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_089302612.1 CHB84_RS16910 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_900188115.1:WP_089302612.1 Length = 422 Score = 280 bits (716), Expect = 6e-80 Identities = 159/404 (39%), Positives = 222/404 (54%), Gaps = 8/404 (1%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q P+ D E ++D GR +LDF GI V +TGH HPKVVAA + Q+ KL H + Sbjct: 10 QATPVEVDYGEGVYLYDHSGRRHLDFTAGIGVTSTGHCHPKVVAAAQEQVGKLIHGQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + ++P L E + +P +GSEAVE A+++AR AT R I F G +HG Sbjct: 70 VMHDPLRSLAERLGDVLPPGL-DSVFFANSGSEAVEAALRLARQATGRPNIIVFQGGFHG 128 Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPL-HGISEDDA----IASIHRIFKNDA 195 RT +LT + AG + V+ A +P +G E A + + +F + Sbjct: 129 RTVGAASLTTSGTRFRAGYAPLMDGVHVAPFPFAYRYGWDEATATRFALQELDYLFATMS 188 Query: 196 APEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAME 255 E+ AAI +EPV GEGG+ ++ F+ LR D+HGI+L+ADEVQ+G GRTG + ME Sbjct: 189 PGEETAAIFVEPVLGEGGYVPANREFLAGLRERADKHGILLVADEVQTGFGRTGKFWGME 248 Query: 256 QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVF 315 V PD+ AK +A GFPL+G+ E+M PG GGTY GN +AC AAL L V Sbjct: 249 HFDVQPDVVITAKGLASGFPLSGIAASTELMGKAWPGSQGGTYGGNAVACAAALATLDVI 308 Query: 316 EQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAE 375 ++E L+ A G +L +G IAEK P+IGDVRGLG M+ E PD A+ Sbjct: 309 QEEGLVNNAATQGARLLEGSRQIAEKFPQIGDVRGLGLMVGSEFVTADGRADPDTAKAAQ 368 Query: 376 IVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419 A ++GL+LL CG + N +R++ L + AQ+ L I S+ Sbjct: 369 --QAAAERGLLLLMCGAWMNTVRMIPALVVSGAQVDDALGIWSE 410 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: 458 Number of extensions: 18 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: 422 Length adjustment: 32 Effective length of query: 394 Effective length of database: 390 Effective search space: 153660 Effective search space used: 153660 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 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