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 PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896 Length = 281 Score = 89.7 bits (221), Expect = 6e-23 Identities = 78/278 (28%), Positives = 125/278 (44%), Gaps = 29/278 (10%) Query: 14 YVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQAGLGTAML 73 Y L + A V L PLV + + ++ + GNL +W G + Sbjct: 18 YATLLLAAAVYLIPLVVMLLTSFKSPEDIRT--------GNLL-----SWPTVIDGIGWI 64 Query: 74 NSVIVAG-------TITVSTVLFST----LAGFAFAKLRFRFSGLLLLLTIGTMMIPPQL 122 + V G ITV VL ST + G+ + RFR S L L + +P Q Sbjct: 65 KAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQT 124 Query: 123 AVVPLYLWMSDLGWSNQLHTVILPSLV--TAFGTFFMRQYLVQALPTELIEAARVDGASS 180 ++P + G +N ++L +V AF T F R Y V ++P L++AAR+DGA Sbjct: 125 VLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYV-SIPDALVKAARLDGAGF 183 Query: 181 LRIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPII--ALNQQNPTVQVGPELARHRVLP 238 I ++ P + P + V + F WNDFL+ ++ + + Q TV + + Sbjct: 184 FTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAK 243 Query: 239 DQAVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIKG 276 + V MA A++ LP L+ ++ GK + G+ GA+KG Sbjct: 244 EYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 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: 227 Number of extensions: 11 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: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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