Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate GFF2903 PS417_14855 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__WCS417:GFF2903 Length = 365 Score = 129 bits (324), Expect = 1e-34 Identities = 102/319 (31%), Positives = 155/319 (48%), Gaps = 51/319 (15%) Query: 65 IEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDA-GVSIFLKPSGHAEPIPAGQ 123 +E +A+ ++W+EGPVW+ +G +LL SD P N + +W +S++ + + Sbjct: 70 VERLATGLRWAEGPVWIGDGRYLLVSDIPNNRIVRWDEVTDSLSVYRENANF-------- 121 Query: 124 FREPGSNGMKVGPDGKIWVADSGT-----RAIMKVDPVTRQRSVVVDNYKGKRFNSPNDL 178 SNGM G++ V + T R I + + +V+ D++ GK FNSPND+ Sbjct: 122 -----SNGMCRDRQGRLLVCEGSTTTREGRRITRTEH-NGSLTVLADSFDGKPFNSPNDI 175 Query: 179 FFSKSGAVYFTDPPYGLTNLDES-DIKEMNYNGVFRLSPD-GRLDLIEAGLSRPNGLALS 236 + G+V+FTDPP+ +N E I +GV+R+ + G + + L+ PNGL S Sbjct: 176 VCKRDGSVWFTDPPFQTSNNYEGHKIAPTQPHGVYRIDGESGTVTRVIDDLNGPNGLCFS 235 Query: 237 PDETKLYVSNSDRASPN--IWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDK 294 PDE LYV RA PN IW + +G +R RK A L DG+ D+ Sbjct: 236 PDEKVLYVVEG-RAKPNRLIWAIDVKDDGTLGAR------RKHIEGFDYAAL-DGIKCDE 287 Query: 295 QGNLFASAPG------------GIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLFI 341 GNL+ G G+ +F P G+ +G IS P N CF G +G LF+ Sbjct: 288 SGNLWCGWGGNGDPKADLEKLDGVRVFNPQGKAIGHISLPERCP--NLCFGGREGNRLFM 345 Query: 342 SASHNV----VRVRTKTFG 356 + SH++ V R FG Sbjct: 346 AGSHSIYSLFVNTRDAGFG 364 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: 437 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: 356 Length of database: 365 Length adjustment: 29 Effective length of query: 327 Effective length of database: 336 Effective search space: 109872 Effective search space used: 109872 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