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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jzta_ | Hypothetical protein YNL200c (YNU0 YEAST) | YjeF N-terminal domain-like | YjeF N-terminal domain-like | α/β |
| Hit | d1b74a2 | Glutamate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
Query <-- 1.058 --> IntermediateDALI alignment (Z-score: 3.6 Raw score:420.50) query 1 ---------------------------------------------------gmENKKMNL 9 ::::::: d1jzta_ 1 lkvvssklaaeidkelmgpqigftlqqlmelagfsvaqavcrqfplrgkteteKGKHVFV 60 query 10 LLfSGDYdKALASLIIANAAREMEIEVTIFCafwGLLLlrdpekasqedkslyeqafssl 69 :: :::: ::::::::::::::::::::::: :::: d1jzta_ 61 IA-GPGN-NGGDGLVCARHLKLFGYNPVVFY---PKRS---------------------- 93 query 70 tpREAEelplskmnlggigkkmllemmkeekapKLSDLLSGARKKEVKFYAXqlsveimg 129 :::: ::::::::::::::::::: d1jzta_ 94 --ERTE---------------------------FYKQLVHQLNFFKVPVLSQ-------- 116 query 130 fkkeelfpevQIMDvkeYLKNAL--ESDLQLFI--------------------------- 160 :::: :::::: :::::::: d1jzta_ 117 ----------DEGN---WLEYLKpeKTLCIVDAifgfsfkppmrepfkgiveelckvqni 163 query 161 ------------------------------------------------------------ 161 d1jzta_ 164 ipivsvdvptgwdvdkgpisqpsinpavlvsltvpkpcsshirenqtthyvggrfiprdf 223 query 161 -------------------- 161 d1jzta_ 224 ankfgfepfgyestdqilkl 243 FAST alignment (Normalized score: 4.04 Raw score:797.30) query 1 G----------------------------------------------------MENKKMN 8 ::::::: d1jzta_ 1 -LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVF 59 query 9 LLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSS 68 :::: ::::::::::::::::::::::::::: d1jzta_ 60 VIAG--PGNNGGDGLVCARHLKLFGYNPVVFYP--------------------------- 90 query 69 LTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP-------KLSDLLSGARKKEVKFYAX 121 :::::::::::::::::: d1jzta_ 91 ----------------------------------KRSERTEFYKQLVHQLNFFKVPVLS- 115 query 122 QLSVEIMGFKKEELFPEVQIMDVK----EYLKNAL---ESDLQLFI-------------- 160 :::::: :::::: d1jzta_ 116 ------------------------QDEGNWLEYL-KPEKTLCIV--DAIFGFSFKPPMRE 148 query 161 ------------------------------------------------------------ 161 d1jzta_ 149 PFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIREN 208 query 161 ----------------------------------- 161 d1jzta_ 209 QTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 243 TMalign alignment (TM-score: 0.44 Raw score:70.86) query 1 --------------------------------------------GME------N-KKMNL 9 ::: : ::::: d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFV 60 query 10 LLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSL 69 :: ::: ::::::::::::::::::::::::: : : d1jzta_ 61 IA-GPG-NNGGDGLVCARHLKLFGYNPVVFYP-K--R----------------------- 92 query 70 TPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMG 129 ::::: :::::::::::::::::::: d1jzta_ 93 -SERTE---------------------------FYKQLVHQLNFFKVPVLSQD------- 117 query 130 FKKEELFPEVQIMDVKEYLKNALESDLQLFI----------------------------- 160 ::::::::: :::::::::: d1jzta_ 118 -----------EGNWLEYLK-PEKTLCIVDAIFGFSFKPPMREPFKGIVEELCKVQNIIP 165 query 161 ------------------------------------------------------------ 161 d1jzta_ 166 IVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFAN 225 query 161 ------------------ 161 d1jzta_ 226 KFGFEPFGYESTDQILKL 243 HHsearch alignment (Probability: 0.06 E-value:0.03) query 4 NKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAF 42 ::::::::::::::::::::::::::::::::::::::: d1jzta_ 53 EKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPK 91
