Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate YP_002823855.1 NGR_b16510 omega-amino acid--pyruvate aminotransferase
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000018545.1:YP_002823855.1 Length = 443 Score = 192 bits (489), Expect = 1e-53 Identities = 137/425 (32%), Positives = 220/425 (51%), Gaps = 34/425 (8%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 ++ AEGVY+ D+DGN +LD ++G+ +N G ++ +A+++QL+ + A +P Sbjct: 28 LLASAEGVYYRDIDGNQVLDGTAGLWCVNAGHARKEISQAVERQLNTLDFAPSFQMGHPI 87 Query: 99 QVELAKKLVEIAPGDIERK---VFLSNSGTEANEAALKIAK------WSTNRKMFIAFIG 149 + A+KL EIAPG+ +K +F + SG+E+ + ALKIA R I Sbjct: 88 AFQFAEKLAEIAPGEPGKKLDRIFYTGSGSESVDTALKIAIAYQRAIGQGTRTRLIGRER 147 Query: 150 AFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPY-RNPWGIDGY-ENPDELINRV 207 +HG G +S+ V R+FP +PG H+ + + RNP+ G E+ EL Sbjct: 148 GYHGVGFGGISVGGL--VNNRRVFPQVPGADHLRHTHDLARNPFTKGGLPEHGAELA--- 202 Query: 208 IDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQ 267 D +E + H AE +A + EP+ G G ++PPK + + L+ ADKHGILLI DEV Sbjct: 203 -DDLERLVALH--GAETIAAVIVEPVAGSTGVLLPPKGYLERLRATADKHGILLIFDEVI 259 Query: 268 MGMGRTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGATIFRADL--------DFGVSGVH 318 G GR G +A+++F + PDI+T AK L G +P+GA + + + + H Sbjct: 260 SGFGRLGAPFAVDYFGVTPDIITTAKGLTNGVVPMGAVFTSSKVHDALMHGPEAQIELFH 319 Query: 319 SNTFGGNTVAAAAALAVIEELQ-NGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLA 377 T+ G+ VA AA LA +E + L+ A +L + + + ++ + +I D+R +GL Sbjct: 320 GYTYSGHPVACAAGLAAMEIYEKEALLTRASELATYWEDAVHGLRSRKNVI-DIRTIGLV 378 Query: 378 WGVEFVKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDI 437 G+E E A ++ V+ KRGL + G I L PPL I E+ + I Sbjct: 379 AGIELA---SRSEAAGARAYDVFVDCFKRGLLIRVTG-DIIALSPPLTIEREQVDELMSI 434 Query: 438 FEEAI 442 +A+ Sbjct: 435 LADAL 439 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: 525 Number of extensions: 29 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: 454 Length of database: 443 Length adjustment: 33 Effective length of query: 421 Effective length of database: 410 Effective search space: 172610 Effective search space used: 172610 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