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 Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= curated2:P94427 (436 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 179 bits (454), Expect = 1e-49 Identities = 130/405 (32%), Positives = 206/405 (50%), Gaps = 48/405 (11%) Query: 34 VKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIHPGFNVMMYPTYI 93 VK G+ ++D G ++D G +++GHSHP + +K Q + + N + P Sbjct: 15 VKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYS-NSVQIPIQK 73 Query: 94 ELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFTRGFHGRTNMTMS 153 ELA KL G G + NSGAEA ENA+K+A T ++G ++FT+GFHGRT+ ++ Sbjct: 74 ELATKL-GQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTSGAVA 132 Query: 154 MTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFFIAS--VAPE 211 +T K APF +++ + I FND +A Sbjct: 133 LTDNPKII-------------APF------------NAHEGVHILPFNDLEAVEKQLATG 167 Query: 212 TVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTYFAIEHFD 271 T+A V++E +QG GG +P F+ +++ K++G + DE+Q+G+AR+G +FA + + Sbjct: 168 TIAGVIVEGIQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVE 227 Query: 272 -VVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALAVLDIIEE 330 + PDLITV+K + G P+ GV+ E A+ G LG T+ G+ L CAAALAVL++I+E Sbjct: 228 GLKPDLITVAKGMGNGFPIGGVLISPEF--KASHGLLGTTFGGNHLACAAALAVLEVIDE 285 Query: 331 EGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKDPDTREPDKTKAAAI- 389 E L + E GK I ++ + ++R G M ++ T+A + Sbjct: 286 ENLITAAAENGKAIMAAL----EKVAGVTEVRGKGLMIGFDLA----------TEAGPVR 331 Query: 390 AAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAGL 434 AA +++ + +AG + IR L PL I L L LE L Sbjct: 332 AALIHEHKIFTGSAG-GKHTIRLLPPLNIEPKALTLFLEKLETVL 375 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: 438 Number of extensions: 25 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: 436 Length of database: 381 Length adjustment: 31 Effective length of query: 405 Effective length of database: 350 Effective search space: 141750 Effective search space used: 141750 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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