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 RR42_RS27380 RR42_RS27380 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS27380 Length = 435 Score = 180 bits (457), Expect = 7e-50 Identities = 123/391 (31%), Positives = 193/391 (49%), Gaps = 15/391 (3%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLS-HTCFQVLA 82 P+ R + ++D G YLD +A + GH HP+VV A+ Q +L+ HT + Sbjct: 32 PLHIVRGDGVWLYDANGERYLDAYNNVA--SVGHCHPQVVQAIARQAAQLNTHTRY---L 86 Query: 83 YEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRT 142 +E L+ + + +P D +L TGSEA + A++IARA T G I AYHG T Sbjct: 87 HEGILDYAQRLLATMP-DALGHAMLTCTGSEANDLAMRIARAHTGAQGLIITRFAYHGVT 145 Query: 143 HYTLALTGKVNPY---SAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPED 199 + + Y + +P + P L + + +I + + P Sbjct: 146 ASIAEASPSLGRYVKLGDNVRTVPAPDSYRVVPAQLGAVFAEGVRHAIEDLRAHGIRP-- 203 Query: 200 IAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLF-AMEQMG 258 AA++++ V G + P F++ A G + IADEVQ G GRTG F ++ G Sbjct: 204 -AALLVDTVFSSDGIFTDPPGFLKDAVAAIRAAGGVFIADEVQPGLGRTGEAFWGFQRHG 262 Query: 259 VAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPG-GLGGTYAGNPIACVAALEVLKVFEQ 317 V PD+ T K + G PLAG+ R EV++A T+ GNP++ A + VL V EQ Sbjct: 263 VVPDIVTMGKPMGNGHPLAGLAVRPEVLEAFGRECRYFNTFGGNPVSVAAGMAVLDVIEQ 322 Query: 318 ENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIV 377 L+ + +G+ L++ L +A + P IGD+RG G +A+E EDGD +P TA IV Sbjct: 323 TQLMAQVRRVGKYLRERLAGVAARRPLIGDIRGAGLFVAVEFVEDGDAARPATARTARIV 382 Query: 378 ARARDKGLILLSCGPYYNVLRILVPLTIEDA 408 R + +++ + G N+L+I P+ +A Sbjct: 383 NGLRRRHVLVGATGEAANILKIRPPMVFTEA 413 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: 462 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 435 Length adjustment: 32 Effective length of query: 394 Effective length of database: 403 Effective search space: 158782 Effective search space used: 158782 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