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 | d1mx3a1 | Transcription corepressor CtbP | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 2.240 --> HitDALI alignment (Z-score: 9.9 Raw score:752.30) d1nyta1 1 --DGVGLLSDLERLS-----------------------------fiRPGLRILLIGAGGA 29 ::::::::::::: :::::::::::::: d1mx3a1 1 eeTADSTLCHILNLYrratwlhqalregtrvqsveqirevasgaarIRGETLGIIGLGRV 60 d1nyta1 30 SRGVLLPLLSLDCAVTITNRTVSraEELAKLFAhtgsIQALSmdELEG--HEFDLIINAT 87 ::::::::::::::::::::::: :::::::: ::::: :::: :::::::::: d1mx3a1 61 GQAVALRAKAFGFNVLFYDPYLS--DGVERALG----LQRVS--TLQDllFHSDCVTLHC 112 d1nyta1 88 SSGISGDIP--aiPSSLIHPGIYCYDMFYqkgkTPFLAW-cEQRG-----SKRNADG--- 136 ::::::::: :::::::::::::::: :::::: :::: ::::::: d1mx3a1 113 GLNEHNHHLindfTVKQMRQGAFLVNTAR----GGLVDEkaLAQAlkegrIRGAALDvhe 168 d1nyta1 137 ---------------------LGMLvaqaahafllwhgvlpdvepvikqlqeels 170 :::: d1mx3a1 169 sepfsfsqgplkdapnlictpHAAW------------------------------ 193 FAST alignment (Normalized score: 6.97 Raw score:1262.00) d1nyta1 1 D---GVGLLSDLERLSFI---------------------------------RPGLRILLI 24 :::::::::: ::::::::: d1mx3a1 1 -EETADSTLCHILN----LYRRATWLHQALREGTRVQSVEQIREVASGAARIRGETLGII 55 d1nyta1 25 GAGGASRGVLLPLLSLDCAVTITNRTVSR-AEELAKLFAHTG-SIQAL-SMDELEGH--- 78 :::::::::::::::::::::::::: ::::::: ::::: :::: d1mx3a1 56 GLGRVGQAVALRAKAFGFNVLFYDPY---LSDGVERA-----LGLQRVSTLQD----LLF 103 d1nyta1 79 EFDLIINATSSGISGDIP--------AIPSSL---IHPGIYCYDMFYQKGKTP------F 121 ::::::::: :::::: :::::::::: : d1mx3a1 104 HSDCVTLHC---------GLNEHNHHLINDFTVKQMRQGAFLVNT--------ARGGLVD 146 d1nyta1 122 LAWCEQR-----GSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS------ 170 :::::: :::::: d1mx3a1 147 EKALAQ-ALKEGRIRGAA------------------------------------LDVHES 169 d1nyta1 171 ------------------------ 171 d1mx3a1 170 EPFSFSQGPLKDAPNLICTPHAAW 193 TMalign alignment (TM-score: 0.60 Raw score:101.76) d1nyta1 1 D--GVGLLSDLERLSF----------------------------I-RPGLRILLIGAGGA 29 : ::::::::::::: : :::::::::::::: d1mx3a1 1 EETADSTLCHILNLYRRATWLHQALREGTRVQSVEQIREVASGAARIRGETLGIIGLGRV 60 d1nyta1 30 SRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHEFDLIINATSS 89 :::::::::::::::::::::::: :: ::::: ::::::::::::::::::::::: d1mx3a1 61 GQAVALRAKAFGFNVLFYDPYLSD-GV-ERALG----LQRVSTLQDLLFHSDCVTLHCGL 114 d1nyta1 90 GISGDIPAI-PS-SLIHPGIYCYDMFYQKGKTPFLAWCE-QR----GSKRNADGL----- 137 ::::::::: :: ::::::::::::::: :::::::: :: ::::::::: d1mx3a1 115 NEHNHHLINDFTVKQMRQGAFLVNTARG---GLVDEKALAQALKEGRIRGAALDVHESEP 171 d1nyta1 138 --------------GMLVAQAAHAFLLWHGVLPDVEPVIKQLQ---EELS 170 ::::: d1mx3a1 172 FSFSQGPLKDAPNL------------------------ICTPHAAW---- 193 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 13 SFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 :::::::::::::::::::::::::::::::::::::::::::::: :::::::: d1mx3a1 44 AARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGVERA------LGLQRVST 97 d1nyta1 73 DELEGHEFDLIINATSSGISGDIPAI---PSSLIHPGIYCYDMFYQKG-KTPFLAWCEQR 128 :::::::::::::::::: ::::::: ::::::::::::::::::: ::::::::::: d1mx3a1 98 LQDLLFHSDCVTLHCGLN-EHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKE 156 d1nyta1 129 GSKRNADGLGMLV 141 ::: ::::::::: d1mx3a1 157 GRI-RGAALDVHE 168