Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_011386476.1 AMB_RS20870 gamma-glutamyl-gamma-aminobutyrate hydrolase
Query= reanno::pseudo5_N2C3_1:AO356_13140 (258 letters) >NCBI__GCF_000009985.1:WP_011386476.1 Length = 237 Score = 137 bits (346), Expect = 2e-37 Identities = 91/244 (37%), Positives = 133/244 (54%), Gaps = 16/244 (6%) Query: 5 PLIGVTTCSRQMGLHA---YHTSGDKYARAVATAAKGLPVLVPSLADLFPPSDILDALDG 61 PLIG+T S + G ++ ++ YA VA A GLPVL+P L + LD +DG Sbjct: 6 PLIGITLDSEEPGGYSRMPWYALRRNYAETVARAG-GLPVLLPHEPRL--AASFLDRIDG 62 Query: 62 ILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVEAGVPVLGICRGFQEMNV 121 +++TG +++P + A A G R L ++R A+E +P+LGIC G Q +NV Sbjct: 63 LVVTGGAFDIDPALFGAEARA-GLVLKRGRTEFELAMVRGALERDMPILGICGGQQLLNV 121 Query: 122 AFGGSLHQKV-HEVGTFIDHREDDTQAVEVQYGPAHAVDIQPGGILAGLGLPQSIEVNSI 180 A GG+L Q + EV + H + ++ P H V+I G LA + I VNS Sbjct: 122 ALGGTLIQHIPDEVNGALSHEQPTPRSE-----PGHWVEIASGTRLAEIVGETRIPVNSA 176 Query: 181 HSQGIERLAPGLRAEAVAPDGLIEAVSVPEGKAFALGVQWHPEWEVSSNPHYLAIFQAFG 240 H Q + +APG A+APDG+IE + G+ F +GVQWHPE+++S P A+ +AF Sbjct: 177 HHQAVRMVAPGCVVNAIAPDGVIEGIEA-AGRTFCIGVQWHPEYDIS--PADSALLRAFV 233 Query: 241 DACR 244 ACR Sbjct: 234 GACR 237 Lambda K H 0.318 0.135 0.406 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: 221 Number of extensions: 16 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: 237 Length adjustment: 24 Effective length of query: 234 Effective length of database: 213 Effective search space: 49842 Effective search space used: 49842 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 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