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_057509163.1 ABB28_RS13760 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:P94427 (436 letters) >NCBI__GCF_001431535.1:WP_057509163.1 Length = 426 Score = 144 bits (363), Expect = 5e-39 Identities = 96/307 (31%), Positives = 157/307 (51%), Gaps = 30/307 (9%) Query: 35 KGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIHPGFNVMMYPTYIE 94 + +GA L+D+DG R+ID+ G+ G + VGH+HP V +AVK+ A+ + G + Sbjct: 40 RADGAYLHDVDGNRYIDYVGSWGPMIVGHNHPAVRQAVKKAADSGLSFG---APCAAEVT 96 Query: 95 LAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFTRGFHGRTNMTMSM 154 +AE L + P + + NSG EA +A+++AR T R +V F +HG + + Sbjct: 97 MAETLTRLVPSCEMVRMV--NSGTEATLSAIRLARGATGRSRIVKFEGCYHGHGDSFL-- 152 Query: 155 TSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFFIAS----VAP 210 K G G V +P PAG+S+ + + +NDF A+ Sbjct: 153 ------VKAGSGMLTLGVPTSP-----GVPAGLSELT----LTLPYNDFDAATALFEAQG 197 Query: 211 ETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTYFAIEHF 270 E +A +++EPV G I P + ++QH+ + C G V + DE+ TGF R A H+ Sbjct: 198 EQIAGLIIEPVVGNANCIPPREGYLQHLRALCTRFGTVLIFDEVMTGF-RVALGGAQAHY 256 Query: 271 DVVPDLITVSKSLAAGLPLSGVIGRAEM---LDAAAPGELGGTYAGSPLGCAAALAVLDI 327 V PDL T K + G+P+ G+ E+ + A P GT +G+P+ AA LA+L++ Sbjct: 257 GVTPDLTTFGKIIGGGMPVGAYGGKRELMQQISPAGPIYQAGTLSGNPVAMAAGLAMLEL 316 Query: 328 IEEEGLN 334 +++ G + Sbjct: 317 VQQPGFH 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: 22 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: 426 Length adjustment: 32 Effective length of query: 404 Effective length of database: 394 Effective search space: 159176 Effective search space used: 159176 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