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 H281DRAFT_02632 H281DRAFT_02632 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__Burk376:H281DRAFT_02632 Length = 283 Score = 123 bits (309), Expect = 4e-33 Identities = 83/266 (31%), Positives = 133/266 (50%), Gaps = 9/266 (3%) Query: 17 LTVFALVSLAPLVWTAIAASRTNHRLAETPPPLW---FGGNLFKNLEAAWEQAGLGTAML 73 L V V L P++ I + R++ L++ W F L N AA Q + Sbjct: 21 LPVALFVWLLPMLAVLITSIRSSDELSQGDYWAWPKHFA--LIDNYGAALTQTPMLHYFA 78 Query: 74 NSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWMSD 133 NS+++ + +L +++AGFA A RFR + ++L + +P Q+ ++P+ Sbjct: 79 NSMLITVPSVLGAILLASMAGFALATYRFRGNIVVLFTFVAGNFVPVQILMIPVRDMALK 138 Query: 134 LGWSNQLHTVIL--PSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFPA 191 +G N + +I+ + T F T F+R ++ Q LP ELIEAARV+GAS I +V P Sbjct: 139 VGLFNTVWALIIFHVAFQTGFCTLFLRNFIKQ-LPFELIEAARVEGASEWTIYARIVLPL 197 Query: 192 ARPAMAVLGLLTFVFAWNDFLWPI-IALNQQNPTVQVGPELARHRVLPDQAVIMAGALLG 250 RPA+A LG+L F F WND+ W + + + VG + + ++ AG++L Sbjct: 198 IRPALAALGILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTAWNLVAAGSVLA 257 Query: 251 TLPLLVAFLLFGKQIVGGIMQGAIKG 276 LP ++ F K V G+ GA KG Sbjct: 258 ALPSVLMFFAMQKHFVAGLTFGASKG 283 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: 267 Number of extensions: 10 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: 283 Length adjustment: 26 Effective length of query: 250 Effective length of database: 257 Effective search space: 64250 Effective search space used: 64250 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