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_010532043.1 ON01_RS16140 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000224785.1:WP_010532043.1 Length = 450 Score = 357 bits (915), Expect = e-103 Identities = 183/427 (42%), Positives = 260/427 (60%), Gaps = 7/427 (1%) Query: 5 KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64 KEL++RR A+P GV P F + A+ + D++G ++DFAG I V N GH H VV Sbjct: 18 KELLERRHNAVPHGVSYGTPTFVESAKGALLKDIDGNHFIDFAGAIGVNNVGHSHDTVVN 77 Query: 65 AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124 A++ Q K HT F V+ Y+ Y+EL E + PG F KK + + +G+EA ENAVKIAR Sbjct: 78 ALQDQAPKYIHTGFNVMMYDSYVELAEKLADLSPGSFDKKVMFLNSGAEANENAVKIARK 137 Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH---GISE- 180 T R ++ +G +HGRT +++TGKV PY G VY A +P G+SE Sbjct: 138 YTGRQAVVSVTGGFHGRTLLAMSMTGKVKPYKYEYGPFAPEVYHAPFPYNYRRPDGMSEE 197 Query: 181 ---DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237 D+ + + F + P +AA +EPVQGE GF + F+Q + LC +HGI+ I Sbjct: 198 AYTDELLKRVKDFFITEVDPSQVAAFFMEPVQGESGFIIPNKKFVQGVYELCKQHGILFI 257 Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297 ADE+Q+G GRTG FAM+ GV PDL T +KS+A G P++G+ GR EVMD G LGGT Sbjct: 258 ADEIQTGFGRTGKYFAMDHFGVEPDLVTVSKSMAAGLPISGIIGRQEVMDFAQKGELGGT 317 Query: 298 YAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAI 357 Y G P+ C A L VL+V E+ENL +A +G+K+ + + + IGD RGLGAM A+ Sbjct: 318 YCGTPLGCRAGLAVLEVMEKENLNDRAVKIGEKVMEKFGKMYDCFDAIGDYRGLGAMCAL 377 Query: 358 ELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417 E +D D +PD LT +++ AR++GLI L+ G + NV+R+L+PL D Q+ +GL+I+ Sbjct: 378 EFVKDRDTKEPDKALTGQVLKEARERGLIALNAGVFDNVVRLLMPLVTTDEQLEEGLDIL 437 Query: 418 SQCFDEA 424 + + A Sbjct: 438 EEAIEAA 444 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: 513 Number of extensions: 21 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: 450 Length adjustment: 32 Effective length of query: 394 Effective length of database: 418 Effective search space: 164692 Effective search space used: 164692 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