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_017753040.1 PN53_RS10390 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000816635.1:WP_017753040.1 Length = 459 Score = 343 bits (881), Expect = 5e-99 Identities = 179/426 (42%), Positives = 258/426 (60%), Gaps = 7/426 (1%) Query: 4 NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63 +KEL+ +R + + +GVG PIF D A+ + D++G ++DFAG I V N GH VV Sbjct: 18 SKELISKRQKYVAKGVGCSAPIFVDEAKGALIKDIDGNVFVDFAGAIGVQNIGHRDDGVV 77 Query: 64 AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123 AV+AQL K H F V YEPY+ L E + + PGD+AKK + +G+EAVENA+KIAR Sbjct: 78 EAVKAQLDKYIHPSFHVNMYEPYINLAEKLVEVTPGDYAKKAMFANSGAEAVENAIKIAR 137 Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRA----LYPCPLHGIS 179 A TK++G I+ G++HGRT+ T+++T K PY G G Y+ Y CPL Sbjct: 138 AYTKKAGVISLQGSFHGRTNMTMSITSKYKPYKNGFGPFSTETYKTDAAYCYRCPLGCKY 197 Query: 180 EDDAIASIHRI---FKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIML 236 + IA ++ K + + IA ++ EPVQGEGGF + + L+ +C+E+GI+ Sbjct: 198 PECGIACAEKLRTMLKTVISSDMIACLIAEPVQGEGGFVVPPKEYFKILQEICNENGIVF 257 Query: 237 IADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG 296 I DEVQ+G RTG LFA E V D+ T +KSIA G PL+ V G+AE+MDA GG+GG Sbjct: 258 IIDEVQAGFARTGKLFAHEHFDVEADIVTMSKSIANGIPLSAVVGKAEIMDAACVGGIGG 317 Query: 297 TYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIA 356 TY G+P+ CVAAL+V++ + + L K+ +G+ + L A+ EK+ IGDVRGLG+MI Sbjct: 318 TYGGSPLGCVAALKVIEKIKNDKLCDKSRKMGEYIIKRLNAMKEKYDVIGDVRGLGSMIG 377 Query: 357 IELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416 +E +D +P +L +I G+I L+ G + NV+R L PL I Q+ GL + Sbjct: 378 LEFVKDRVTKEPYGELVKQITEYCFKHGVIFLNAGLFGNVVRFLPPLVITKEQLDYGLNV 437 Query: 417 ISQCFD 422 + + D Sbjct: 438 LDKAID 443 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: 498 Number of extensions: 17 Number of successful extensions: 2 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: 459 Length adjustment: 32 Effective length of query: 394 Effective length of database: 427 Effective search space: 168238 Effective search space used: 168238 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