Align Gluconolactonase; EC 3.1.1.-; EC 3.1.1.17 (characterized, see rationale)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase
Query= uniprot:Q88NN7 (293 letters) >FitnessBrowser__Koxy:BWI76_RS21470 Length = 290 Score = 147 bits (372), Expect = 2e-40 Identities = 100/278 (35%), Positives = 138/278 (49%), Gaps = 13/278 (4%) Query: 15 ESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIA-RSGQGWVAGMESGI 73 E P W EQALYW DI ++HR+ G+HQ Q E C A R+ G++ + SGI Sbjct: 16 ECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFALRAKGGFIVALRSGI 75 Query: 74 FQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLLDMQQGAHVGALY-R 132 + A G L ++ N + Q RFNDG DR GRF+AGT G GAL R Sbjct: 76 WLTDAH--GLLQRKVCDNPSNPQLA-RFNDGGTDRDGRFYAGTF---WGPGDFNGALLMR 129 Query: 133 HDGEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYDTDSGTPHGKHLFV 192 D + + Q + NGLAFS D + MY SD+ V D ++G + +F Sbjct: 130 IDSDLSPQVIQCDIHGANGLAFSEDKRWMYTSDTPNAVIYRTPLDKRGEAGK---REVFR 186 Query: 193 DMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVPVKKPAMCAFGGASL 252 G PDGAAID +GCYW D +I RF+P G +PV+ P M FGG + Sbjct: 187 RFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSPTGEQLEEHRLPVRCPTMVCFGGTDM 246 Query: 253 DILYVTSIRPT--GIDLSDQPLAGGVFALDPGTKGLEE 288 LY+T+ R +++ PL+G +F L G+++ Sbjct: 247 KTLYITTTRENMDAEEVAKYPLSGAIFTLPVSVAGMKK 284 Lambda K H 0.320 0.139 0.455 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: 380 Number of extensions: 28 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: 293 Length of database: 290 Length adjustment: 26 Effective length of query: 267 Effective length of database: 264 Effective search space: 70488 Effective search space used: 70488 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