Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_068173905.1 HTA01S_RS16835 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_4510 (258 letters) >NCBI__GCF_001592305.1:WP_068173905.1 Length = 280 Score = 110 bits (275), Expect = 3e-29 Identities = 88/238 (36%), Positives = 119/238 (50%), Gaps = 19/238 (7%) Query: 30 RAVATAAKGLPVLIPSLADLFPPSDILDALDGILLTGSPSNVEPFHYQGPASAPGTAHDP 89 RA+A + P A+ P ++++D LDG++L G ++ P Y P A D Sbjct: 41 RAIALMVPFIDEESPLSANRAPMTELVDLLDGLVLQGG-IDICPETYGDTLRDPAWAGDA 99 Query: 90 ARDATTLPLIRAAVDAGIPVLGICRGFQEMNVAFGGSLHQKV--HEVGTFIDHREDDTQA 147 RD L L+R + AG PVLG+CRG Q +NV FGGSL Q + GT I H+ DT Sbjct: 100 VRDRYELNLLRGFIAAGKPVLGVCRGAQLINVYFGGSLVQDIPSQRPGT-IQHQ--DTTR 156 Query: 148 VDVQYGPAHAVHIQPGGVLA---GLGLPQRIEVNSIHSQGIERLAPGLRAEAV-APDGLI 203 D H VH + G L G +P R V SIH Q ++RL GL EAV + DG+I Sbjct: 157 YD---RLTHEVHFETGSSLQRLYGNSVPHR--VTSIHHQCVDRLGEGLVVEAVSSKDGII 211 Query: 204 EAVSVPGGKAFALGVQWHPEWEVSSNPHYLAIFQA---FGDACRARAAQRDADASNNA 258 EA+ G + LGVQWHPE+ ++ + + D RA A+ D S A Sbjct: 212 EAIR-HTGPGYVLGVQWHPEFHLTPGEEMQGLLDSGPMMMDFLRAALARADRHQSGAA 268 Lambda K H 0.319 0.136 0.413 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: 249 Number of extensions: 21 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: 258 Length of database: 280 Length adjustment: 25 Effective length of query: 233 Effective length of database: 255 Effective search space: 59415 Effective search space used: 59415 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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