Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_028316962.1 G491_RS0128595 acetylornithine transaminase
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000429905.1:WP_028316962.1 Length = 395 Score = 345 bits (886), Expect = 1e-99 Identities = 183/395 (46%), Positives = 250/395 (63%), Gaps = 12/395 (3%) Query: 21 DQYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK 80 DQ + +TY R P+ + KG+G +LWD +GK Y DF+AGIA C LGHAHPA+ QAVS Q K Sbjct: 9 DQVIANTYARNPICLVKGQGVKLWDEDGKEYTDFLAGIAVCILGHAHPAVTQAVSEQAAK 68 Query: 81 LHHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP 140 L H+SNL+Y Q LA ++ AD+VFFCNSGAEANEAAIK+ RKY + ++ Sbjct: 69 LVHVSNLFYTEPQTLLADQLINSCFADRVFFCNSGAEANEAAIKMARKY-FSEKGQPDKY 127 Query: 141 VILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRR 200 +++ + SFHGRT AT+ ATGQ +K F+P+ DGF +VP+ND+ A+E+AITD Sbjct: 128 RVIAMEKSFHGRTFATMAATGQDAIKKGFEPMMDGFDHVPFNDLEAVEKAITD------E 181 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 A++ E +Q EGGV Y +R +CD+ GILL+ DEVQ G+GRTG + ++ +G Sbjct: 182 TCAVLTEPIQAEGGVMVPFPGYLPGLRELCDKKGILLIFDEVQTGMGRTGALFAHQQMGA 241 Query: 261 EPDIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQEN 319 PDI T AKGLA G+PIGA + + A F PG HA+TFGG P AAA AV+ TL ++ Sbjct: 242 VPDIMTLAKGLANGLPIGAALATEEVASAFTPGAHATTFGGTPLVTAAARAVMITLMDQD 301 Query: 320 LLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGL 379 LLE + G+ + L L EK+ +VRG GL+ G++ L + + AME G Sbjct: 302 LLEMSISVGDYFKNQLLLLKEKFDCVEEVRGMGLLLGLK----LNMPGGPIAAKAMEMGY 357 Query: 380 LLAPAGPKVLRFVPPLIVSAAEINEAIALLDQTLA 414 + VLRFVPPLI++ +++ I LD+ LA Sbjct: 358 IFNVTQGDVLRFVPPLIITRKDVDGLIETLDKILA 392 Lambda K H 0.319 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: 443 Number of extensions: 19 Number of successful extensions: 5 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: 418 Length of database: 395 Length adjustment: 31 Effective length of query: 387 Effective length of database: 364 Effective search space: 140868 Effective search space used: 140868 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: 50 (23.9 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