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 Ac3H11_3991 Glutamate-1-semialdehyde aminotransferase (EC 5.4.3.8)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3991 Length = 434 Score = 146 bits (369), Expect = 1e-39 Identities = 112/358 (31%), Positives = 166/358 (46%), Gaps = 39/358 (10%) Query: 4 NKELMQRRSQAIPRGVGQI---------HPIFADRAENCRVWDVEGREYLDFAGGIAVLN 54 N L +R IP GV P F RA+ WD + ++D+ G + Sbjct: 8 NIPLFERAKALIPGGVNSPVRAFKAVGGTPRFVKRAQGAYFWDANDQRFIDYIGSWGPMI 67 Query: 55 TGHLHPKVVAAVE-AQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSE 113 GH HP V+ AV+ A L+ S E +EL E + VP + LV++G+E Sbjct: 68 LGHGHPAVLEAVQSAALEGFSFGA----PTEREVELAEEILGLVPS--MEMIRLVSSGTE 121 Query: 114 AVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKV-----NPYSAGMGLMPGHVYR 168 A +A+++AR AT RS I F G YHG L G N SAG+ P V + Sbjct: 122 AGMSAIRLARGATGRSKFIKFEGCYHGHADSLLVKAGSGLATFGNATSAGV---PPEVVQ 178 Query: 169 ALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRAL 228 + +++ + ++H +++A ++IEP+ G +S FM+R R L Sbjct: 179 HTIVLEYNNVAQLEEAFALHG--------KELACVMIEPIAGNMNLVRASVPFMKRCREL 230 Query: 229 CDEHGIMLIADEVQSG----AGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAE 284 C EHG +L+ DEV +G G +++A G PDLT K I GG PLA G Sbjct: 231 CTEHGALLVLDEVMTGFRVALGSAQSVYAKSIPGFKPDLTVLGKVIGGGMPLAAFGGPRA 290 Query: 285 VMDAVAP-GGL--GGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIA 339 +M+ +AP GG+ GT +GNP+A L L+ ++ + + L DGL A A Sbjct: 291 IMEHLAPLGGVYQAGTLSGNPVATACGLATLREIKKPGFFDALSARTRSLVDGLAAAA 348 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: 476 Number of extensions: 28 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: 434 Length adjustment: 32 Effective length of query: 394 Effective length of database: 402 Effective search space: 158388 Effective search space used: 158388 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