Align 1,4-lactonase (EC 3.1.1.25) (characterized)
to candidate RR42_RS23435 RR42_RS23435 gluconolactonase
Query= BRENDA::B2LYJ5 (401 letters) >FitnessBrowser__Cup4G11:RR42_RS23435 Length = 317 Score = 94.0 bits (232), Expect = 6e-24 Identities = 66/207 (31%), Positives = 101/207 (48%), Gaps = 23/207 (11%) Query: 202 TTLLNNYFGRQFNSLNDVGINPRNGDLYFTDT---LYGYLQDFRPVPGLRNQVYRYNFDT 258 T L + Y G+ NS NDV + +G ++FTD + G+ Q + V L +VYR + T Sbjct: 118 TVLADQYDGKPLNSPNDVVVKS-DGSVWFTDPPFGIVGFYQGEKAVAELPERVYRIDPHT 176 Query: 259 GAVTVVADDFTLPNGIGFGPDGKKVYVTDTGIALGFYGRNLSSPASVYSFDVNQDG-TLQ 317 G ++VVADD + PNG+ F PD K +YV + + + P + +F V+ DG +L Sbjct: 177 GELSVVADDVSGPNGLAFSPDEKLLYVIE----------SRTRPRRIRAFHVSGDGESLT 226 Query: 318 NRKTFAYVASFIPDGVHTDSKGRVYAGCG------DGVHVWNPSGKLIGKIYTGTVAANF 371 + K PDG D G ++ G G DGV V+ P G+ IG I AN Sbjct: 227 DSKVLIDAGPGTPDGFRVDVDGNLWCGWGMGTPELDGVRVFAPDGEAIGHIGLPERCANL 286 Query: 372 QFAG--KGRMIITGQTKLFYVTLGASG 396 F G + R+ + T ++ + + G Sbjct: 287 CFGGRHRNRLFMASCTSIYALYVNTQG 313 Lambda K H 0.317 0.138 0.415 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: 395 Number of extensions: 28 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: 401 Length of database: 317 Length adjustment: 29 Effective length of query: 372 Effective length of database: 288 Effective search space: 107136 Effective search space used: 107136 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 (21.6 bits) S2: 49 (23.5 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