Align gamma-glutamyl-gamma-aminobutyrate hydrolase (EC: 3.5.1.94) (characterized)
to candidate 5210088 Shew_2532 peptidase C26 (RefSeq)
Query= reanno::SB2B:6936606 (267 letters) >FitnessBrowser__PV4:5210088 Length = 267 Score = 379 bits (973), Expect = e-110 Identities = 178/252 (70%), Positives = 207/252 (82%) Query: 1 MPLQQESARQERKPVILMSMGQQDRNGHAYQVMTHKYMQPVVDISDCIPLLIPTCFGVAD 60 MP+ Q ++ ++ KP+ILM+MGQQDRN H YQVMTHKYMQP+V+I+ IPLL+PTCFG+ D Sbjct: 1 MPITQTTSAKKSKPIILMTMGQQDRNQHPYQVMTHKYMQPIVEIAGAIPLLMPTCFGIED 60 Query: 61 IEQYLDMADGVYLSGAASNIDPSLYGQENLTPEKKQDLARDLVDIALIKGAVKRGLPILG 120 +++YLDM DGVYLSGA SNIDPSLYGQENLTPEK QD+ RD VD+A+I GA+KR LPILG Sbjct: 61 VDRYLDMVDGVYLSGAGSNIDPSLYGQENLTPEKSQDVNRDTVDLAIIAGALKRKLPILG 120 Query: 121 ICRGMQEMNIAFGGDLYQKVHDEDHLNDHREDPDTPPDVQYGASHSISMVKGSWLHKLLG 180 ICRGMQE+NIA GG LYQKV+ E +DHREDP TP VQYG H I V GSWL KL+G Sbjct: 121 ICRGMQELNIALGGTLYQKVYSEPGFDDHREDPQTPNHVQYGPRHPIKTVPGSWLAKLIG 180 Query: 181 DTIEVNSLHGQGIKTLGKGLEALALAEDGLVEALHAPYLPQFTLGVQWHPEWKALENPDS 240 D VNSLHGQGI TLGKGLEALA EDGL+EA+H P QF LGVQWHPEW+A +NPDS Sbjct: 181 DKTMVNSLHGQGICTLGKGLEALAYGEDGLIEAIHGPDYGQFILGVQWHPEWQANDNPDS 240 Query: 241 IKIFKAFGEACR 252 IK+F+AFG ACR Sbjct: 241 IKLFQAFGSACR 252 Lambda K H 0.318 0.137 0.412 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: 314 Number of extensions: 10 Number of successful extensions: 1 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: 267 Length of database: 267 Length adjustment: 25 Effective length of query: 242 Effective length of database: 242 Effective search space: 58564 Effective search space used: 58564 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: 47 (22.7 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