Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::Q2Z0F8 (466 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 132 bits (332), Expect = 2e-35 Identities = 125/417 (29%), Positives = 190/417 (45%), Gaps = 40/417 (9%) Query: 56 PLPVVFDSASGAKVYDPEGNEYIDMLSAYSAVNQGHCHPRIVATLVQQAQKLT-LSSRAF 114 PLPVV + G ++ +G E ID +S++ G+ HP I A + +Q L + Sbjct: 25 PLPVV--ATQGVRIRLADGRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGL 82 Query: 115 YNSVFGRFAQKITTMFGYDM--VLPMNTGAEAVETCVKLARKWAYMKKGVPEGKAIVFSV 172 + R AQ++ + D+ V +G+ AVE +K+A ++ + KG E + IV+ Sbjct: 83 VHEPAARLAQRLAALLPGDLERVFFTESGSVAVEVALKMAIQY-WRNKGQAEKQRIVYFR 141 Query: 173 SGNFHGRTLGIISMSTDPESRTGFGPYLQNVGP--VYEDGGMMKTIRYGVLEDLERALEL 230 G +HG T +++ DPE G P + + +T+R E LE Sbjct: 142 HG-YHGDTFATMALC-DPEE--GMHSLFAGAMPDQIMAELPSDETMRRA----FELLLET 193 Query: 231 YGEHTAAFLIEP-IQGEAGIVVPEPGYLAQVHQLCKKHNVLLICDEIQTGLCRTGKMLAC 289 +GE AA +IEP +QG G+ + + LA + C +H +LLI DEI TG RTG+M AC Sbjct: 194 HGERLAAVIIEPLVQGAGGMQMHDAATLAFIAAACARHKLLLIADEIMTGFGRTGRMFAC 253 Query: 290 ----EYEGIRPDVVLLGKALSGGLYPVSAVLADSDVMLCIRPGE------HGSTYGGNPL 339 E PD+V L KAL+GG P++A +A V + HG TY N L Sbjct: 254 EEADELTSTIPDIVCLSKALTGGTLPLAATVARRHVFEAFLADDPAAALMHGPTYMANAL 313 Query: 340 GCAVAMTALDVLVDE-KLADRAMRLGEYFRSAVQSLNSPLVECVRGRGLLNAVVID---E 395 CA A +LD+ E +LA A + + V VR +G + AV + E Sbjct: 314 ACAAANASLDLFESEPRLAQVAAIEAQLAAELGPCRDLAGVAEVRVKGAIGAVELAGRIE 373 Query: 396 KKSTKGRTAWQLCLLLKSRGVLAKPTHVNIIRFAPPLVIEEEDLKRAVRIIGECLAD 452 + + R A GV +P ++ PP VI EDL + + L + Sbjct: 374 LDALRRRFA--------ELGVWVRP-FGKVVYLMPPFVIAAEDLTTLTAAVRQVLTE 421 Lambda K H 0.319 0.136 0.401 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: 430 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 426 Length adjustment: 32 Effective length of query: 434 Effective length of database: 394 Effective search space: 170996 Effective search space used: 170996 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 (21.8 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