Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate 3610544 Dshi_3925 peptidase C26 (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_13140 (258 letters) >FitnessBrowser__Dino:3610544 Length = 240 Score = 115 bits (288), Expect = 8e-31 Identities = 93/253 (36%), Positives = 122/253 (48%), Gaps = 37/253 (14%) Query: 5 PLIGVTTCSRQ-------MGLHAYHTSGDKYARAVATAAKGLPVLVPSLADLFPPSDILD 57 PLIGVTT SR + L+ + T G +GL ADL D Sbjct: 4 PLIGVTTSSRSGWRVFPFINLNLWLTGG-----------RGLRWGAGRPADL-------D 45 Query: 58 ALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVEAGVPVLGICRGFQ 117 +DGI++ G ++ P Y G DPARDA L R A+ +PVLGICRG Q Sbjct: 46 KVDGIVIGGG-DDISPELY-GTEVLTTARLDPARDALEHGLAREALIRNIPVLGICRGAQ 103 Query: 118 EMNVAFGGSLHQKVHEVGTFIDHREDDTQAVEVQYGPAHAVDIQPGGILAGLGLPQSIEV 177 +NVA GGSLHQ +V T P V++Q LA + + + V Sbjct: 104 MLNVAAGGSLHQNAWQV--------HPTSRPVKTVLPKRMVEVQANARLALIAGTEPMRV 155 Query: 178 NSIHSQGIERLAPGLRAEAVAPDGLIEAVSVPEGKAFALGVQWHPEWEVSSNPHYLAIFQ 237 N++HSQ ++RL G R A G+++A+ E FALGVQWHPE+ V + AIF+ Sbjct: 156 NALHSQAVDRLGDGFRVAARDTGGMVQAIERVE-DPFALGVQWHPEYLVYAR-RQRAIFR 213 Query: 238 AFGDACRARATQR 250 A A RARA R Sbjct: 214 ALVTAARARAQHR 226 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: 194 Number of extensions: 12 Number of successful extensions: 5 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: 240 Length adjustment: 24 Effective length of query: 234 Effective length of database: 216 Effective search space: 50544 Effective search space used: 50544 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