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 Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 196 bits (498), Expect = 1e-54 Identities = 134/406 (33%), Positives = 195/406 (48%), Gaps = 41/406 (10%) Query: 21 QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80 ++ P+ R E C + G YLDFA GIAV GH HP+ A+ Q L H Sbjct: 14 EVRPV---RGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHV--SN 68 Query: 81 LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAF 134 L P E + + V FA +G EA+E A+K AR +R I F Sbjct: 69 LYGSPQGEA--LAQRIVDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITF 126 Query: 135 SGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194 A+HGR+ ++ T + L+PG Y + +D +I +I Sbjct: 127 KNAFHGRSIGAISATDQPKMRDGFEPLLPGFDY----------VKFNDLEGAIAKI---- 172 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 ++ A ++E VQGEGG A + F+Q LR CDEHG++LI DE+Q G GRTG ++A Sbjct: 173 --DDETAGFLVETVQGEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAY 230 Query: 255 EQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKV 314 E G+ PD+ T AK I GFPL E + G G TY GNP+A A VL V Sbjct: 231 EHYGITPDILTAAKGIGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDV 290 Query: 315 FEQENLLQKANDLGQKLKDGLLAIAEKHPEIGD-VRGLGAMIAIELFEDGDHNKPDAKLT 373 + + +G++L+ G + H + D +RG G M+ I+L E ++ Sbjct: 291 MLEPGFFEHVEKMGERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPA--------VS 342 Query: 374 AEIVARARDK-GLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIS 418 + VA R+ GL+ ++ G NV R+L PL IE++ I + +E +S Sbjct: 343 RDFVAHLRENHGLLTVAAGE--NVFRVLPPLVIEESHIAECIEKLS 386 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: 446 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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