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 | d1qsga_ | Enoyl-ACP 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 <-- 1.041 --> HitDALI alignment (Z-score: 6.5 Raw score:634.20) d1nyta1 1 dgvgllsdlerlsfiRPGLRILLIGAG---GASRGVLLPLLSLDCAVTITNR---TVSRA 54 :::::::::::: :::::::::::::::::::::: ::::: d1qsga_ 1 -------------gfLSGKRILVTGVAsklSIAYGIAQAMHREGAELAFTYQndkLKGRV 47 d1nyta1 55 EELAKLFAhtgSIQALSM---------DELEGH-----EFDLIINATS------------ 88 :::::::: ::::::: :::::: :::::::::: d1qsga_ 48 EEFAAQLG---SDIVLQCdvaedasidTMFAELgkvwpKFDGFVHSIGfapgdqldgdyv 104 d1nyta1 89 --------sgISGD----ipAIPSSLIH---PGIYCYDMF----------------yQKG 117 :::: :::::::: ::::::::: ::: d1qsga_ 105 navtregfkiAHDIssysfvAMAKACRSmlnPGSALLTLSylgaeraipnynvmglaKAS 164 d1nyta1 118 KTPFLAWCEQRG---sKRNADGLgmLVAQ-----------aaHAFLLWH----------- 152 :::::::::::: ::::::: :::: ::::::: d1qsga_ 165 LEANVRYMANAMgpegVRVNAIS--AGPIrtlaasgikdfrkMLAHCEAvtpirrtvtie 222 d1nyta1 153 --------------------gvlpdVEPVikqlqeels 170 :::: d1qsga_ 223 dvgnsaaflcsdlsagisgevvhvdGGFS--iaamnel 258 FAST alignment (Normalized score: 4.36 Raw score:913.90) d1nyta1 1 DGVGLLSDLERLSFI--RPGLRILLIGAG---GASRGVLLPLLSLDCAVTITNR---TVS 52 :::::::::::: :::::::::::::::::::::: ::: d1qsga_ 1 ---------------GFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKG 45 d1nyta1 53 RAEELAKLFAHTGSIQAL-------------------SMDELEG--HEFDLIINATSSGI 91 :::::::: ::::::: ::::::::: d1qsga_ 46 RVEEFAAQ----------LGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHS----- 90 d1nyta1 92 SGDIPAI---------------------------------------PSSLIHPGIYCYDM 112 :::::::::::::: d1qsga_ 91 -------IGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTL 143 d1nyta1 113 FYQKGK----------------------TPFLAWCEQRGS------KRNADGLGMLVAQA 144 ::::::::: :::::: d1qsga_ 144 ------SYLGAERAIPNYNVMGLAKASLEANVRYMAN---AMGPEGVRVNAI-------- 186 d1nyta1 145 AHAFLLWHGVLPDVEPVIKQLQEELS---------------------------------- 170 d1qsga_ 187 --------------------------SAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVT 220 d1nyta1 171 -------------------------------------- 171 d1qsga_ 221 IEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL 258 TMalign alignment (TM-score: 0.59 Raw score:100.65) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAG---GASRGVLLPLLSLDCAVTITNRTVSRAEEL 57 : ::::::::::::: :::::::::::::::::::::::::::::: d1qsga_ 1 ---------G----FLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRV 47 d1nyta1 58 AKLFAHTGSIQALSM---------DELE--G--H-EFDLIINATSSG------------- 90 ::::::::::::::: :::: : : :::::::::::: d1qsga_ 48 EEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAV 107 d1nyta1 91 ------ISGD----IP-AIPSSLI--HPG-IYCYDMFY--QK-------------GKTPF 121 :::: :: ::::::: ::: :::::::: :: ::::: d1qsga_ 108 TREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEA 167 d1nyta1 122 LAWCEQRGSK----RNADGLGMLV-AQ---------------------AAHAFLL----- 150 :::::::::: :::::: :: : ::::::: d1qsga_ 168 NVRYMANAMGPEGVRVNAIS--AGP-IRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDV 224 d1nyta1 151 ---------------------WHGVLPDVEPVIKQL-----QEELS 170 :::::::: d1qsga_ 225 GNSAAFLCSDLSAGISGEVVH-------VDGGFSIAAMNEL----- 258 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 16 RPGLRILLIGAG---GASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSM 72 :::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: d1qsga_ 3 LSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQC 62 d1nyta1 73 D--------------ELEGHEFDLIINATSSG 90 : ::::::::::::::::: d1qsga_ 63 DVAEDASIDTMFAELGKVWPKFDGFVHSIGFA 94