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 WP_005458846.1 SACCYDRAFT_RS19655 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000244975.1:WP_005458846.1 Length = 418 Score = 299 bits (765), Expect = 1e-85 Identities = 157/401 (39%), Positives = 228/401 (56%), Gaps = 8/401 (1%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q P+ D E ++D GR +LDF GI V +TGH HP+VVAA + Q+ KL H + Sbjct: 10 QATPVVVDHGEGAYLYDTSGRRHLDFTAGIGVTSTGHCHPRVVAAAQEQVGKLIHGQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + + P LEL E + + +P +GSEAVE A+++ R AT R + F G +HG Sbjct: 70 VMHRPLLELSERLGEVLPKGL-DSLFFANSGSEAVEAALRLTRQATGRPNVVVFQGGFHG 128 Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH-----GISEDDAIASIHRIFKNDA 195 RT ++T +SAG + G V+ A +P H + + A+ + +F Sbjct: 129 RTVAAASMTTSGTRFSAGFSPLMGGVHVAPFPYAYHYGWDERTATEFALRELDYLFATQT 188 Query: 196 APEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAME 255 +P++ AA +EP+ GEGG+ ++ FM LR DEHGI+L+ DE+Q+G GRTG + E Sbjct: 189 SPQETAAFFVEPMLGEGGYVPANTEFMAGLRRRADEHGILLVVDEIQTGFGRTGRFWGHE 248 Query: 256 QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVF 315 V PD+ AK +A GFPL+G+ ++M PG GGTY GN ++C AA+ L V Sbjct: 249 HFDVRPDVVLIAKGLASGFPLSGIAASKDLMGKAWPGSQGGTYGGNAVSCAAAIATLDVI 308 Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375 +ENL++ A G++L DG A+ EK P IGDVRGLG ++ E F D KPD Sbjct: 309 REENLVENAAARGRQLLDGAKAVGEKTPGIGDVRGLGLLVGSE-FVTAD-GKPDGATAQA 366 Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416 + A +KGL+LL+CG + NV+R++ PL + QI + LEI Sbjct: 367 VQKAAAEKGLLLLTCGAFMNVVRMIPPLVVTAEQIDEALEI 407 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: 477 Number of extensions: 20 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: 426 Length of database: 418 Length adjustment: 32 Effective length of query: 394 Effective length of database: 386 Effective search space: 152084 Effective search space used: 152084 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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