Align Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94) (characterized)
to candidate CA265_RS24855 CA265_RS24855 peptidase C26
Query= reanno::pseudo3_N2E3:AO353_29305 (253 letters) >FitnessBrowser__Pedo557:CA265_RS24855 Length = 234 Score = 92.0 bits (227), Expect = 9e-24 Identities = 77/228 (33%), Positives = 104/228 (45%), Gaps = 24/228 (10%) Query: 1 MALKPLIGVTACVKQIGLHPYHVSGDKYLRAVSVAALGLPVVIPSLGELTEIDELLAHLD 60 M+ K +IGV+ C K + +S Y ++V V LG +L +E+ D Sbjct: 1 MSDKIIIGVSDCSKFDIYRDWVLS---YNKSVEVIQLGY--------KLNNFEEI-KKCD 48 Query: 61 GLLLTGSPSNVEPFHYQGPASAP---GTDHDPARDSTTLPLLRAAIAAGVPVLGICRGFQ 117 G++LTG +V P Y P P D D RD +L A VPVLGICRG Q Sbjct: 49 GIVLTGG-EDVHPRFYNHPEYYPYCYEDDIDEKRDEFEFKVLTYTEAHSVPVLGICRGMQ 107 Query: 118 EMNVAFGGSLHQKVHELPGMLDHREADHPDLAVQYAPAHAVSVQPGGVFQALELPPVFQV 177 NV FGG+L +P + + DH + + H + V P + V Sbjct: 108 VGNVFFGGTL------IPDIPTWGKFDHSKMHDKSDRYHEIMVNPSSWLNQIVNTDKGLV 161 Query: 178 NSIHSQGIDRLAPGLRAEAIAPDGLIEAIS--VEHSKAFALGVQWHPE 223 NS H Q D+ GL AI+PDG+ EA+ K+F L VQWHPE Sbjct: 162 NSNHHQSTDKTGKGLVVSAISPDGVTEAMERIEPEGKSFLLFVQWHPE 209 Lambda K H 0.320 0.138 0.419 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: 180 Number of extensions: 16 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: 253 Length of database: 234 Length adjustment: 23 Effective length of query: 230 Effective length of database: 211 Effective search space: 48530 Effective search space used: 48530 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 (21.8 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