Intermediate <-- 0.852 --> HitDALI alignment (Z-score: 3.6 Raw score:352.70) d1jzta_ 1 lkvvssklaaeidkelmgpqigftlqqlmelagfsvaqavcrqfplrgktetekGKHVFV 60 :::::: d1b74a2 1 ------------------------------------------------------NKKIGV 6 d1jzta_ 61 IAGPGnnggdgLVCARHLKLFGYNPVVFYPKRsertefykqlvhqlnffkvpvlsqdegN 120 ::::: ::::::::::::::::::::: : d1b74a2 7 IGTPA--tvksGAYQRKLEEGGADVFAKACPL-------faplaeegllegeitrkvveH 57 d1jzta_ 121 WLEYLKPeKTLCIVDAIfgfsfkppmrepFKGI-VEELCKVQNIIPIVSVDvptgwdvdk 179 ::::::: ::::::::: :::: ::::::::::::::::: d1b74a2 58 YLKEFKG-KIDTLILGC-----------tHYPLlKKEIKKFLGDAEVVDSS--------- 96 d1jzta_ 180 gpisqpsinpavLVSLtvpkpcsshirenqtthyVGGR-FIPRDfaNKFG---------- 228 :::: :::: ::::: :::: d1b74a2 97 ------------EALS------------------LSLHnFIKDD--GSSSlelfftdlsp 124 d1jzta_ 229 --------fepfgyestdqilkl 243 d1b74a2 125 nlqfliklilgrdypvklaegvf 147 FAST alignment (Normalized score: 2.24 Raw score:422.90) d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFV 60 :::::: d1b74a2 1 ------------------------------------------------------NKKIGV 6 d1jzta_ 61 IAGPGNNGGDG-LVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLSQDEG 119 ::: ::::: ::::::::::::::::: d1b74a2 7 IGT-PATVK--SGAYQRKLEEGGADVFAK------------------------------- 32 d1jzta_ 120 N--------------------------WLEYLKPEKTLCIVDAIFGFSFKPPMRE----- 148 ::::: :::::::: d1b74a2 33 -ACPLFAPLAEEGLLEGEITRKVVEHYLKEFK--GKIDTLIL-------------GCTHY 76 d1jzta_ 149 --PFKGIVEELCKVQN--IIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSH 204 :::::::: ::::::: d1b74a2 77 PLLKKEIKKF------LGDAEVVDS----------------------------------- 95 d1jzta_ 205 IRENQTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL--------------------- 243 d1b74a2 96 ---------------------------------------SEALSLSLHNFIKDDGSSSLE 116 d1jzta_ 244 ------------------------------- 244 d1b74a2 117 LFFTDLSPNLQFLIKLILGRDYPVKLAEGVF 147 TMalign alignment (TM-score: 0.30 Raw score:73.99) d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFV 60 :: :::: d1b74a2 1 ----------------------------------------------------NK--KIGV 6 d1jzta_ 61 IAGPGNNGG-DGLVCARHLKLFGYNPVVFYPKR-----------------SERTEFYKQL 102 ::::: :: :::::::::::::::::::::: d1b74a2 7 IGTPA--TVK-SGAYQRKLEEGGADVFAKACPLFAPLAEEGLLEGEITRK---------- 53 d1jzta_ 103 VHQLNFFKVPVLSQD--EGNWLEYLKPEKTLCIVDAIFGFSFKPPMREPFKGIV-EELCK 159 : ::::::: ::::::::::: ::::: ::::: d1b74a2 54 --------------VVE--HYLKEFK-GKIDTLILGCT-----------HYPLLKKEIKK 85 d1jzta_ 160 VQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFI 219 ::::::::::: :: : : :::::: d1b74a2 86 FLGDAEVVDSS---------------------EA-L-S----------------LSLHNF 106 d1jzta_ 220 PRDFANKFGF---------------------------------EPFGYESTDQILKL 243 :: :::::: d1b74a2 107 IK--DDGSSSLELFFTDLSPNLQFLIKLILGRDYPVKLAEGVF-------------- 147 HHsearch alignment (Probability: 0.03 E-value:0.17) d1jzta_ 77 H 77 : d1b74a2 58 Y 58