Align Gluconolactonase; EC 3.1.1.-; EC 3.1.1.17 (characterized, see rationale)
to candidate RR42_RS09940 RR42_RS09940 gluconolactonase
Query= uniprot:Q88NN7 (293 letters) >FitnessBrowser__Cup4G11:RR42_RS09940 Length = 313 Score = 74.7 bits (182), Expect = 2e-18 Identities = 82/258 (31%), Positives = 109/258 (42%), Gaps = 33/258 (12%) Query: 15 ESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIARSGQGWVAGMESGIF 74 E PVW P Q++ W DIP +L RW AA G Q + QG + E G Sbjct: 37 EGPVWVPRLQSVLWSDIPNNRLLRWSAA-GMEVFRQPAQFTNGHTLDLQGRLVSCEHGRR 95 Query: 75 QL-QAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFW------------AGTMLLDM 121 + + +ADG + +L++ + ND G W G Sbjct: 96 CISRTEADGKVV--ILADRYKGKRLNSPNDVVVRSDGSIWFTDPSYGILSDREGYKADQE 153 Query: 122 QQGAHVGALYRHDG-EGHLHLQQDGMIVPNGLAFSPDGKRMYLSD---SH--PNVQKVWA 175 Q G HV YR D G L + D + PNGLAFSPD ++Y+SD SH V Sbjct: 154 QPGRHV---YRMDPVTGALEVVADDFVQPNGLAFSPDESKLYISDTSASHDPDGNHHVRV 210 Query: 176 FDYDTDSGTPHGKHLF---VDMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLD 232 D T +G P GK L V PG PDG +D+ G +I D +H P+G Sbjct: 211 LDVAT-NGRP-GKRLASGGVFTVISPGLPDGLRVDRQGRVYITAEDGVHVH--APDGTAL 266 Query: 233 RSLSVPVKKPAMCAFGGA 250 ++VP +K C FG A Sbjct: 267 GHIAVP-EKTGNCTFGSA 283 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: 400 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 293 Length of database: 313 Length adjustment: 27 Effective length of query: 266 Effective length of database: 286 Effective search space: 76076 Effective search space used: 76076 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