Align CbtC, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AZOBR_RS25280 AZOBR_RS25280 ABC transporter permease
Query= TCDB::Q97VF6 (290 letters) >FitnessBrowser__azobra:AZOBR_RS25280 Length = 264 Score = 108 bits (270), Expect = 1e-28 Identities = 69/220 (31%), Positives = 110/220 (50%), Gaps = 5/220 (2%) Query: 67 GTGPFAESILVQIIQGAKSVIEISFLAGLFATLIGIVVGIIAGYLGGIIDNILMGITDII 126 GT + Q++ GA+ + + A ATLIG+ +G +AGY GG+ D++L + D + Sbjct: 46 GTDQLGRDVAAQLLFGARVSLAVGVGAAAVATLIGVGLGAVAGYFGGVADHLLSRLCDYV 105 Query: 127 LTLPSLILIIIIVSAFKTSNPIFLSLILSITSWAGLARAVRSQVLVIRNSPAVEVLRVLG 186 TLPS +L +++V+ S + L + +TSW +AR R++VL IRN+ V R +G Sbjct: 106 QTLPSFLLSMVLVAVLAPSIGSVM-LAIGLTSWPEIARLTRAEVLRIRNADWVLAARTMG 164 Query: 187 LSRKYIIFREVVPTLGSYIAIHYIFNVEAAVYAEVGLYYLGVLPYNPNNWGAMIQQALSY 246 L +I+ V+P + + V AV E L +LG+ N +WGAMI A Sbjct: 165 LGHGHILLNHVLPNGIAPVVAMITAVVAHAVLVEAALAFLGLGDPNLVSWGAMIGNARPL 224 Query: 247 GAAAGGKAIYYLAFPTIVVAGFMSGLILLSYGIDEISNPR 286 Y +A P + + + LL G+ E +PR Sbjct: 225 LRTLW----YLMALPGLAIFATVMVFTLLGNGLSERLDPR 260 Lambda K H 0.328 0.146 0.429 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: 176 Number of extensions: 9 Number of successful extensions: 3 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: 290 Length of database: 264 Length adjustment: 25 Effective length of query: 265 Effective length of database: 239 Effective search space: 63335 Effective search space used: 63335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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