Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate AO353_25125 AO353_25125 sugar ABC transporter permease
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25125 Length = 280 Score = 109 bits (272), Expect = 8e-29 Identities = 78/268 (29%), Positives = 132/268 (49%), Gaps = 8/268 (2%) Query: 14 YVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQAGLGTAML 73 + ++ + L ++ P + + + + + L E W F N A Q+ A+ Sbjct: 16 WCLIGILLLYAVFPFYYAIVTSLKPSSALFEVS--YWIDSPDFSNYAAVLHQSSFLRAIG 73 Query: 74 NSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWMSD 133 NS++VA + + S A +A +++FR G +L++ +G M P + L+ + Sbjct: 74 NSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRA 133 Query: 134 LGWSNQLHTVILP-SLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFPAA 192 LG N +IL ++ T T ++ + LP EL EAA +DGAS + V+ P Sbjct: 134 LGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLL 193 Query: 193 RPAMAVLGLLTFVFAWNDFLWPI-IALNQQNPTVQVGPEL---ARHRVLPDQAVIMAGAL 248 PA+ GLL F+ AWN+FL+ + L TV V L LP ++MA ++ Sbjct: 194 WPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELP-WGLLMAASV 252 Query: 249 LGTLPLLVAFLLFGKQIVGGIMQGAIKG 276 L T+PL++ L+F ++IV G+ GA+KG Sbjct: 253 LVTVPLVILVLIFQRRIVSGLTAGALKG 280 Lambda K H 0.327 0.140 0.434 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: 189 Number of extensions: 8 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: 276 Length of database: 280 Length adjustment: 25 Effective length of query: 251 Effective length of database: 255 Effective search space: 64005 Effective search space used: 64005 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