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 | d1hrda1 | Glutamate dehydrogenase | 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 <-- 1.855 --> HitDALI alignment (Z-score: 7.6 Raw score:714.70) d1nyta1 1 --------------DGVGLLSDLERLS----fIRPGLRILLIGAGGASRGVLLPLLSLDC 42 ::::::::::::: :::::::::::::::::::::::::::: d1hrda1 1 karsfggslvrpeaTGYGSVYYVEAVMkhendTLVGKTVALAGFGNVAWGAAKKLAELGA 60 d1nyta1 43 AVTITNRTvSRAE--elaklFAHT---------------------gsiqalsmdelegHE 79 :::::::: :::: :::: :: d1hrda1 61 KAVTLSGP-DGYIydpegitTEEKinymlemrasgrnkvqdyadkfgvqffpgekpwgQK 119 d1nyta1 80 FDLIINATSSgisgDIPA--IPSSLI-HPGIYCYDMFYqkgktpfLAWCEQRGSKRNADG 136 :::::::::: :::: :::::: ::::::::::: ::::::::::::::: d1hrda1 120 VDIIMPCATQ----NDVDleQAKKIVaNNVKYYIEVANmpttneaLRFLMQQPNMVVAPS 175 d1nyta1 137 LGMLVAQAAHAFLLWHG--------------vlpDVEPVI-KQLQEELS----------- 170 ::::::::::::::::: :::::: :::::::: d1hrda1 176 KAVNAGGVLVSGFEMSQnserlswtaeevdsklhQVMTDIhDGSAAAAEryglgynlvag 235 d1nyta1 171 -------------------- 171 d1hrda1 236 anivgfqkiadammaqgiaw 255 FAST alignment (Normalized score: 6.89 Raw score:1435.00) d1nyta1 1 D---------------GVGLLSDLERLSFI--------RPGLRILLIGAGGASRGVLLPL 37 :::::::::: :::::::::::::::::::::: d1hrda1 1 -KARSFGGSLVRPEATGYGSVYYVEA----VMKHENDTLVGKTVALAGFGNVAWGAAKKL 55 d1nyta1 38 LSLDCA-VTITNRTVS----------------------------RAEELAKLFAHTGS-- 66 :::::: :::::: :::::::: d1hrda1 56 AELGAKAVTLSGP---DGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADK------FG 106 d1nyta1 67 IQALSMD---ELEGHEFDLIINATSSGISGDIP--AIPSSLIHPG---------IYCYDM 112 :::: ::::::::::::::: :::::: :::::: d1hrda1 107 VQFF---PGEKPWGQKVDIIMPCAT--------QNDVDLEQ----AKKIVANNVKYYIEV 151 d1nyta1 113 FYQKGK------TPFLAWCEQRGS--KRNADGLGMLVAQAAHAFLLWHGVL--------- 155 :::::::::: ::::::::::::::::::::: d1hrda1 152 ------ANMPTTNEALRFLMQQ--PNMVVAPSKAVNAGGVLVSGFEM----SQNSERLSW 199 d1nyta1 156 ----------PDVEPVIKQLQEELS--------------------------------- 170 ::::::::::::: d1hrda1 200 TAEEVDSKLHQVMTDIHDGSAAA--AERYGLGYNLVAGANIVGFQKIADAMMAQGIAW 255 TMalign alignment (TM-score: 0.65 Raw score:110.58) d1nyta1 1 --------------DGVGLLSDLERLS----FIRPGLRILLIGAGGASRGVLLPLLSLDC 42 ::::::::::::: ::::::::::::::::::::::::::::: d1hrda1 1 KARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGA 60 d1nyta1 43 AVTITN-RTV-------------------------SRAEELAKLFAHTGSIQALS--MDE 74 :::::: ::: ::::::::: : ::::: ::: d1hrda1 61 KAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADK-F----GVQFFPGEKP 115 d1nyta1 75 LEGHEFDLIINATSSGISGDIP-AIPSSLI-HPGIYCYDMFYQKGKTPF-LAWCEQRG-S 130 :: ::::::::::::: ::: ::::::: :::::::::::: :::: :::::::: : d1hrda1 116 WG-QKVDIIMPCATQN---DVDLEQAKKIVANNVKYYIEVANM--PTTNEALRFLMQQPN 169 d1nyta1 131 KRNADGLGMLVAQAAHAFLLW-H------G----V--LP--DV-EPV-IK---------- 163 ::::::::::::::::::::: : : : :: :: ::: :: d1hrda1 170 MVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLG 229 d1nyta1 164 -----QLQE-EL--------------S 170 :::: :: d1hrda1 230 YNLVAGANIVGFQKIADAMMAQGIAW- 255 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 3 VGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVT-ITNRT-------VSRA 54 ::::::::::::::::::::::::::::::::::::::::::: ::::: :::: d1hrda1 21 YYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITT 80 d1nyta1 55 EELAKLF--------------AHTGSIQALSMDELEGHEFDLIINATSSGISGDIPAIPS 100 ::::::: :::::::::::::::::::::::::: :::::::::: d1hrda1 81 EEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCA---TQNDVDLEQA 137 d1nyta1 101 SLIHP--GIYCYDMFYQKGKTPFLAWC-EQRGSKRNADGLGMLVAQAAHAFLLW----HG 153 ::::: :::::::::::::::::::: :::::: ::::::::::::::::::: :: d1hrda1 138 KKIVANNVKYYIEVANMPTTNEALRFLMQQPNMV-VAPSKAVNAGGVLVSGFEMSQNSER 196 d1nyta1 154 VLPDVEPVIKQLQEE 168 ::::::::::::::: d1hrda1 197 LSWTAEEVDSKLHQV 211