Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_010964736.1 CA_RS07495 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000008765.1:WP_010964736.1 Length = 445 Score = 310 bits (795), Expect = 5e-89 Identities = 173/443 (39%), Positives = 272/443 (61%), Gaps = 13/443 (2%) Query: 7 VKEIPGPKARKVIEEHHKYMATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVM 66 V ++PGPK+R+++++ KY+A + Y + +E A+G D+DGNV +DF+ GIGV Sbjct: 9 VTKVPGPKSRELLKKREKYVAKGVSC--SYPVFVEEAKGALVKDIDGNVFVDFAGGIGVQ 66 Query: 67 NVGLRNPKVIEAIKKQLDLVLHAA-GTDYYNPYQVELAKKLVEIAPGDIERKVFLSNSGT 125 N+G R+ V+EA+K+QLD +HA + Y PY V+LA+KL EI PG+ +K +NSG Sbjct: 67 NIGHRDDGVVEAVKEQLDKYIHACFHVNMYEPY-VDLAEKLTEITPGNFAKKAMFANSGA 125 Query: 126 EANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYP 185 EA E A+KIA+ T + I+ G+FHGRT+ TMS+T+ ++ P + Y Sbjct: 126 EAVENAIKIARAYTKKSGIISMNGSFHGRTNMTMSITSKYKPYKNGFGPFVCETYKADYA 185 Query: 186 NPYRNPWGIDGYENPDELINRVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKN 245 YR P G + ++ + + + V + +A + EP+QGEGG+VVPPK+ Sbjct: 186 YCYRCPLGCKFKDCGIACAEKL-----KTMLKTVVSPDMIACLIVEPVQGEGGFVVPPKD 240 Query: 246 FFKELKKLADKHGILLIDDEVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGGIPIGATI 305 +FK L+++ +++ I+ I DEVQ G RTG+ +A E+FD+ DI+T++K++ G+PI A + Sbjct: 241 YFKALQQICNENNIVFIVDEVQAGFARTGKFFAHEYFDVDADIITMSKSIANGLPISAVV 300 Query: 306 FRAD-LDFGVSGVHSNTFGGNTVAAAAALAVIEELQN-GLIENAQKLEPLFRERLEEMKE 363 +A+ +D G T+GGN ++ AA+ VI++++ L E + +L RL EMKE Sbjct: 301 GKAEIMDAACVGGIGGTYGGNPLSCVAAIKVIDKIKEANLNEKSIELGKSIMNRLNEMKE 360 Query: 364 KYEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGEIVVEALKRGLALLGCG--KSAIRLI 421 KY +IGDVRGLG GVEFVKD+ TKE + I+ K G+ L G + +R + Sbjct: 361 KYNVIGDVRGLGAMIGVEFVKDKDTKEPNKEIVSSILDYCFKHGVIFLNAGLLGNVLRFL 420 Query: 422 PPLIISEEEAKMGLDIFEEAIKV 444 PP+++++E+ K GLD EEAI++ Sbjct: 421 PPVVMTDEQLKYGLDTLEEAIRI 443 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: 565 Number of extensions: 29 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: 454 Length of database: 445 Length adjustment: 33 Effective length of query: 421 Effective length of database: 412 Effective search space: 173452 Effective search space used: 173452 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