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_011372884.1 SUDEN_RS06570 aspartate aminotransferase family protein
Query= curated2:P94427 (436 letters) >NCBI__GCF_000012965.1:WP_011372884.1 Length = 394 Score = 173 bits (438), Expect = 1e-47 Identities = 127/407 (31%), Positives = 205/407 (50%), Gaps = 53/407 (13%) Query: 34 VKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIHPGFNVMMYPTYI 93 V G A + D +G+++IDFA I +VGH++ +V +A+ +Q + H N+ Sbjct: 24 VSGNNAIVVDANGKKYIDFASGIAVCSVGHANKRVNDAICKQLSNITHTS-NLYYIAPQA 82 Query: 94 ELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQG------VVSFTRGFHGR 147 + A+K+ + ++ K F NSGAEA E A+KIARK+ ++ G V++ FHGR Sbjct: 83 KAAQKI--VEASGYDMKCFFGNSGAEANEGAIKIARKFGEKDGELKRYKVITLQHSFHGR 140 Query: 148 TNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFFIAS 207 T T+ T + K + + FGP Y D + A N +AS Sbjct: 141 TITTVKATGQEKMHNY-FGP------------------------YPDGFVYADNIDHVAS 175 Query: 208 VAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTYFAI 267 + + V++E VQGEGG + VQ +A F KE ++ + DE+QTG RTG + A Sbjct: 176 LVDDHTCAVMIELVQGEGGVQPLDRDSVQKLAKFLKEKNVLLIIDEVQTGIYRTGKFLAS 235 Query: 268 EHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALAVLDI 327 ++D+ PD++T++K L G+P+ V+ + D G+ G T+ G+ L AA V+DI Sbjct: 236 NYYDIKPDVVTLAKGLGGGVPIGVVM--TTLKDVFGAGDHGSTFGGNFLSTTAACEVVDI 293 Query: 328 IEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRR----LGAMAAIEIVKDPDTREPDK 383 + E +NE S E+ K I+ E ++ + DI +G M + VKD DT Sbjct: 294 LNE--MNE-SGELQKGIDYFDSELEKFYNAHRDIFTSKVGIGMMCGLR-VKDGDT----- 344 Query: 384 TKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSIL 430 I + A + G+++L AG + +R L L I+ ++EG + L Sbjct: 345 --LTKIISNAREEGVIVLKAG--RDTLRLLPALTITKEEIDEGFTSL 387 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: 375 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: 436 Length of database: 394 Length adjustment: 31 Effective length of query: 405 Effective length of database: 363 Effective search space: 147015 Effective search space used: 147015 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 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