Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate AZOBR_RS04080 AZOBR_RS04080 cytochrome C
Query= BRENDA::Q5FRK5 (437 letters) >FitnessBrowser__azobra:AZOBR_RS04080 Length = 288 Score = 118 bits (296), Expect = 2e-31 Identities = 95/305 (31%), Positives = 137/305 (44%), Gaps = 45/305 (14%) Query: 6 VIACFLGMGLTAEATAQDSDKAIVEKGRYLA-AASDCAACHSVHGKP------EYSGGVS 58 V AC + G+ A A A+ ++ VE+GR L C CH+ G E +GG Sbjct: 10 VAACLMLSGMIATAGAETPPESPVERGRALVNGIVACGNCHTPQGPNGPVAGRELAGGTP 69 Query: 59 FSLPMGKIYSTNITPDPDHGIGRYTEAQFGQALRQGIRRDGSTLYPAMPFPSYARLTDSD 118 F Y++NITPDP+ GIGR+T+ Q A+R+G R DGS + P MPF Y L+D D Sbjct: 70 FVEEPFTAYASNITPDPETGIGRWTDEQLIAAIREGRRPDGSLIGPPMPFGFYRGLSDGD 129 Query: 119 IHALFVYFRDGVKAVPVSAPRNEIPWPLSIRWPLTFWRWAFAPTPHKAITSTAGEF--TD 176 + A+ Y R V V S P++E L P + + E TD Sbjct: 130 LRAIVAYLR-SVPPVRHSVPKSEYRMAL--------------PAAYGPPVGSVAEIPRTD 174 Query: 177 PLLARGAYLVEGPAHCGACHSPRAITMQEKALIAHDGSLYL----AGGAPVDG-W---TP 228 P + GAY+ HC CH+P + DG L + AGG G W Sbjct: 175 P-VTYGAYMAGPLGHCMECHTP----------MLPDGRLDMTRMGAGGRNFTGPWGNAVS 223 Query: 229 PSLRQENRTGLGRWSEEDIVSFLRTGRSNPGSVFGSMTSAVLHGTQKLTDNDLHAIAHYL 288 ++ Q+ GLG W++ +I + G G H + ++D +L A+ YL Sbjct: 224 RNITQDKEHGLGGWTDAEIRKAITEGVRPDGHRLSPPMG--YHYYKSMSDGELGALVAYL 281 Query: 289 KSLPP 293 ++LPP Sbjct: 282 RTLPP 286 Lambda K H 0.319 0.133 0.420 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: 497 Number of extensions: 39 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 437 Length of database: 288 Length adjustment: 29 Effective length of query: 408 Effective length of database: 259 Effective search space: 105672 Effective search space used: 105672 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: 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