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 | d2pgda2 | 6-phosphogluconate 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 <-- 2.079 --> HitDALI alignment (Z-score: 9.1 Raw score:677.80) d1nyta1 1 dgvgllsdlerlsfirpglRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 ::::::::::::::::::::::::::::::::::::::::: d2pgda2 1 ----------------aqaDIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLAN 44 d1nyta1 61 -FAHTgSIQALSMDEL-EGHEF--DLIINATSsGISG-DIPA-IPSSLIHPGIYCYDMF- 113 :::: :::::::::: ::::: :::::::: :::: :::: :::::::::::::::: d2pgda2 45 eAKGT-KVLGAHSLEEmVSKLKkpRRIILLVK-AGQAvDNFIeKLVPLLDIGDIIIDGGn 102 d1nyta1 114 YQKGKT-pfLAWCEQRGSkRNADGlGMLV---------------------------aqaa 145 :::::: ::::::::: ::::: :::: d2pgda2 103 SEYRDTmrrCRDLKDKGI-LFVGS-GVSGgedgarygpslmpggnkeawphikaifqgia 160 d1nyta1 146 HAFLlwhgVLPDVepviKQLQeels 170 :::: ::::: :::: d2pgda2 161 AKVG----TGEPC---cDWVG--dd 176 FAST alignment (Normalized score: 6.88 Raw score:1190.00) d1nyta1 1 DGVGLLSDLERLSFIRPGL---RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEEL 57 :::::::::::::::::::::::::::::::::::::: d2pgda2 1 -------------------AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDF 41 d1nyta1 58 AK-LFAHTGSIQAL-SMDELEGHEF-----DLIINATSSGISGDIPAI-----------P 99 :: :::: :::::: ::::::: :::::::: : d2pgda2 42 LANEAKG-TKVLGAHSLEEMVS---KLKKPRRIILLVK----------AGQAVDNFIEKL 87 d1nyta1 100 SSLIHPGIYCYDM-FYQKGK---TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVL 155 ::::::::::::: :::: ::::::::::: :::::: d2pgda2 88 VPLLDIGDIIIDGGNSEY--RDTMRRCRDLKDKG-ILFVGS------------------- 125 d1nyta1 156 PDVEPVIKQLQEELS--------------------------------------------- 170 d2pgda2 126 ---------------GVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIAAKVGTGEPCC 170 d1nyta1 171 ------ 171 d2pgda2 171 DWVGDD 176 TMalign alignment (TM-score: 0.60 Raw score:101.70) d1nyta1 1 -DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 :::::::::::::::::::::::::::::::::::::::::: d2pgda2 1 A-----------------QADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLA 43 d1nyta1 60 L-FAHTGSIQALSMDELEGHEF---DLIINATSSGISG-DIP-AIPSSLIHPGIYCYDMF 113 : :::: ::::::::::::::: :::::::: :::: ::: ::::::::::::::::: d2pgda2 44 NEAKGT-KVLGAHSLEEMVSKLKKPRRIILLVK-AGQAVDNFIEKLVPLLDIGDIIIDGG 101 d1nyta1 114 -YQKGKT-PFLAWCEQRGSKRNADGLGML---------VAQA------------------ 144 :::::: :::::::::::: ::::: :: :::: d2pgda2 102 NSEYRDTMRRCRDLKDKGIL-FVGSG-VSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGI 159 d1nyta1 145 AH-AFLLWHGVLPDVEPVIKQLQEELS 170 :: : :::::::: :: :: : d2pgda2 160 AAK--V---GTGEPCCD-WV--GD--D 176 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 18 GLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQA-LSMDE-- 74 :::::::::::::::::::::::::::::::::::::::::::::::::::: ::::: d2pgda2 2 QADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMV 61 d1nyta1 75 LEGHEFDLIINATSSGIS-GDIPAIPSSLIHPGIYCYDMFY-QKGKTPFL-AWCEQRGSK 131 :::::::::::::::::: :::::::::::::::::::::: :::::::: ::::::::: d2pgda2 62 SKLKKPRRIILLVKAGQAVDNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGIL 121 d1nyta1 132 RNAD-GLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEEL 169 ::: :::::::::::::::::::::::::::::::::: d2pgda2 122 -FVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGI 159