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_037574263.1 BS73_RS19430 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000744815.1:WP_037574263.1 Length = 425 Score = 286 bits (733), Expect = 6e-82 Identities = 160/410 (39%), Positives = 237/410 (57%), Gaps = 18/410 (4%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 Q P+ A+R E +++ GR +LDF GI V +TGH HPKVVAA + Q+ +L H + Sbjct: 10 QATPVLAERGEGVYLYEESGRRHLDFTAGIGVTSTGHCHPKVVAAAQEQVGRLVHGQYTT 69 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140 + ++P L L E + + +P V +GSEAVE A+++A+ AT R + F G++HG Sbjct: 70 VMHKPLLTLSERLGEVLPAGL-DSLFFVNSGSEAVEAAMRLAKQATARPNIVVFQGSFHG 128 Query: 141 RTHYTLALTGKVNPYSAGMG-LMPGHVYRALYPCPLH----GISEDDA----IASIHRIF 191 RT ++T + +G G LMPG V A +P H G+ E+ A + + + Sbjct: 129 RTLAAASMTTSATKFRSGYGPLMPG-VAIAPFPHAAHYARYGMDEEAATRFALRELDELL 187 Query: 192 KNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTL 251 +AP D AA ++EPV GEGG+ ++ AF++ LR D HGI+LI DEVQ+G GRTG Sbjct: 188 ATVSAPADTAAFIVEPVLGEGGYVPANSAFLRGLRERADRHGILLILDEVQTGFGRTGRF 247 Query: 252 FAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEV 311 + + PD+ AK +A GFPL+ + +M+ PG GGTY GN +AC AA+ Sbjct: 248 WGHDHFDGRPDILVTAKGLASGFPLSAIAAPRALMEKAWPGSQGGTYGGNAVACAAAIAT 307 Query: 312 LKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-----IGDVRGLGAMIAIELFEDGDHN 366 L V ++E L++ A + G++L GL +A HP IGDVRGLG M E F D Sbjct: 308 LDVIQEEKLVENAAERGEQLFAGLREVAAAHPAGGRGGIGDVRGLGLMAGTE-FTTAD-G 365 Query: 367 KPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416 +PD A++ A A ++GL+LL+CGP V+R++ PL ++ QI +GL + Sbjct: 366 EPDGATAAKVHAAAAERGLLLLTCGPRGEVVRMIPPLVVDAEQIDEGLRL 415 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: 485 Number of extensions: 21 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: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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 Jul 26 2024. The underlying query database was built on Jul 25 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