Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate RR42_RS09940 RR42_RS09940 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS09940 Length = 313 Score = 152 bits (385), Expect = 9e-42 Identities = 101/316 (31%), Positives = 163/316 (51%), Gaps = 34/316 (10%) Query: 54 RLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPS 113 R +L +E +A+ WSEGPVWV +L+SD P N + +W+ AG+ +F +P+ Sbjct: 15 RFQDVLQPGQLLERLATGAIWSEGPVWVPRLQSVLWSDIPNNRLLRWSA-AGMEVFRQPA 73 Query: 114 GHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFN 173 QF +NG + G++ + G R I + + + ++ D YKGKR N Sbjct: 74 ---------QF----TNGHTLDLQGRLVSCEHGRRCISRTE-ADGKVVILADRYKGKRLN 119 Query: 174 SPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNYNG--VFRLSP-DGRLDLIEAGLSRP 230 SPND+ G+++FTDP YG+ + E + G V+R+ P G L+++ +P Sbjct: 120 SPNDVVVRSDGSIWFTDPSYGILSDREGYKADQEQPGRHVYRMDPVTGALEVVADDFVQP 179 Query: 231 NGLALSPDETKLYVSNSDRA-----SPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAG 285 NGLA SPDE+KLY+S++ + + ++ V + +NG P R F G Sbjct: 180 NGLAFSPDESKLYISDTSASHDPDGNHHVRVLDVATNGRPGKRLASGG----VFTVISPG 235 Query: 286 LPDGMNIDKQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCFGE-----KGQTLF 340 LPDG+ +D+QG ++ +A G+++ APDG LG I+ + NC FG L+ Sbjct: 236 LPDGLRVDRQGRVYITAEDGVHVHAPDGTALGHIA--VPEKTGNCTFGSAPGSAARNRLY 293 Query: 341 ISASHNVVRVRTKTFG 356 I+AS ++ + T G Sbjct: 294 IAASSSLYAITLITTG 309 Lambda K H 0.317 0.135 0.409 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: 452 Number of extensions: 24 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: 356 Length of database: 313 Length adjustment: 28 Effective length of query: 328 Effective length of database: 285 Effective search space: 93480 Effective search space used: 93480 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