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_164924739.1 NGR_RS30780 diaminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000018545.1:WP_164924739.1 Length = 424 Score = 181 bits (458), Expect = 5e-50 Identities = 123/401 (30%), Positives = 207/401 (51%), Gaps = 19/401 (4%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKK---LSHTCFQV 80 P+ ++A + D GRE++DF G VLN GH P + L+ + Sbjct: 28 PVVFEKAAGAILHDESGREFIDFLSGSGVLNYGHNDPYFLDEATQYLRSNGIIHGLDMAT 87 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 A ++E + + + G K TG+ AVE A+K+AR AT R ++F+ +HG Sbjct: 88 PAKREFMECFDAIILRPRGLTYKFQFCGPTGANAVEAALKLARKATGRHSIVSFTNGFHG 147 Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDI 200 + LA+TG Y G P V A P + +++D + ++ + ++ D+ Sbjct: 148 MSLGALAVTGN-RYYRDAAGFPPAGV--AFMPYDGYWGADNDTSEYLDKVLADASSGVDV 204 Query: 201 -AAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGV 259 AAI++E VQGEGG A+ ++Q ++ +C HGI+LI D++Q+G GR G F+ E G+ Sbjct: 205 PAAIILETVQGEGGINAARKEWLQSIQRICRSHGILLIVDDIQAGCGRAGNFFSFEFAGL 264 Query: 260 APDLTTFAKSIAG-GFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVL-KVFEQ 317 +PD+ +KSI+G G PL+ + + E +D PG GT+ GN +A V L K + Sbjct: 265 SPDVVVLSKSISGCGLPLSLLLLKPE-LDVWRPGEHNGTFRGNNLAFVTGAAALRKYWTN 323 Query: 318 ENLLQKANDLGQKLKDGLLAIAEKHPEIG-DVRGLGAMIAIELFEDGDHNKPDAKLTAEI 376 + L + + G+ + + L +A+ + VRG G M+ + N KL I Sbjct: 324 DALSARVMETGRIIAERLRQVAQTNRARSLSVRGRGMMLGL--------NCGTGKLAERI 375 Query: 377 VARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 V +A ++GL++ CG V+++L PLT ++ +R+GL+I+ Sbjct: 376 VRKAFEEGLVVERCGAEDQVIKLLPPLTTDEQTLRRGLDIL 416 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: 469 Number of extensions: 26 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: 424 Length adjustment: 32 Effective length of query: 394 Effective length of database: 392 Effective search space: 154448 Effective search space used: 154448 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