Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900115975.1:WP_207545101.1 Length = 434 Score = 303 bits (777), Expect = 5e-87 Identities = 164/434 (37%), Positives = 249/434 (57%), Gaps = 11/434 (2%) Query: 17 EVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVV 76 E++ R + +A + + + +E+ +G + DV+G + DF G+G +N GH VV Sbjct: 7 ELVARKHQLIARGISN--STEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVV 64 Query: 77 EAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK 136 EAIK QAEK H YE + LAEKLIEL PG+ +++V++ NSGAE E A+K+ + Sbjct: 65 EAIKNQAEKLLHTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIAR 124 Query: 137 YGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDG 196 R ++F AFHGRT +SLT+ + GF P P V IP YR T+ Sbjct: 125 SYAKRTGIISFECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTY---- 180 Query: 197 YEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEY 256 E L+ + VPP I A+ EP+QGEGG++VPP F L+K D++ Sbjct: 181 RSTYPECGLHCLEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKH 240 Query: 257 GILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPG 315 GI+L DEVQ G GRTGK +A EHFG+EPDL+ K+I G+PL+ V+ +ADI PG Sbjct: 241 GIILIADEVQTGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPG 300 Query: 316 RHATTFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLG 373 T+ GNPV+ AAG+ ++ +++ L+ +GD + + +EKY +IGD RGLG Sbjct: 301 EIGGTYSGNPVSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKYPIIGDVRGLG 360 Query: 374 LAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDV 431 A+E+VK + TKE E ++K G++++G G N +R + PL++T E+++ Sbjct: 361 AMNAMELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEK 420 Query: 432 AMEIFEEALKAALK 445 +++ E+A+ + K Sbjct: 421 GLDVLEQAVASVSK 434 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: 512 Number of extensions: 27 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 413 Effective length of database: 402 Effective search space: 166026 Effective search space used: 166026 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 Apr 09 2024. 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