Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_046010708.1 OLEAN_RS01080 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:P94427 (436 letters) >NCBI__GCF_000967895.1:WP_046010708.1 Length = 434 Score = 154 bits (390), Expect = 4e-42 Identities = 107/323 (33%), Positives = 169/323 (52%), Gaps = 35/323 (10%) Query: 23 KGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIHP 82 KGV G +GEG+ L+D DG R+ID+ G+ G + +GH+ V+EAVK + ++ + Sbjct: 27 KGVG-GTPIFFERGEGSCLFDADGNRYIDYVGSWGPMIMGHARGDVIEAVKARLDQGLSF 85 Query: 83 GFNVMMYPTYIEL--AEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSF 140 G PT IE+ A+ +CGI PG + + NSG EA +A+++AR +T R +V F Sbjct: 86 GA-----PTEIEIDMAQTVCGIMPGMDMVRMV--NSGTEATMSAIRLARGFTGRDKLVKF 138 Query: 141 TRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAF 200 +HG + + K G G V +P PAG ++ D + + Sbjct: 139 EGCYHGHADSLL--------VKAGSGALTLGVPSSP-----GVPAGAAN----DTITLDY 181 Query: 201 NDFFIASVA----PETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQT 256 ND + +AC+++E V G I PSK F+Q + C ++G V + DE+ T Sbjct: 182 NDIDDVKACFAEQGDKIACIIVEAVAGNMNCIPPSKEFLQGLRDVCDQYGAVLIFDEVMT 241 Query: 257 GFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAP-GEL--GGTYAG 313 GF R A ++DV PDL T+ K + GLP+ G+ E+++ AP G + GT +G Sbjct: 242 GF-RVSLTGAQGYYDVQPDLTTLGKVIGGGLPVGAFGGKREIMEYLAPIGPVYQAGTLSG 300 Query: 314 SPLGCAAALAVLDIIEEEGLNER 336 +PL AA LA++ +++ GL E+ Sbjct: 301 NPLAMAAGLAMMKSVQQPGLYEQ 323 Lambda K H 0.319 0.136 0.393 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: 462 Number of extensions: 25 Number of successful extensions: 6 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: 436 Length of database: 434 Length adjustment: 32 Effective length of query: 404 Effective length of database: 402 Effective search space: 162408 Effective search space used: 162408 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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