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_052717833.1 OLEAN_RS03755 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000967895.1:WP_052717833.1 Length = 294 Score = 144 bits (362), Expect = 5e-39 Identities = 89/285 (31%), Positives = 136/285 (47%), Gaps = 29/285 (10%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAY 83 PI+ + + C + +G +YLD GIAV N GH H + AA+ Q KL H V Sbjct: 26 PIYFSKGKGCWLTSDDGIDYLDAISGIAVTNLGHTHAAINAALVEQTNKLWHVSNTVHIQ 85 Query: 84 EPYL---ELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSG-----TIAFS 135 E L +LC + N +G+EA E A+K+AR + G I S Sbjct: 86 EQQLLGEKLCHLANMD-------NAFFCNSGAEANETALKLARLHGHKKGIKNPLVIVMS 138 Query: 136 GAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDA 195 GA+HGRT L+ T N L+ G + P + ++ D + + Sbjct: 139 GAFHGRTLAMLSATDSPNARHGFGPLVEGFL-----ELPFNDMNALDNLGENKK------ 187 Query: 196 APEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAME 255 DI A++IEP+QGE G +SP ++ +L +C ++ +L+ DE+QSG GRTG+ F+ + Sbjct: 188 ---DIVAVLIEPIQGESGVRIASPEYLNKLSTMCSDNDWLLMLDEIQSGIGRTGSWFSYQ 244 Query: 256 QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300 + PD+ T AK++ GFP+ + PG G T+ G Sbjct: 245 NFNLKPDIITLAKALGNGFPIGACLASGKAASLFTPGSHGSTFTG 289 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: 297 Number of extensions: 13 Number of successful extensions: 4 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: 294 Length adjustment: 29 Effective length of query: 397 Effective length of database: 265 Effective search space: 105205 Effective search space used: 105205 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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