Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate GFF2792 PGA1_c28350 peptidase C26
Query= reanno::pseudo5_N2C3_1:AO356_13140 (258 letters) >FitnessBrowser__Phaeo:GFF2792 Length = 232 Score = 90.9 bits (224), Expect = 2e-23 Identities = 65/199 (32%), Positives = 97/199 (48%), Gaps = 16/199 (8%) Query: 56 LDALDGILLTGSPSNVEPFHYQGPASAPGTAHDPARDATTLPLIRAAVEAGVPVLGICRG 115 L +D +++ G ++ P Y G P DP RDA ++R A VP+LGICRG Sbjct: 43 LATVDAVVIGGG-DDIAPTLYNGQIM-PEVRLDPDRDALEAGIVREASRQDVPLLGICRG 100 Query: 116 FQEMNVAFGGSLHQKVHEVGTFIDHREDDTQAVEVQYGPAHAVDIQPGGILAGLGLPQSI 175 Q +NVA GG L+Q + +++ P V I L + + Sbjct: 101 AQMLNVARGGRLYQDAYAFYGLENYK---------TVLPRKKVTITNNSTLRRILGVSEL 151 Query: 176 EVNSIHSQGIERLAPGLRAEAVAPDGLIEAVSVPEGKAFALGVQWHPEWEVSSNPHYLAI 235 +VN++HSQ + L GLR G+++A+ P G+ FA+GVQWHPE + +L + Sbjct: 152 KVNALHSQSVSSLGQGLRVTGRDQSGMVQAIEDP-GRRFAVGVQWHPE-HLFYRAAHLNL 209 Query: 236 FQAFGDACRARATQRDADA 254 F+A A R T+RD A Sbjct: 210 FRALVAAAR---TKRDTPA 225 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: 172 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: 258 Length of database: 232 Length adjustment: 24 Effective length of query: 234 Effective length of database: 208 Effective search space: 48672 Effective search space used: 48672 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