Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase
Query= BRENDA::Q64374 (299 letters) >FitnessBrowser__BFirm:BPHYT_RS24170 Length = 309 Score = 133 bits (334), Expect = 6e-36 Identities = 97/308 (31%), Positives = 150/308 (48%), Gaps = 24/308 (7%) Query: 5 KVECVLRENYRCGESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALR 64 +VE + GESPVW A Q+L +VDIP++ I R S + + V+ +A Sbjct: 11 RVEAAGQAPAAVGESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLLPEKVACIAFD 70 Query: 65 QLGGYVATIGTKFCALNW-----ENQSVFV----LAMVDEDKKNNRFNDGKVDPAGRYFA 115 G +A T AL ++V V LA D + RFNDG+ D GR++A Sbjct: 71 HRGTVLAGCETGLFALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDGRCDRQGRFWA 130 Query: 116 GTMAEETAPAVLERHQGSLYSLFPDHSVKK--YFDQVDISNGLDWSLDHKIFYYIDS--L 171 GTM ++ A A + G+LY F + + +++ NGL WS D Y DS L Sbjct: 131 GTMVQDMAAA---KPAGALYR-FDERGMLSAPVVEELITQNGLAWSPDGATMYLSDSHPL 186 Query: 172 SYTVDAFDYDLQTGQISNRRIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPET 231 + AFDYD+++G+ NRR+ + + PDG +DA+G W+ + G ++R PE Sbjct: 187 RRQIWAFDYDIESGEPRNRRVFADLNQHAGRPDGAAVDADGCYWICANDAGLLLRFTPE- 245 Query: 232 GKRLQTVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKG 291 GK + + +P K C FGG++ ++VT R NA G++F + G+ G Sbjct: 246 GKLDRQIAVPAIKPAMCAFGGRELDTLFVTSIRPAANA-----SEHDGHLFAVRP-GITG 299 Query: 292 IAPYSYAG 299 + +AG Sbjct: 300 LPEPEFAG 307 Lambda K H 0.319 0.137 0.419 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: 270 Number of extensions: 17 Number of successful extensions: 5 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: 299 Length of database: 309 Length adjustment: 27 Effective length of query: 272 Effective length of database: 282 Effective search space: 76704 Effective search space used: 76704 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