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 | d1vi2a1 | Putative shikimate dehydrogenase YdiB | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1vkza2 | Glycinamide ribonucleotide synthetase (GAR-syn), N-domain | PreATP-grasp domain | PreATP-grasp domain | α/β |
Query <-- 0.883 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:365.80) query 1 --------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI-EVTIFCAFWgl 45 ::::::::::: :::::::::::::::: ::::::::: d1vi2a1 1 dgtghiraikesgfDIKGKTMVLLG------aGGASTAIGAQGAIEGLkEIKLFNRRD-- 52 query 46 LLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllemmkeekapkls 105 :::: d1vi2a1 53 EFFD-------------------------------------------------------- 56 query 106 dlLSGARKKE------VKFYAXQlsveimgfkkeelfpevqimDVKEYLKNALESDLQLF 159 :::::::: ::::::: ::::::::::::::::: d1vi2a1 57 kaLAFAQRVNentdcvVTVTDLA--------------------DQQAFAEALASADILTN 96 query 160 ------------------------------------------------------------ 160 d1vi2a1 97 gtkvgmkpleneslvndisllhpgllvtecvynphmtkllqqaqqagcktidgygmllwq 156 query 160 -------------------------i 160 d1vi2a1 157 gaeqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.17 Raw score:711.70) query 1 --------------GMENKKMNLLLFSGDYDK---ALASLIIANAAREME-IEVTIFCA- 41 ::::::::: ::::::::::::::: :::::::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVL---------LGAGGASTAIGAQGAIEGLKEIKLFNRR 51 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKA 101 ::::: d1vi2a1 52 DEFFD------------------------------------------------------- 56 query 102 PK-LSDLLSGARK---KEVKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALESD 155 :::::::::: ::::::: ::::::::::::: d1vi2a1 57 --KALAFAQRVNENTDCVVTVTD----------------------LADQQAFAEALASAD 92 query 156 LQLFI------------------------------------------------------- 160 ::: d1vi2a1 93 ILT--NGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGY 150 query 161 -------------------------------- 161 d1vi2a1 151 GMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.31 Raw score:49.46) query 1 ------GMENKKMNL------------LLFSGDYD-KALASLIIAN-AAR--EMEIEVTI 38 :::: ::::: :::::::::: ::: d1vi2a1 1 DGTGHI-----RAIKESGFDIKGKTMV---LLGAGGASTAIGAQGAIEGLKE-------- 44 query 39 FCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE 98 ::::::::: : ::::::::::::: d1vi2a1 45 ----------------------------------IKLFNRRDE-F--FDKALAFAQRVNE 67 query 99 EK-APKLS------------DLLSGARKKEVKFYA----XQLS----VEIMG--FKKEEL 135 :: ::::: ::::: : ::: : :::: :::::: d1vi2a1 68 NTDCVVTVTDLADQQAFAEA--LASAD---I-LTNGTKV---GMKPL-ENESLVNDISLL 117 query 136 FPEV-Q---------------IMD-----VKEYLKNALESDLQL---------------- 158 :::: : ::: ::: ::: ::::: d1vi2a1 118 HPGLLVTECVYNPHMTKLLQQAQQAGCKT--IDG-YGM-LLWQGAEQFTLWTGKDFPLEY 173 query 159 ---------FI 160 d1vi2a1 174 VKQVMGFGA-- 182 HHsearch alignment (Probability: 0.01 E-value:0.14) query 102 PKLSDLLSGARKKEVKFY 119 :::::::::::::::::: d1vi2a1 130 PHMTKLLQQAQQAGCKTI 147
Intermediate <-- 0.781 --> HitDALI alignment (Z-score: 5.5 Raw score:356.60) d1vi2a1 1 dgtghiraikesgfdikgKTMVLLGAGGASTAIGAQGAIEGLkEIKLFNrrdeffdkALA 60 :::::::::::::::::::::::: :::::: ::: d1vkza2 1 ------------------VRVHILGSGGREHAIGWAFAKQGY-EVHFYP--------GNA 33 d1vi2a1 61 FAQRVnentdcvVTVTDLADQQAFAEaLASAdILTNGTKVGmkplenESLVndisllhpg 120 ::::: :::::::::::::: :::: ::::::::: :::: d1vkza2 34 GTKRD-------GTNHPYEGEKTLKA-IPEE-DIVIPGSEE------FLVE--------r 70 d1vi2a1 121 LLVTE---cvYNPHMtkllqqaqqagcktidgygmllwqgaeqftlwtgkdfpleyvkqv 177 ::::: ::::: d1vkza2 71 SNVFGpvkevARLEG--------------------------------------------- 85 d1vi2a1 178 mgfga 182 d1vkza2 86 ----- 86 FAST alignment (Normalized score: 3.94 Raw score:490.70) d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEF---FDK 57 ::::::::::::::::::::::: ::::: ::: d1vkza2 1 ------------------VRVHILGSGGREHAIGWAFAKQG-YEVHF-------YPGNAG 34 d1vi2a1 58 ALAFAQRVNENTDCV-VTVTDLADQQAFAEALASA--DILTNGTKVGMKPLENESLVNDI 114 ::: :::::: ::::::::: ::::::: d1vkza2 35 TKR------------DGTNHPY----EGEKTLKAIPEEDIVIPG---------------- 62 d1vi2a1 115 SLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYV 174 d1vkza2 63 ------------------------------------------------------------ 63 d1vi2a1 175 KQVMGFGA----------------------- 182 d1vkza2 63 --------SEEFLVERSNVFGPVKEVARLEG 85 TMalign alignment (TM-score: 0.36 Raw score:65.60) d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALA 60 :::::::::::::::::::::::: :::::: : ::: d1vkza2 1 ------------------VRVHILGSGGREHAIGWAFAKQGY-EVHFYP-----G--NAG 34 d1vi2a1 61 FAQRVNENTDCVVTVTDLADQQAF-AEALASADILTNGTKV-GMKPLENESLVNDISLLH 118 :: :: :::::::::: : :: :: ::::::: :: : :: : : :: d1vkza2 35 TK-RD-------GTNHPYEGEK-TLKA-IP-EEDIVIP-GSEE------FL-V--E--RS 71 d1vi2a1 119 PGLLVTECVYNPHMTKLLQQ-AQ-----QAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLE 172 ::: : ::: : d1vkza2 72 --NVF-G----------PVKE-VARLEG-------------------------------- 85 d1vi2a1 173 YVKQVMGFGA 182 d1vkza2 86 ---------- 86 HHsearch alignment (Probability: 0.88 E-value:0.00) d1vi2a1 19 KTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDE 53 ::::::::::::::::::::::: ::::::::::: d1vkza2 1 VRVHILGSGGREHAIGWAFAKQG-YEVHFYPGNAG 34