :::: d1kyha_ 166 ewaaqlqtviVLKGnqtviafpdgdcwlnptGNGAlakggtgdtltgmilgmlcchedpk 225 d1nyta1 150 -------------------lWHGV---lpdvepvikqlqeels 170 :::: d1kyha_ 226 havlnavylhgacaelwtdeHSAHtllahelsdilprvwkrfe 268 FAST alignment (Normalized score: 4.30 Raw score:918.40) d1nyta1 1 DGVGLLSDLERLSFIRP------------------GLRILLIGA------GGASRGVLLP 36 ::::::: :::::::::: d1kyha_ 1 -----------------NVPFWTEEHVRATLPERTYGTALLL--AGSDDMPGAALLAGLG 41 d1nyta1 37 LLSLD-CAVTITNRTVSRAEELAKLFAHTGSIQAL--SMDEL-----EGHEFDLIINATS 88 ::::: ::::::: ::::::::::: ::::::: :::: ::::::::: d1kyha_ 42 AMRSGLGKLVIGT-SENVIPLIVPV---LPEATYWRDGWKK-AADAQLEETYRAIA---- 92 d1nyta1 89 SGISGDIPAI--------------PSSLIH--PGIYCYDMFYQKGKTPFLAWCE------ 126 :::: ::::::: d1kyha_ 93 ----------IGPGLPQTESVQQAVDHV--LTADCPVIL---------------DAGALA 125 d1nyta1 127 ---QRGSK-RNAD----------------------------------------------- 135 ::::: :::: d1kyha_ 126 KRTYPKREGPVILTPHPGEFFRMTGVPVNELQKKRAEYAKEWAAQLQTVIVLKGNQTVIA 185 d1nyta1 136 ------------------------------------------GLGMLVAQAAHAFLLWHG 153 ::::::::::::::::: d1kyha_ 186 FPDGDCWLNPTGNGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAELWTD- 244 d1nyta1 154 VLPDVEPVIKQLQEELS------------------------ 170 d1kyha_ 245 -----------------EHSAHTLLAHELSDILPRVWKRFE 268 TMalign alignment (TM-score: 0.55 Raw score:92.84) d1nyta1 1 ---------DGVGLLSDLE--RLS-FIRP-GLRILLIGA----GGASRGVLLPLLSLDC- 42 : : ::: ::::::::: :::::::::::::::: d1kyha_ 1 NVPFWTEEH---------VRA--TL-PERTYGTALLLAGSDDMPGAALLAGLGAMRSGLG 48 d1nyta1 43 AVTITNRTVSRAEELAKLFAHTGSIQALS-M--DE---LEGHEFDLIIN-ATSSGISGDI 95 :::::: ::::::::::::: : ::::: : :: ::::::::::: ::::: :::: d1kyha_ 49 KLVIGT-SENVIPLIVPVLP-E--ATYWRDGWKKAADAQLEETYRAIAIGPGLPQ-TESV 103 d1nyta1 96 PAI-PSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGL----------------- 137 ::: ::::::: :::::::: :::::: :::::::::::: d1kyha_ 104 QQAVDHVLTAD-CPVILDAG---ALAKRT--YPKREGPVILTPHPGEFFRMTGVPVNELQ 157 d1nyta1 138 ------------------GMLV--A-------------QAAHAF---------------- 148 :::: : :::::: d1kyha_ 158 KKRAEYAKEWAAQLQTVIVLKGNQTVIAFPDGDCWLNPTGNGALAKGGTGDTLTGMILGM 217 d1nyta1 149 ----------------------L--L----WH-------------------GVLPDVEPV 161 : : :: d1kyha_ 218 LCCHEDPKHAVLNAVYLHGACAELWTDEHSAHTLLAHELSDILPRVWKRFE--------- 268 d1nyta1 162 IKQLQEELS 170 d1kyha_ 269 --------- 269 HHsearch alignment (Probability: 0.29 E-value:0.01) d1nyta1 17 PGLRILLIGA----GGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG 65 :::::::::: ::::::::::::::::::::::::::::::::::::::: d1kyha_ 18 TYGTALLLAGSDDMPGAALLAGLGAMRSGLGKLVIGTSENVIPLIVPVLPEAT 70