Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_102106348.1 C0029_RS13280 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_002869505.1:WP_102106348.1 Length = 454 Score = 177 bits (450), Expect = 5e-49 Identities = 133/437 (30%), Positives = 221/437 (50%), Gaps = 51/437 (11%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY-- 96 V+ R E I +Y +G+ D SG+ N+G+S +V+A+ +Q + +Y+ +FF Sbjct: 35 VMSRAEHIYIYTAEGHKMLDGMSGLWCCNLGYSQRSIVDAVTEQLGQLPYYN--NFFQCS 92 Query: 97 -ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFYH 149 + AI LA+ L+++ P V + NSG+EAN+ ++LV +K ++ + Sbjct: 93 NQPAIELAKALVDITPERFNH-VFFTNSGSEANDTNLRLVSRYYQCQGRPEKKLIISRKN 151 Query: 150 AFHGRTQAVLSL--TASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRV 207 A+HG T A L Q +G + V HI P+ + + E+P+E RV Sbjct: 152 AYHGSTIAAACLGGMGPMHEQTNG----IDYVHHIEQPHWFE----VGPDEDPNEFGLRV 203 Query: 208 LDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQM 267 +EE + + + A EP+QG GG ++PP ++ +++ +E ILL DEV Sbjct: 204 ARQLEEKI-DELGEENVAAFIAEPVQGAGGVIIPPDSYWPEVQRICNERDILLIADEVIC 262 Query: 268 GIGRTGKFWAIEHFGVEPDLIQFGKAIGGGL-PLAGVI---HRADITFDKPGR--HATTF 321 G GRTG++W E +G+EPDL+ F KA+ G PL GV+ AD+ G H T+ Sbjct: 263 GFGRTGQWWGSETYGIEPDLMTFAKAVTNGFQPLGGVMVADKVADVLLAHEGEFAHGLTY 322 Query: 322 GGNPVAIAAGIEVVEIVKE---LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 G+P A AAG+ + I+KE + + + + L+E + ++++G RG G+ AV Sbjct: 323 SGHPAAAAAGLATLNILKEGNVIADAAANIAPHFQRRLQELAD-HKIVGQVRGRGMFAAV 381 Query: 379 EIVKSKETKEKYPELRDRIVKESA----------KRGLVLLGCGDNSIRFIPPLIVTKEE 428 E+VK K ++E + ESA + GL++ G N++ PPLI + E Sbjct: 382 ELVKDKSSREP-------LAAESAGALFCRNTANELGLMVRQTG-NAMIMAPPLICSTSE 433 Query: 429 IDVAMEIFEEALKAALK 445 ID +++ +AL K Sbjct: 434 IDSLIDMLGQALDVTAK 450 Lambda K H 0.320 0.141 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 505 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 454 Length adjustment: 33 Effective length of query: 412 Effective length of database: 421 Effective search space: 173452 Effective search space used: 173452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory