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 | d1cyda_ | Carbonyl 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 <-- 1.358 --> HitDALI alignment (Z-score: 7.7 Raw score:697.60) d1nyta1 1 dgvgllsdlerlsfiRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 :::::::::: :::::::::::::::::::::::::::::::::: d1cyda_ 1 -------------lnFSGLRALVTGaGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAK 47 d1nyta1 60 LFAhtgSIQALSM---------DELEGH-EFDLIINATSS--------------giSGDI 95 ::: ::::::: :::::: ::::::::::: :::: d1cyda_ 48 ECP---GIEPVCVdlgdwdateKALGGIgPVDLLVNNAALvimqpflevtkeafdrSFSV 104 d1nyta1 96 -----pAIPSSLIH------pGIYCYDMFY----------------QKGKTPFLAWCEQR 128 :::::::: ::::::::: :::::::::::::: d1cyda_ 105 nlrsvfQVSQMVARdminrgvPGSIVNVSSmvahvtfpnlitysstKGAMTMLTKAMAME 164 d1nyta1 129 G---sKRNADGLgmLVAQA---ahafLLWH------------------------------ 152 : ::::::: ::::: :::: d1cyda_ 165 LgphkIRVNSVN--PTVVLtdmgkkvSADPefarklkerhplrkfaevedvvnsilflls 222 d1nyta1 153 --------gvlpdVEPVIKQlqeels 170 ::::::: d1cyda_ 223 drsastsgggilvDAGYLAS------ 242 FAST alignment (Normalized score: 5.49 Raw score:1114.00) d1nyta1 1 DGVGLLSDLERLSFI--RPGLRILLI-GAGGASRGVLLPLLSLDCAVTITNRTVSRAEEL 57 ::::::::: ::::::::::::::::::::::::::::::::: d1cyda_ 1 ---------------LNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSL 45 d1nyta1 58 AKLFAHTGSIQALSM-----------DELEG-HEFDLIINATSSGISGDIPAI------- 98 ::: ::::::: ::::: ::::::::: d1cyda_ 46 AKE---CPGIEPV--CVDLGDWDATEKALGGIGPVDLLVNN------------AALVIMQ 88 d1nyta1 99 ------------------------PSSLIH--------PGIYCYDMFYQKGK-------- 118 :::: ::::::::: d1cyda_ 89 PFLEVTKEAFDRSFSVNLRSVFQVSQMV--ARDMINRGVPGSIVNVS-----SMVAHVTF 141 d1nyta1 119 -------------TPFLAWCEQRGS------KRNADGLGMLVAQAAHAFLLWHGVLPDVE 159 ::::::::: :::::: d1cyda_ 142 PNLITYSSTKGAMTMLTKAMAM---ELGPHKIRVNSV----------------------- 175 d1nyta1 160 PVIKQLQEELS------------------------------------------------- 170 d1cyda_ 176 -----------NPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVVNSILFLLSDR 224 d1nyta1 171 ------------------ 171 d1cyda_ 225 SASTSGGGILVDAGYLAS 242 TMalign alignment (TM-score: 0.58 Raw score:98.47) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 : ::::::::::: ::::::::::::::::::::::: : : ::::: d1cyda_ 1 ---------L----NFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVT-R--T-NSDLV 43 d1nyta1 60 LFAH-TGSIQAL-S-------MD-ELEG-HEFDLIINATSSGI--------------SG- 93 :::: ::::::: : :: :::: :::::::::::::: :: d1cyda_ 44 SLAKECPGIEPVCVDLGDWDATEKALGGIGPVDLLVNNAALVIMQPFLEVTKEAFDRSFS 103 d1nyta1 94 --DIP--AIPSSLI--HP----GIYCYDMFY--QK-------------G-KTPFLAWCEQ 127 ::: ::::::: :: ::::::::: :: : :::::::::: d1cyda_ 104 VNLRSVFQVSQMVARDMINRGVPGSIVNVSSMVAHVTFPNLITYSSTKGAMTMLTKAMAM 163 d1nyta1 128 RGS---KRNADGLGM-----------------------------LV-AQA-AH------- 146 ::: ::::::::: :: ::: : d1cyda_ 164 ELGPHKIRVNSVNPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVV-NSILFLLS 222 d1nyta1 147 ----------AFLLWHGVLPDVEPVIK-QL---QEEL-S 170 :: : :: d1cyda_ 223 DRSASTSGGG---------------ILV-DAGY--LAS- 242 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 14 FIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQA--- 69 :::::::::::: :::::::::::::::::::::::::::::::::::::::::::: d1cyda_ 1 LNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLG 60 d1nyta1 70 ----LSMDELEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQ 115 :::::::::::::::::::::::::::::::::::: ::::::: d1cyda_ 61 DWDATEKALGGIGPVDLLVNNAALVIMQPFLEVTKEAFDR---SFSVNLR 107