Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate AZOBR_RS27880 AZOBR_RS27880 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__azobra:AZOBR_RS27880 Length = 438 Score = 168 bits (426), Expect = 3e-46 Identities = 122/397 (30%), Positives = 200/397 (50%), Gaps = 21/397 (5%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLS-HTCFQVLA 82 PI R E ++D EG YLD +A + GH P+VV A+ Q L+ HT + Sbjct: 41 PIHVVRGEGSSLYDAEGNRYLDAYNNVA--SVGHSRPEVVEAMARQAAVLNTHTRYLT-- 96 Query: 83 YEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRT 142 + L+ E + P + + +L TGSEA + A+++AR T +G + AYHG T Sbjct: 97 -DGILDFAEAFLAEFPAELSH-LMLTCTGSEANDLALRVARVHTGGTGVVIAHNAYHGVT 154 Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKN---DAAPED 199 + +++P S G + G R + + + E + A+ R + D + Sbjct: 155 ----SALAEMSP-SLGAAVKLGDHVRVVPAPDGYRMPEAEVGAAFARSVEEAIADLREKG 209 Query: 200 I--AAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGT-LFAMEQ 256 I AA++++ + G + F+ + + G + IADEVQ G GR GT ++ + Sbjct: 210 ITPAALLVDTIFSSSGVFTDPAGFLAPAVEVMRKAGGVFIADEVQPGFGRLGTHMWGFAR 269 Query: 257 MGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGG-LGGTYAGNPIACVAALEVLKVF 315 G+ PD+ T K + G P+AG R EV++A T+ GNP++C AL VL+V Sbjct: 270 HGLVPDIVTVGKPMGNGHPVAGAVFRPEVIEAFGKSQRYFNTFGGNPVSCAVALAVLRVI 329 Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375 +++ L + A +G ++ DGL A+A KH IGDVRG G I +E+ D P ++ TA Sbjct: 330 KEDRLQENALTVGTEMIDGLRALAAKHELIGDVRGSGLFIGVEMVRDRKLKTPASEETAR 389 Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTI--EDAQI 410 +V R + +++ + G ++L+I PL EDA++ Sbjct: 390 VVNGMRQRRVLISATGQEGHILKIRPPLVFSSEDAKL 426 Lambda K H 0.320 0.137 0.401 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: 472 Number of extensions: 27 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: 426 Length of database: 438 Length adjustment: 32 Effective length of query: 394 Effective length of database: 406 Effective search space: 159964 Effective search space used: 159964 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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