Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate GFF3393 PS417_17365 gluconolactonase
Query= BRENDA::Q15493 (299 letters) >FitnessBrowser__WCS417:GFF3393 Length = 291 Score = 139 bits (349), Expect = 1e-37 Identities = 94/291 (32%), Positives = 139/291 (47%), Gaps = 15/291 (5%) Query: 7 ECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQS 66 E ++ GE PVW N+L +VDIP + RW + T V T ++ +A + Sbjct: 4 ELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDA 63 Query: 67 GGYVATIGTKFCAL---NWKEQSAVVLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETA 123 G +VA + T F L N +LA V++ +++ R NDG+ D GR++AG+M Sbjct: 64 GNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMG 123 Query: 124 PAVLERHQGALYSLFPDHHVKKYFDQVDISNGLDWSLDHKIFYYIDS--LSYSVDAFDYD 181 L +G LY D NGL +S D + Y DS L + AFDYD Sbjct: 124 ---LNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYD 180 Query: 182 LQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTVKLP 241 + TG SNRR + K PDG +DA+G W+ + G + R P G+ +++ +P Sbjct: 181 IDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSP-DGRLDRSLTVP 239 Query: 242 VDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGI 292 V K T C FGG ++VT RD + L +GG+F + GV G+ Sbjct: 240 VKKPTMCAFGGSRLDTLFVTSIRDDQSEQSL-----SGGVFALNP-GVVGL 284 Lambda K H 0.319 0.136 0.421 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: 260 Number of extensions: 17 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: 291 Length adjustment: 26 Effective length of query: 273 Effective length of database: 265 Effective search space: 72345 Effective search space used: 72345 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 (21.7 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