Align Gluconolactonase (characterized, see rationale)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__Koxy:BWI76_RS21470 Length = 290 Score = 148 bits (374), Expect = 1e-40 Identities = 101/286 (35%), Positives = 138/286 (48%), Gaps = 18/286 (6%) Query: 35 LGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAPGFIVTLR 94 L E WS EQA+YW DI+ E+HR+D TG HQ F EE A RA GFIV LR Sbjct: 14 LPECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFALRAKG-GFIVALR 72 Query: 95 RGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSMDFACEAPTGALYRYD 154 G L D + + P + RFNDG D GRF+AG+ + L R D Sbjct: 73 SGIWLTDAHGLLQRKVCDNPSNPQLA-RFNDGGTDRDGRFYAGTFWGPGDFNGALLMRID 131 Query: 155 SDGS-----CTRHD-DGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATGTVSNK 208 SD S C H +G A + W M+ + T YR D G + Sbjct: 132 SDLSPQVIQCDIHGANGLAFSEDKRW--------MYTSDTPNAVIYRTPLD-KRGEAGKR 182 Query: 209 TLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQVTTCAF 268 +++ + P +G+PDG DA+G W A + GW + P T +L RLPV T F Sbjct: 183 EVFRRFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSP-TGEQLEEHRLPVRCPTMVCF 241 Query: 269 GGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPF 314 GG D++TL+I++ R + E++A PL+GA+F + G+ PF Sbjct: 242 GGTDMKTLYITTTRENMDAEEVAKYPLSGAIFTLPVSVAGMKKLPF 287 Lambda K H 0.321 0.137 0.457 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: 353 Number of extensions: 17 Number of successful extensions: 4 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: 316 Length of database: 290 Length adjustment: 27 Effective length of query: 289 Effective length of database: 263 Effective search space: 76007 Effective search space used: 76007 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: 48 (23.1 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