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 | d1gu7a2 | 2,4-dienoyl-CoA reductase | 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 <-- 0.788 --> HitDALI alignment (Z-score: 7.3 Raw score:599.30) d1nyta1 1 -----------DGVGLLSDLERLsFIRP--GLRILLIG-AGGASRGVLLPLLSLDCAVTI 46 :::::::::::: :::: :::::::: ::::::::::::::::::::: d1gu7a2 1 ltinqgatisvNPLTAYLMLTHY-VKLTpgKDWFIQNGgTSAVGKYASQIGKLLNFNSIS 59 d1nyta1 47 TNRT----vSRAEELAKLFahtgsIQALSMDEL------EGHE---------FDLIINAT 87 :::: :::::::::: ::::::::: :::: :::::::: d1gu7a2 60 VIRDrpnldEVVASLKELG----aTQVITEDQNnsrefgPTIKewikqsggeAKLALNCV 115 d1nyta1 88 ssgisgdIPAI---psSLIHPGIYCYDMFyqkgktPFLAWcEQRG---SKRNADGlgmLV 141 :::: ::::::::::::: ::::: :::: ::::::: :: d1gu7a2 116 -------GGKSstgiaRKLNNNGLMLTYG-gmsfqPVTIP-TSLYifkNFTSAGF--wVT 164 d1nyta1 142 AQAahafllwhgVLPDV----epvikqlqeels 170 ::: ::::: d1gu7a2 165 ELL--------kNNKELktstlnqiiawyeegk 189 FAST alignment (Normalized score: 5.58 Raw score:999.50) d1nyta1 1 -----------DGVGLLSDLERLS--FIRP-GLRILLI-GAGGASRGVLLPLLSLDCAVT 45 ::::::::::: :::: ::::::: ::::::::::::::::::::: d1gu7a2 1 LTINQGATISVNPLTAYLMLTH--YVKLTPGKDWFIQNGGTSAVGKYASQIGKLLNFNSI 58 d1nyta1 46 ITNR-----TVSRAEELAKLFAHTGS---IQALSMDELEGH------------------E 79 ::: :::::::::: ::::::::: : d1gu7a2 59 SVI-RDRPNLDEVVASLKE-------LGATQVITEDQN---NSREFGPTIKEWIKQSGGE 107 d1nyta1 80 FDLIINATSSGISGDIPAI---------PSSLIHPGIYCYDMFYQKGKTPF--------- 121 :::::: ::::::::::::: d1gu7a2 108 AKLALN-------------CVGGKSSTGIARKLNNNGLMLT----------YGGMSFQPV 144 d1nyta1 122 --LAWCE-QRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS-------- 170 ::::: ::: :::::: :::::::: d1gu7a2 145 TIPTSLYIFKN-FTSAGF-WVTELLKN-------------------------NKELKTST 177 d1nyta1 171 ------------ 171 d1gu7a2 178 LNQIIAWYEEGK 189 TMalign alignment (TM-score: 0.59 Raw score:99.59) d1nyta1 1 -----------DGVGLLSDLERLSFIRPG-LRILLIG-AGGASRGVLLPLLSLDCAVTIT 47 :::::::::::::::::: ::::::: :::::::::::::::::::::: d1gu7a2 1 LTINQGATISVNPLTAYLMLTHYVKLTPGKDWFIQNGGTSAVGKYASQIGKLLNFNSISV 60 d1nyta1 48 NRTVS-RAEELAKLFAHTGSIQALS---M-D-ELEG-HE---------FDLIINATSSGI 91 : ::: ::::::::::::::::::: : : :::: :: :::::::: : d1gu7a2 61 I-RDRPNLDEVVASLKELGATQVITEDQNNSREFGPTIKEWIKQSGGEAKLALNCV-G-- 116 d1nyta1 92 SGDIP-AIPSSLIHPGIYCYDMFY---QKGKTPFLAWCEQRG---SKRNADGLGMLVAQA 144 ::: :::::::::::::::::: ::: ::::::: :::::::: :::::: d1gu7a2 117 --GKSSTGIARKLNNNGLMLTYGGMSF----QPV-TIPTSLYIFKNFTSAGFW-VTELLK 168 d1nyta1 145 AHAFLLWHGVLPDVE---------------PVIKQLQEELS 170 : ::::: d1gu7a2 169 N---------NKELKTSTLNQIIAWYEEGK----------- 189 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 6 LSDLERLSFIRPGLRILLI--GAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAH 63 ::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: d1gu7a2 17 YLMLTHYVKLTPGKDWFIQNGGTSAVGKYASQIGKLLNFNSISVIRDRPNLDEVVASLKE 76 d1nyta1 64 TGSIQALSMDEL---------------EGHEFDLIINATSSGISGDIPAIPSSLIHPGIY 108 :::::::::::: :::::::::::::: ::::::::::::::: d1gu7a2 77 LGATQVITEDQNNSREFGPTIKEWIKQSGGEAKLALNCVGG----KSSTGIARKLNNNGL 132 d1nyta1 109 CYDM 112 :::: d1gu7a2 133 MLTY 136