Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_013010405.1 DACET_RS05585 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000025725.1:WP_013010405.1 Length = 441 Score = 179 bits (454), Expect = 2e-49 Identities = 138/434 (31%), Positives = 227/434 (52%), Gaps = 35/434 (8%) Query: 31 QDPENLPIV-IERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHY 89 +D E PI+ IERGEGI +YD N + D S V GH++PR+ +AIK Q +K H Sbjct: 15 KDHETYPIIKIERGEGIYLYDDKNNKYIDAVSSWWVNIFGHNNPRLKDAIKNQLDKIEHV 74 Query: 90 SLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYG-------TGRK 142 ++ A+ L E+L+ + P ++ KV Y + G+ A E+AMKL YG T +K Sbjct: 75 IFAGITHDPALKLTEQLLSVTPENL-TKVFYADIGSAAVESAMKL-SYGYRKNNGVTSKK 132 Query: 143 QFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDE 202 ++L +HG T LS+ + + + + M + P+ YR +G + +E Sbjct: 133 RYLYLDSGYHGETLGALSVCGEE-LYTELYGDIMIENIRVQGPDCYRCPYG----KTRNE 187 Query: 203 LTNRVLDFIEEYVFRHVPPHEIGAIFFEP-IQGEGGYVVPPKGFFKALKKFADEYGILLA 261 + + + +E + +H +EI A+ EP +Q GG + P + + L + A Y I Sbjct: 188 CSAQCFEHMERTIEKHA--NEITAVIIEPLLQCAGGMKMYPPLYLQKLCEAAKAYDIHTI 245 Query: 262 DDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRA---DITFD 312 DE+ G GRTG +A+E GV+PD I K + G LP++ V I+ A D T Sbjct: 246 FDEIASGFGRTGTMFALEQAGVQPDFICVSKGLTSGYLPMSAVLTTDEIYSAFYDDYTTL 305 Query: 313 KPGRHATTFGGNPVAIAAGIEVVEIVKEL--LPHVQEVGDYLHKYLEEFKEKYEVIGDAR 370 K H+ +F GNP+A A E +++ KEL + ++ +H+Y+ + + +G+ R Sbjct: 306 KAFLHSHSFTGNPLACAVANETMKMFKELNIIEENRKKFPVMHEYINKKFKGQPHVGEIR 365 Query: 371 GLGLAQAVEIVKSKETKEKYPELRDR----IVKESAKRGLVLLGCGDNSIRFIPPLIVTK 426 LG AVE+VK +TKE + + +DR I ++S +G L GD I F+PP ++T+ Sbjct: 366 HLGCVSAVELVKDVKTKESF-DWKDRTGFQIFRKSITKGAYLRNLGD-VIYFMPPYVITE 423 Query: 427 EEIDVAMEIFEEAL 440 +E+ ++I E++ Sbjct: 424 DEMIKLVDIAHESI 437 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: 520 Number of extensions: 31 Number of successful extensions: 7 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: 441 Length adjustment: 32 Effective length of query: 413 Effective length of database: 409 Effective search space: 168917 Effective search space used: 168917 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 10 2024. The underlying query database was built on Apr 09 2024.
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