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_078716203.1 B5D49_RS03155 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_900167125.1:WP_078716203.1 Length = 433 Score = 415 bits (1066), Expect = e-120 Identities = 215/425 (50%), Positives = 282/425 (66%), Gaps = 9/425 (2%) Query: 1 MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60 M SN +L++RR +AIP+G + P FA +A + DVEGREY+DFAGGI V+NTGH HP Sbjct: 1 MVSNNDLLRRRQEAIPQGPANMLPAFAAQARGATITDVEGREYIDFAGGIGVVNTGHCHP 60 Query: 61 KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120 KVV AV+ Q +K HTCF V+ YE Y+EL E +N PGDFAKK+ + +G+EAVENAVK Sbjct: 61 KVVRAVQEQAEKFLHTCFHVVMYEGYVELAERLNALAPGDFAKKSFFLNSGAEAVENAVK 120 Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRA----LYPCPLH 176 IAR T R IAF +HGR+ T++LT KV PY G VYRA Y CPL Sbjct: 121 IARYETGRPAVIAFQNGFHGRSLLTMSLTSKVKPYKYRFGPFAPEVYRAPYAYCYRCPL- 179 Query: 177 GISEDDAIAS----IHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEH 232 G++ A+ + F + A E AA+V+EP+QGEGGF P + RLR++CD++ Sbjct: 180 GLTHPACGAACADYLEEFFVSHVAAERTAALVVEPIQGEGGFATPPPEYFPRLRSICDKY 239 Query: 233 GIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPG 292 GI LI DEVQSG GRTGTLFA+E GVAPD+ T AKS+AGG PL+GV GRAE+MDA G Sbjct: 240 GIRLIVDEVQSGFGRTGTLFAIEHWGVAPDMITVAKSLAGGMPLSGVVGRAEIMDAPHVG 299 Query: 293 GLGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLG 352 GLGGTY G+P AC AAL VL + ++ LL +A +LG+ ++ ++ +GDVRGLG Sbjct: 300 GLGGTYGGSPTACAAALAVLDILLEDGLLHRAQELGRHVRKVFDGFQQEFEIVGDVRGLG 359 Query: 353 AMIAIELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQ 412 M+A+EL +D P A +VA R +GLI+L+CG + NV+R L+PL I D ++ + Sbjct: 360 PMLALELVQDRQTKTPAADKAKALVAHCRAQGLIILACGNFGNVIRTLMPLVITDQELDR 419 Query: 413 GLEII 417 GL I+ Sbjct: 420 GLSIL 424 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: 531 Number of extensions: 27 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: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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