Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate 7025360 Shewana3_2520 aminotransferase (RefSeq)
Query= BRENDA::P31893 (426 letters) >FitnessBrowser__ANA3:7025360 Length = 452 Score = 104 bits (260), Expect = 5e-27 Identities = 85/286 (29%), Positives = 136/286 (47%), Gaps = 42/286 (14%) Query: 52 YGAHNYHHCSAYRAKGVSLDM-EGKRYFDFLSAYSAVNQGHCHPKIVNTMVEQAQRLT-- 108 YG H+ A+G L++ +G++ D S++ A G+ HP I+ M Q +L+ Sbjct: 28 YGVHS--------AQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMERQLHQLSHV 79 Query: 109 ----LTSRAFYT---DVLGEYEEFLTKLFNYDKVLPMNTGVEGGETACKIA-RCWAYMKK 160 +T T +L E LTK+F D +G E A K+A + W Sbjct: 80 MFGGITHEPAITLCKKLLAMTCEPLTKVFLCD------SGSIAVEVAIKMALQYWQGQDL 133 Query: 161 KVPENQAK--IIFAENNFWGRTLSAISASTDPMSYDEL------------RPYMPGFEIV 206 + + K I+ + + G T +A+S + P P E + Sbjct: 134 PLAQKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVTKQCFVDAPQTPFGEPL 193 Query: 207 KYNDTAALEKAF--QDPNVCAYMVEPI-QGEAGVVALDAGYLTEVRELCTKYNVLFIADE 263 + +D A +++ Q P + A ++EPI QG G+ + YL +R LC +YNVL I DE Sbjct: 194 RQDDLAPMQRILREQHPEIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDE 253 Query: 264 VQTGLARTGRMLAVDHEDVKPDLLILGKALSGGLYPVSAVLRDDHI 309 + TG RTG++ A +H D+ PD+L LGKAL+GG ++A L D++ Sbjct: 254 IATGFGRTGKLFAYEHADITPDILCLGKALTGGYISLAATLCTDNV 299 Lambda K H 0.322 0.137 0.424 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: 424 Number of extensions: 21 Number of successful extensions: 2 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: 426 Length of database: 452 Length adjustment: 32 Effective length of query: 394 Effective length of database: 420 Effective search space: 165480 Effective search space used: 165480 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 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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