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 | d1vima_ | Hypothetical protein AF1796 | SIS domain | SIS 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 <-- 0.809 --> HitDALI alignment (Z-score: 3.8 Raw score:353.20) d1nyta1 1 ------------------------dgvgllSDLErlSFIRpgLRILLIG---aGGASRGV 33 :::: :::: ::::::: ::::::: d1vima_ 1 hgghmsllrflevvsehiknlrnhidletvGEMI--KLIDsaRSIFVIGagrsGYIAKAF 58 d1nyta1 34 LLPLLSLDCAVTITNrtvsraeelaklfahtgsiQALSmdelegHEFDLIINATSSGIsg 93 ::::::::::::::: :::: :::::::::::::: d1vima_ 59 AMRLMHLGYTVYVVG-----------------etVTPR-----iTDQDVLVGISGSGEtt 96 d1nyta1 94 dIPAIpSSLIHPGIYCYDMFYQkgKTPFLAWCeqrgskrNADGL---------------- 137 :::: :::::::::::::::: :::::::: ::::: d1vima_ 97 sVVNIsKKAKDIGSKLVAVTGK-rDSSLAKMA-------DVVMVvkgkmkqerdeilsql 148 d1nyta1 138 --------gmLVAQ---aahafllwhgvlpdvepvikqlqeels 170 :::: d1vima_ 149 aplgtmfeltAMIFldalvaeimmqkhltekdlearhavleegg 192 FAST alignment (Normalized score: 1.99 Raw score:359.70) d1nyta1 1 DGVGLLSDLERLSFIRPG----------------------------------------LR 20 :: d1vima_ 1 ------------------HGGHMSLLRFLEVVSEHIKNLRNHIDLETVGEMIKLIDSARS 42 d1nyta1 21 ILLIGA------GGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDE 74 ::: :::::::::::::::::::: d1vima_ 43 IFV---IGAGRSGYIAKAFAMRLMHLGYTVYV---------------------------- 71 d1nyta1 75 LEGHEFDLIINATSSGISGDIPAIPSS-------LIHPGIYCYDMFYQKGK--------T 119 :::::::::::: : d1vima_ 72 ---------------------------VGETVTPRITDQDVLVGIS-----GSGETTSVV 99 d1nyta1 120 PFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS--------- 170 :::::::::: ::::: d1vima_ 100 NISKKAKDIG-SKLVA-----------------------------------VTGKRDSSL 123 d1nyta1 171 ------------------------------------------------------------ 171 d1vima_ 124 AKMADVVMVVKGKMKQERDEILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEA 183 d1nyta1 171 --------- 171 d1vima_ 184 RHAVLEEGG 192 TMalign alignment (TM-score: 0.45 Raw score:76.46) d1nyta1 1 --------------------------DGVGLLSDLERL--SFIRPGLRILLIGA---GGA 29 :::::: :::::::::::::: ::: d1vima_ 1 HGGHMSLLRFLEVVSEHIKNLRNHID------LETVGEMIKLIDSARSIFVIGAGRSGYI 54 d1nyta1 30 SRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE-FDLIINATS 88 :::::::::::::::::: : :: ::: : :: ::::::::: d1vima_ 55 AKAFAMRLMHLGYTVYVV---G--ET------------VTP----R--ITDQDVLVGISG 91 d1nyta1 89 SGISGDI-P-AIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLG-------- 138 :: ::: : ::::::::::::::::::: ::::::: :: ::::::: d1vima_ 92 SG--ETTSVVNISKKAKDIGSKLVAVTGK-RDSSLAK-MA-----DVVMVVKGKMKQERD 142 d1nyta1 139 ---------------MLVAQAAH---------------------------AFLLWHGVLP 156 :::::::: d1vima_ 143 EILSQLAPLGTMFELTAMIFLDALVAEIMMQKHLTEKDLEARHAVLEEGG---------- 192 d1nyta1 157 DVEPVIKQLQEELS 170 d1vima_ 193 -------------- 193 HHsearch alignment (Probability: 0.47 E-value:0.00) d1nyta1 17 PGLRILLIGAGGA---SRGVLLPLLSLDCAVTITNR 49 ::::::::::::: :::::::::::::::::::: d1vima_ 39 SARSIFVIGAGRSGYIAKAFAMRLMHLGYTVYVVGE 74