Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_212636831.1 B9A12_RS05520 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900176285.1:WP_212636831.1 Length = 449 Score = 191 bits (484), Expect = 5e-53 Identities = 131/432 (30%), Positives = 225/432 (52%), Gaps = 32/432 (7%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYEN 98 V++RGEGI ++D DGN + D + G V+++GH P ++EA+K+QA + + + F E Sbjct: 21 VVDRGEGIHIWDKDGNRYIDGSGGACVVSLGHGVPEILEAMKEQAARISFAHGSHFTSEA 80 Query: 99 AIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY---GTGRK---QFLAFYHAFH 152 A A++L+ LAP +V + + G+EA E A+K+V+ GR + ++ + +FH Sbjct: 81 ARECADRLVRLAPDPSLSRVYFLSGGSEAVETAVKVVRQYWREVGRPDKYKVISRWVSFH 140 Query: 153 GRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIE 212 G T ++L ++ + P HI YR +G EP + + +E Sbjct: 141 GNTMGAVAL-GGHTARRRHYHPHFLHTPHIEPAYCYRCPFG----REPQTCSLECAEQLE 195 Query: 213 EYVFRHVPPHEIGAIFFEPIQG-EGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271 + ++ P + A EP+ G G +VP G+++ +++ D Y + L DEV G+GR Sbjct: 196 RTI-KYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICDTYEVKLIADEVMTGVGR 254 Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGV-----IHRADITFDKPGRHATTFGGNP 325 TG+ + ++H+ V PD+I K + G PL V IH A + H T+ NP Sbjct: 255 TGRNFCLDHWSVVPDVIVSAKGLSSGYTPLGAVIVKEEIHDAIRSGSGAFVHGHTYSQNP 314 Query: 326 VAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKS 383 +++A G V+ + K+L+ +G+ + L E+ ++GD RGLGL VE+V++ Sbjct: 315 LSVAVGAAVLRYLEEKDLIARCATMGEVFLEKLRGLLER-PMVGDVRGLGLFAGVELVQN 373 Query: 384 KETKEKYP---ELRDRIVKESAKRGLVLL-------GCGDNSIRFIPPLIVTKEEIDVAM 433 KETK + ++ R+ +E+ +RGL+ G + I PP I+T+EE+D + Sbjct: 374 KETKAPFAPSGKISARVAQEAFRRGLITYPGSGGADGINGDHILLAPPFIITEEELDEIV 433 Query: 434 EIFEEALKAALK 445 I EA++A K Sbjct: 434 RILGEAIQAVEK 445 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: 555 Number of extensions: 32 Number of successful extensions: 4 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: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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 Jul 25 2024. The underlying query database was built on Jul 25 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