Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate HSERO_RS19370 HSERO_RS19370 gluconolactonase
Query= BRENDA::Q64374 (299 letters) >FitnessBrowser__HerbieS:HSERO_RS19370 Length = 302 Score = 162 bits (411), Expect = 7e-45 Identities = 97/302 (32%), Positives = 156/302 (51%), Gaps = 14/302 (4%) Query: 2 SSIKVECVLRENYRCGESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSV 61 S+ V E GESP+W +L ++DIP K + R S Q +R + S+ Sbjct: 7 SAAAVTVAFPEPMLLGESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLPEEPGSI 66 Query: 62 ALRQLGGYVATIGTKFCALNWENQSVFVLAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEE 121 GG V I T LN + ++ +L D RFNDG+ D +GR++ GT+ E Sbjct: 67 VRHAQGGLVVAIRTGMFHLNTDTGALTLLLAAPYDSSRIRFNDGRCDASGRFWCGTIYEP 126 Query: 122 TAPAVLERHQGSLYSLFPDHSVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYD 181 +R G+LY F ++++ V SNGL +S D ++ Y+ ++ ++ ++ +DYD Sbjct: 127 R-----DRDGGTLY-CFERNALRDAHHAVVTSNGLAFSSDQRLMYHANTPAHRINLYDYD 180 Query: 182 LQTGQISNRRIVYKMEKDEQI------PDGMCIDAEGKLWVACYNGGRVIRLDPETGKRL 235 L TG SN R++ + + D+ PDG +D++G W A + GGRV+RL P+ G+ L Sbjct: 181 LATGATSNCRLLRQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSPQ-GEIL 239 Query: 236 QTVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKGIAPY 295 Q ++LP T FGG D +Y+T R+G + L + P++G + + + V G Y Sbjct: 240 QEIRLPARCPTMVAFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVR-VDVPGQLEY 298 Query: 296 SY 297 SY Sbjct: 299 SY 300 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: 256 Number of extensions: 14 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: 299 Length of database: 302 Length adjustment: 27 Effective length of query: 272 Effective length of database: 275 Effective search space: 74800 Effective search space used: 74800 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