Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 258 bits (658), Expect = 3e-73 Identities = 165/407 (40%), Positives = 226/407 (55%), Gaps = 17/407 (4%) Query: 41 ERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQV 100 ERAE DV+G +DF++GI V N G R+PK++ AI+ QLD H A V Sbjct: 27 ERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQIVPYASYV 86 Query: 101 ELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMS 160 ELA+KL E APGD +K +G EA E A+KIA+ +T R IAF G FHGRT M+ Sbjct: 87 ELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMA 146 Query: 161 LTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFEHYV 220 LT + P V H P+PNP + G D L + I E+LF+ + Sbjct: 147 LTGKVAPYKIGFGPFPSDVFHAPFPNP------LHGVTTADSL--KAI----EFLFKADI 194 Query: 221 PAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMWAIE 280 + VA I FEP+QGEGG+ P F + L+KL ++HGILLI DEVQ G RTG+++A+ Sbjct: 195 DPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMH 254 Query: 281 HFDIVPDIVTVAKALGGGIPIGATIFRAD-LDFGVSGVHSNTFGGNTVAAAAALAVIEEL 339 H+D+VPD++TVAK+L GG+P+ I RAD +D G T+ GN +A AAA AV++ + Sbjct: 255 HYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAAHAVLDII 314 Query: 340 -QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGE 398 + L E A L + +L ++ I DVRG G VEF K T+ A + Sbjct: 315 DEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCKAGGTEPDAEFTK-R 373 Query: 399 IVVEALKRGLALLGCG--KSAIRLIPPLIISEEEAKMGLDIFEEAIK 443 + AL+RGL LL CG + +R + PL I + + I E+ IK Sbjct: 374 VQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIK 420 Lambda K H 0.319 0.139 0.410 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: 526 Number of extensions: 34 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: 454 Length of database: 427 Length adjustment: 32 Effective length of query: 422 Effective length of database: 395 Effective search space: 166690 Effective search space used: 166690 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 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