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_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:P94427 (436 letters) >NCBI__GCF_002869505.1:WP_084199387.1 Length = 467 Score = 216 bits (549), Expect = 2e-60 Identities = 139/420 (33%), Positives = 216/420 (51%), Gaps = 15/420 (3%) Query: 22 SKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIH 81 SKG + + + EG ++DLDG ++IDF T +G+ HP+++EAV + Sbjct: 36 SKGYVPPAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQRQY-- 93 Query: 82 PGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFT 141 GF +P I LAE+L I P + F SG EA E+A+ +A +T+R+ +VSFT Sbjct: 94 -GFQ-WEHPLRIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLALCHTQRRYIVSFT 151 Query: 142 RGFHGR---TNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQ 198 FHG T M + S Y G+ A V +APFPY + PAGM Y + + Sbjct: 152 SCFHGEGLGTKMVSAYNSDNNLYMEGW---AGGVLKAPFPYSEEIPAGMDQAQYTEYCLW 208 Query: 199 AFNDFFIASVAP-ETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTG 257 V P E +A +++EP EGG IPSK F+Q + C + + +ADE+ TG Sbjct: 209 YIETHLTEYVVPAENIAAILVEPGLAEGGNWIPSKAFMQGLRRICDKFDWLLIADEVLTG 268 Query: 258 FARTGTYFAIEHFDVVPDLITVSKSLAAGL-PLSGVIGRAEMLDAAAPGELGGTYAGSPL 316 RTGT +A+EHFDVVPD++ K+L+ G+ P +GV R E+L G T+AG+P Sbjct: 269 LGRTGTMWAVEHFDVVPDILVAGKNLSGGIEPCAGVAARDEILGDNPRATAGSTFAGTPG 328 Query: 317 GCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKDP 376 GCAAAL L+I E + + ++ + + + +W+ + + +R LG + + Sbjct: 329 GCAAALKTLEIYERDAVLTHTQHLAGVAMQRMSDWESRYEIVSQVRGLGLLLGVSFRAGR 388 Query: 377 DTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAGLRA 436 + E D A ++ + GL + N +R L +++ +L EGLS +E + A Sbjct: 389 EDIE-DFHIARSVRDEMLKRGLWAICD--NEPQVRMYPALNMAEDVLLEGLSRMEEAIEA 445 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: 467 Number of extensions: 23 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: 467 Length adjustment: 33 Effective length of query: 403 Effective length of database: 434 Effective search space: 174902 Effective search space used: 174902 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