Align 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 Dsui_0664 Dsui_0664 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:P63505 (449 letters) >FitnessBrowser__PS:Dsui_0664 Length = 427 Score = 117 bits (292), Expect = 9e-31 Identities = 103/332 (31%), Positives = 150/332 (45%), Gaps = 36/332 (10%) Query: 39 PVFVARAGGGIVEDVDGNRLIDLGSGIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPY 98 P F R G V D +G +D +G++ V AV+ A P Sbjct: 34 PRFFTRGEGPRVWDAEGKSYLDYVGSWGPLILGHAHAPTVKAVQEAAALGLS---FGAPT 90 Query: 99 EGYVAVAEQLNRITPGSGPKRSVLFNSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTN 158 E + +A+ L I P R L +SG EA +A+++AR +TG+ +V F+ YHG ++ Sbjct: 91 EAEIEIADLLCDILPSLDMVR--LVSSGTEATMSAIRLARGHTGRDLLVKFEGCYHGHSD 148 Query: 159 LTMALTAKSMPYKSGFGPFA---PEIYRAPLSYPYRDGLLDKQLATNGELAAARAIGVID 215 S+ K+G G P P +L+ A +LA A A Sbjct: 149 --------SLLVKAGSGLLTFGNPSSGGVPADVAKHTLVLEYNNAE--QLAEAFA----- 193 Query: 216 KQVGANNLAALVIEPIQGEGGFIVPAEGFLPALLDWCRKNHVVFIADEVQTGFARTGAMF 275 KQ + +AA+++EP+ G I P F+ A+ + C K+ V I DEV TGF R G Sbjct: 194 KQ--GSEIAAVIVEPVAGNMNLIAPKPEFMQAMRELCSKHGAVLIFDEVMTGF-RVGPQC 250 Query: 276 ACEHEGPDGLEPDLICTAKGIADGLPLSAVTGRAEIMNAPHVGGLG-----GTFGGNPVA 330 A +G G+ PDL K I G+P++A G+ EIM + LG GT GNPVA Sbjct: 251 A---QGLFGITPDLTTLGKVIGGGMPVAAFGGKREIME--KIAPLGPVYQAGTLSGNPVA 305 Query: 331 CAAALATIATIESDGLIERARQIERLVTDRLT 362 AA L T+ + G + + +TD LT Sbjct: 306 VAAGLVTLKATRAPGFYDSLAARTKQLTDGLT 337 Lambda K H 0.319 0.137 0.397 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: 512 Number of extensions: 32 Number of successful extensions: 4 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: 449 Length of database: 427 Length adjustment: 32 Effective length of query: 417 Effective length of database: 395 Effective search space: 164715 Effective search space used: 164715 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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