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 3607838 Dshi_1246 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__Dino:3607838 Length = 282 Score = 123 bits (309), Expect = 4e-33 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 14/276 (5%) Query: 9 AGPVTYVVLTVFALVS-LAPLVWTAIAASRTNHRLAETPPPLW---FGGNLFKNLEAAWE 64 A +TY + AL+ L PL+ AI + + A W F G F+N + Sbjct: 12 AAQLTYQGMIPLALILWLLPLIAVAIFSVKPAGDFAAGNYWGWPAEFAG--FENYARVFT 69 Query: 65 QAGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAV 124 + + +LNS ++ + V S + GFA RFR + L+ + I +P Q+ + Sbjct: 70 DSEMPRYILNSFMITIPTVIGAVALSCMTGFALGIYRFRGNLLIFFMFIAGNFVPFQILM 129 Query: 125 VPLYLWMSDLGWSNQLHTVILPSLV--TAFGTFFMRQYLVQALPTELIEAARVDGASSLR 182 VP+ D+G N ++L + T F T FMR + ++ALP ELIEAARV+G + R Sbjct: 130 VPVRDLTVDMGLYNTKTGLVLFHIAFQTGFCTLFMRNF-IRALPYELIEAARVEGVAEWR 188 Query: 183 IVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIAL---NQQNPTVQVGPELARHRVLPD 239 I W VV P +PA+A L +L F F WND+ W ++ N Q T + A+ + + Sbjct: 189 IFWFVVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGPNAQPVTAGITSFNAQFGIAYN 248 Query: 240 QAVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIK 275 ++ AG+L+ LP ++ F L K + G+ GA+K Sbjct: 249 --MLSAGSLIAALPPVMMFFLMQKHFIAGLTLGAVK 282 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: 239 Number of extensions: 12 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: 282 Length adjustment: 26 Effective length of query: 250 Effective length of database: 256 Effective search space: 64000 Effective search space used: 64000 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