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 | d1q1ra1 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 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 <-- 1.690 --> HitDALI alignment (Z-score: 5.0 Raw score:397.30) d1nyta1 1 dgvgllsdlerlsfiRPGLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSR----- 53 :::::::::::::::::::::::: :::::::::::::: d1q1ra1 1 ---------------NANDNVVIVGTGLAGVEVAFGLRAsgWEGNIRLVGDATVIphhlp 45 d1nyta1 54 ----------------aeelaKLFAHTgSIQAL--SMDE-------------lEGHEFDL 82 :::::: ::::: :::: ::::::: d1q1ra1 46 plskaylagkataeslylrtpDAYAAQ-NIQLLggTQVTainrdrqqvilsdgRALDYDR 104 d1nyta1 83 IINATSSGISGDIP--------------aipsslihpgIYCYDM---FYQK------GKT 119 :::::::::::::: :::::: :::: ::: d1q1ra1 105 LVLATGGRPLIPNCelasaaglqvdngivinehmqtsdPLIMAVgdcARFHsqlydrWVR 164 d1nyta1 120 Pflawceqrgskrnadglgmlvaqaahafllwhgvlpdvepvikqlqeels 170 : d1q1ra1 165 I------------------------------esvpnaleqarkiaailcgk 185 FAST alignment (Normalized score: 3.78 Raw score:670.20) d1nyta1 1 DGVGLLSDLERLSFIR-PGLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSRAEEL 57 ::::::::::::::::::::::: ::::::::::::: d1q1ra1 1 ----------------NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATV----- 39 d1nyta1 58 --------------------------AKLFAHTGSIQALSMDEL---------------- 75 ::::::: :::: d1q1ra1 40 IPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQ-NIQL------LGGTQVTAINRDRQQV 92 d1nyta1 76 -----EGHEFDLIINATSSG--ISGDIPAIPSSLIHPGIYCYDMFYQKGK--TPFLAWCE 126 :::::::::::: :::: :::::: d1q1ra1 93 ILSDGRALDYDRLVLAT---GGRPLI------------------------PNCELASA-- 123 d1nyta1 127 QR-----------------GSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEEL 169 :::::: d1q1ra1 124 --AGLQVDNGIVINEHMQTSDPLIM----------------------------------- 146 d1nyta1 170 S--------------------------------------- 170 d1q1ra1 147 -AVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGK 185 TMalign alignment (TM-score: 0.44 Raw score:75.43) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSRA---- 54 :::::::::::::::::::::::: ::::::::::::::: d1q1ra1 1 ---------------NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLP 45 d1nyta1 55 ----------------EE-LAK-LFAHTGSIQAL-SM-------------DELEGHEFDL 82 : ::: ::::::::::: :: :::::::::: d1q1ra1 46 PLSKAYLAGKATAESL-YLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDR 104 d1nyta1 83 IINATSSG-ISGDIPAI-PSS-LI---------------HPGIYCYDM---FYQ------ 115 :::::::: :::::::: :: : ::::::: ::: d1q1ra1 105 LVLATGGRPLIPNCELAS-AAG-LQVDNGIVINEHMQTS--DPLIMAVGDCARFHSQLYD 160 d1nyta1 116 -KGKT------PFLAWCEQRGSKRNADG-LGMLVAQ-------AAHAFLLWHGVLPDVEP 160 :: : : :::::: d1q1ra1 161 RWV-RIESVPN----------------AL-EQARKIAAILCGK----------------- 185 d1nyta1 161 VIKQLQEELS 170 d1q1ra1 186 ---------- 186 HHsearch alignment (Probability: 0.94 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSLDCAVTITNRT 50 :::::::::::::::::::::::::::::::::: d1q1ra1 2 ANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVG 35