Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate GFF363 Psest_0364 Gluconolactonase
Query= BRENDA::Q15493 (299 letters) >FitnessBrowser__psRCH2:GFF363 Length = 296 Score = 142 bits (358), Expect = 9e-39 Identities = 98/294 (33%), Positives = 149/294 (50%), Gaps = 17/294 (5%) Query: 7 ECVLPENCRCGESPVWEEVSNSLLFVDIPAKKVCRWDSFTKQVQRVTMDAPVSSVALRQS 66 E ++ C GESPVW +L +VDIP +++ RW++ Q+ R D ++ +A R Sbjct: 6 ELIVDLGCATGESPVWVAAEQALYWVDIPNRELLRWNAADGQISRWQGDEMLACIA-RHG 64 Query: 67 GGYVATIGTKFCALNWKEQSAV---VLATVDNDKKNNRFNDGKVDPAGRYFAGTMAEETA 123 G+VA + + F +L + + +LAT+D+ R NDG+ D GR++AG+MA + A Sbjct: 65 DGWVAGMESGFFSLQTRPDGRLDSHLLATIDHQLPAMRMNDGRCDREGRFWAGSMALDMA 124 Query: 124 PAVLERHQGALYSLFP---DHHVKKYFDQVDISNGLDWSLDHKIFYYIDS--LSYSVDAF 178 GALY L D + D + NGL +S D + Y DS + AF Sbjct: 125 AG---HPVGALYRLDSKSIDAPLVPQLDGFIVPNGLAFSPDGRTMYLSDSHPSVQKIWAF 181 Query: 179 DYDLQTGQISNRRSVYKLEKEEQIPDGMCIDAEGKLWVACYNGGRVIRLDPVTGKRLQTV 238 DYD+ +G S RR + PDG +DA+G W+ + G + R P G+ +++ Sbjct: 182 DYDIDSGTPSRRRLFVDMLDHPGRPDGAAVDADGCYWICGNDAGFIHRFTP-DGRLDRSL 240 Query: 239 KLPVDKTTSCCFGGKNYSEMYVTCARDGMDPEGLLRQPEAGGIFKITGLGVKGI 292 +PV K + C FGG ++VT R G D L QP AGG+F + GV G+ Sbjct: 241 AVPVKKPSMCAFGGARLDTLFVTSIRPGGD---LSDQPLAGGVFALNP-GVTGL 290 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: 307 Number of extensions: 22 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: 296 Length adjustment: 26 Effective length of query: 273 Effective length of database: 270 Effective search space: 73710 Effective search space used: 73710 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