Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_086511038.1 BZY95_RS16770 gamma-glutamyl-gamma-aminobutyrate hydrolase
Query= reanno::Koxy:BWI76_RS10705 (254 letters) >NCBI__GCF_002151265.1:WP_086511038.1 Length = 223 Score = 92.4 bits (228), Expect = 7e-24 Identities = 67/211 (31%), Positives = 99/211 (46%), Gaps = 25/211 (11%) Query: 34 AIVNAGGVPIALPHALAEPELLSALLPKLDGIYLPGSPSNVQPHLYG-ENGDEPDADPGR 92 A+ GG P+ L + P+ L DG+ + G ++Q HLYG E + DP R Sbjct: 25 AVWRHGGRPLRLSPSRPLPQAL-------DGLIIGGG-DDIQAHLYGGEVQLDVRLDPQR 76 Query: 93 DLLSMALIDAALERRIPIFAICRGLQELVVATGGTLYRRLFEQPELLEHREDPELPVEQQ 152 D L + L++ + + P+ ICRG Q L V GGTL ++ E L+ R + Sbjct: 77 DELELELMERFIPQGKPVLGICRGAQMLNVHLGGTLDPDIYTTHEGLKRR--------RT 128 Query: 153 YAPSHEVQVQEGGLLSQLIPGCNTFW--VNSLHGQGAKTTGPRLRVEARSPDGLAEAVSV 210 P V + L +++ W +NSLH Q + G + + AR DGL + + Sbjct: 129 VLPRKTVDIVADTQLRRIL---KVSWCRINSLHHQAVQEAGRGIEIVARDRDGLVQGIES 185 Query: 211 NDHPFALGVQWHPEW---NSSEYALSRMLFE 238 DH F +GVQWHPEW N + L R L + Sbjct: 186 RDHEFLIGVQWHPEWLIFNRPQQRLIRALVD 216 Lambda K H 0.318 0.137 0.415 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: 153 Number of extensions: 11 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: 254 Length of database: 223 Length adjustment: 23 Effective length of query: 231 Effective length of database: 200 Effective search space: 46200 Effective search space used: 46200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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