Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_028316962.1 G491_RS0128595 acetylornithine transaminase
Query= BRENDA::Q9SR86 (481 letters) >NCBI__GCF_000429905.1:WP_028316962.1 Length = 395 Score = 213 bits (543), Expect = 7e-60 Identities = 137/409 (33%), Positives = 209/409 (51%), Gaps = 40/409 (9%) Query: 79 FYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVVKQLKLINHSTIL 138 + P+ +V+ + ++DE+G+ Y D GIA GH HP V +V +Q + H + L Sbjct: 16 YARNPICLVKGQGVKLWDEDGKEYTDFLAGIAVCILGHAHPAVTQAVSEQAAKLVHVSNL 75 Query: 139 YLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLY---TGCND---IVSLR 192 + + A+ L+++ D VFF NSG EANE A+ MAR Y G D ++++ Sbjct: 76 FYTEPQTLLADQLINSCFADR--VFFCNSGAEANEAAIKMARKYFSEKGQPDKYRVIAME 133 Query: 193 NSYHGNAAATMGATAQSNWK--FNVVQSGVHHAINPDPYRGIFGSDGEKYASDVHDLIQF 250 S+HG ATM AT Q K F + G H P+ + + ++ Sbjct: 134 KSFHGRTFATMAATGQDAIKKGFEPMMDGFDHV----PFNDL-------------EAVEK 176 Query: 251 GTSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWG 310 + + + E IQ GG++ PGYLP ++ K G + I DEVQ+G RTG F Sbjct: 177 AITDETCAVLTEPIQAEGGVMVPFPGYLPGLRELCDKKGILLIFDEVQTGMGRTGALF-A 235 Query: 311 FQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLR 370 Q G +PDI+T+AKG+ NG+P+GA + T E+A + ++ TFGG P+ TAA AV+ Sbjct: 236 HQQMGAVPDIMTLAKGLANGLPIGAALATEEVASAFTPGAHATTFGGTPLVTAAARAVMI 295 Query: 371 VLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAET 430 L ++ L E + VG + K +L LLK K++ + +VRG GL+LG++ L P Sbjct: 296 TLMDQDLLEMSISVGDYFKNQLLLLKEKFDCVEEVRGMGLLLGLK------LNMPGGPIA 349 Query: 431 LHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVMDHAMS 479 M EMG + G+V R PPL T D D L++ +D ++ Sbjct: 350 AKAM----EMGYIFNV--TQGDVLRFVPPLIITRKDVDGLIETLDKILA 392 Lambda K H 0.320 0.136 0.406 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: 415 Number of extensions: 18 Number of successful extensions: 7 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: 481 Length of database: 395 Length adjustment: 32 Effective length of query: 449 Effective length of database: 363 Effective search space: 162987 Effective search space used: 162987 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 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