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 3608623 Dshi_2016 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__Dino:3608623 Length = 284 Score = 116 bits (291), Expect = 5e-31 Identities = 76/254 (29%), Positives = 130/254 (51%), Gaps = 16/254 (6%) Query: 29 VWTAIAASRTNH-RLAETPPPLWFGGNLFKNLEAAWE---QAGLGTAMLNSVIVAGTITV 84 +W A AS + + P PL G L +N A A + + NS+I+A I + Sbjct: 33 IWLAFVASTVSQPEIVRPPMPLLPGDQLVENYTRALTAGINAPVALMLGNSLIMALGIAL 92 Query: 85 STVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWMSDLGWSNQLHTVI 144 + S L+ FA RF L L T+M+P ++ +VP Y +++ G N +I Sbjct: 93 GKIAISLLSAFAIVYFRFPGRMLFFWLIFLTLMLPVEVRIVPTYEVIANFGMLNSYQGLI 152 Query: 145 LPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFPAARPAMAVLGLLTF 204 LP + +A TF RQ+ + +P EL EAARVDGA +R + ++ P +R +A L ++ F Sbjct: 153 LPLVASATATFLFRQFFM-TVPDELAEAARVDGARPMRFFFDILLPMSRTNIAALFVILF 211 Query: 205 VFAWNDFLWP-IIALNQQNPTVQVGPELARHRVLP------DQAVIMAGALLGTLPLLVA 257 ++ WN +LWP +I + + T+ +G + ++ P D VIMA ++L +P ++ Sbjct: 212 IYGWNQYLWPLLITTDPEMNTIVMGIK----QMFPSGDDTADWPVIMATSILAMVPPVIV 267 Query: 258 FLLFGKQIVGGIMQ 271 + + V G+++ Sbjct: 268 VITMQRLFVRGLVE 281 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: 235 Number of extensions: 15 Number of successful extensions: 2 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: 284 Length adjustment: 26 Effective length of query: 250 Effective length of database: 258 Effective search space: 64500 Effective search space used: 64500 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