Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000025485.1:WP_043795594.1 Length = 392 Score = 346 bits (888), Expect = e-100 Identities = 184/387 (47%), Positives = 250/387 (64%), Gaps = 11/387 (2%) Query: 24 VMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHH 83 +M TY R PV +GEG LWDT GK YLD ++GIA C LGHAHPA+ A+ Q +L H Sbjct: 5 LMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIH 64 Query: 84 ISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVIL 143 SN+Y + EQ L + E + D+VFF NSGAEANEAAIKL R +AH +E P IL Sbjct: 65 TSNIYGVAEQERLGALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRG--IENPAIL 122 Query: 144 SAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVAA 203 A+ SFHGRTLAT++ATG K Q F+PL GF VPY+D+ A+E A T+ + A Sbjct: 123 VAEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATN----RPNIVA 178 Query: 204 IMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEPD 263 I++E +QGEGG+R +Y +R ICD +G LL+LDE+Q G+GRTG+ + +++ GI+PD Sbjct: 179 ILIEPIQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPD 238 Query: 264 IFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLLE 322 + T AKGL G+PIGA + + + A VF+PG H STFGGNP +C AV+ETL ENL E Sbjct: 239 VVTLAKGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRVGRAVLETLIDENLTE 298 Query: 323 NVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLLA 382 N A+G L L+ + ++RG GL+ G+E L+ E+V A++ GLL+ Sbjct: 299 NAAAQGAYLLDSLRAALGETHGLVEIRGRGLMVGIE----LDRPCGELVGRALDAGLLIN 354 Query: 383 PAGPKVLRFVPPLIVSAAEINEAIALL 409 +V+R +PPLI+ A+I+E +A L Sbjct: 355 VTAERVIRLLPPLIIDRAQIDELVATL 381 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: 435 Number of extensions: 20 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: 392 Length adjustment: 31 Effective length of query: 387 Effective length of database: 361 Effective search space: 139707 Effective search space used: 139707 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 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