Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate WP_053938627.1 WG78_RS14775 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_4510 (258 letters) >NCBI__GCF_001294205.1:WP_053938627.1 Length = 265 Score = 288 bits (736), Expect = 1e-82 Identities = 144/247 (58%), Positives = 172/247 (69%), Gaps = 1/247 (0%) Query: 5 PLIGVTTCSRQIGLHAYHISGEKYSRAVATAAKGLPVLIPSLADLFPPSDILDALDGILL 64 P++GV +QIG H +H +G KY AV A V++P LA + LD +DG+LL Sbjct: 12 PVVGVIADLKQIGAHGFHAAGHKYIAAVVGGAHAFAVVLPVLAPQQDIAQTLDLVDGLLL 71 Query: 65 TGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVDAGIPVLGICRGFQEMNVAFG 124 TGS SNVEP HY GPASAPGT HDP RDA +LPLI AA+ AG+P+LGICRGFQEMNVA G Sbjct: 72 TGSYSNVEPHHYAGPASAPGTLHDPDRDANSLPLINAAIAAGVPLLGICRGFQEMNVALG 131 Query: 125 GSLHQKVHEVGTFIDHREDDTQAVDVQYGPAHAVHIQPGGVLAG-LGLPQRIEVNSIHSQ 183 GSLHQ+VHEV + H+E D +D QYGPAH V + GG LAG L +I VNS+HSQ Sbjct: 132 GSLHQRVHEVAGMLLHKERDEDPLDTQYGPAHPVSVVAGGQLAGWLDGASQITVNSLHSQ 191 Query: 184 GIERLAPGLRAEAVAPDGLIEAVSVPGGKAFALGVQWHPEWEVSSNPHYLAIFQAFGDAC 243 G++ LA RAEA+APDGL+EA SVP FA VQWHPEW + NP LA+F AFG+AC Sbjct: 192 GVQTLALRARAEAIAPDGLVEAFSVPEASRFAFAVQWHPEWRYADNPVSLALFAAFGEAC 251 Query: 244 RARAAQR 250 AR A R Sbjct: 252 AARRAAR 258 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: 289 Number of extensions: 10 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: 258 Length of database: 265 Length adjustment: 25 Effective length of query: 233 Effective length of database: 240 Effective search space: 55920 Effective search space used: 55920 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 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