Align Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_089136150.1 CES79_RS01915 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
Query= reanno::Koxy:BWI76_RS10705 (254 letters) >NCBI__GCF_002217945.1:WP_089136150.1 Length = 239 Score = 132 bits (332), Expect = 6e-36 Identities = 86/242 (35%), Positives = 123/242 (50%), Gaps = 14/242 (5%) Query: 5 MYKPVIGVVMCRNRLKGHQTQTLQEKYLNAIVNAGGVPIALPHALAEPELLSALLPKLDG 64 M KP+IG+ R + G ++ + + A+V AGGVP+ +P E +L + +DG Sbjct: 1 MAKPIIGIPAERRLVDGSYLNSVNQGEVAAVVKAGGVPVLIP--TRESDLATNYSQLIDG 58 Query: 65 IYLPGSPSNVQPHLYGENGDEP-----DADPGRDLLSMALIDAALERRIPIFAICRGLQE 119 + LPG +V P YGE EP +D D +AL + A+ PI ICRG Q Sbjct: 59 LLLPGGV-DVAPRFYGE---EPLPKMAASDDRLDATEIALTNQAVTAGKPILGICRGTQV 114 Query: 120 LVVATGGTLYRRLFEQPELLEHREDPELPVEQQYAPSHEVQVQEGGLLSQLIPGCNTFWV 179 L VA GG LY+ + Q + ++ + +Q +H + V EG LL + G V Sbjct: 115 LNVALGGNLYQDIGTQVDHQTYQHSQKASFDQG---THYIDVAEGSLLQGIFQGQQHVLV 171 Query: 180 NSLHGQGAKTTGPRLRVEARSPDGLAEAVSVNDHPFALGVQWHPEWNSSEYALSRMLFEG 239 NSLH Q KT P+L++ A++ DG+ E V D + VQWHPE E AL +FE Sbjct: 172 NSLHHQAIKTPAPQLKITAKASDGIIECVESKDSNLIVAVQWHPELMFKEDALQFAIFED 231 Query: 240 FI 241 FI Sbjct: 232 FI 233 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: 163 Number of extensions: 9 Number of successful extensions: 3 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: 239 Length adjustment: 24 Effective length of query: 230 Effective length of database: 215 Effective search space: 49450 Effective search space used: 49450 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