Align CbtB, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3684 PGA1_262p00880 ABC transporter, integral inner membrane component
Query= TCDB::Q97VF8 (333 letters) >FitnessBrowser__Phaeo:GFF3684 Length = 347 Score = 116 bits (291), Expect = 7e-31 Identities = 74/241 (30%), Positives = 118/241 (48%), Gaps = 1/241 (0%) Query: 78 YIWNTLHGNLGFSIISNVPVAELIAVALPWTLFIVVTSILISFFLGIRLGQKLGYLRGTK 137 Y+ L G+LG+SI PV +L+ ALPWT +++ ++ + G G + G L G Sbjct: 98 YLSRLLAGDLGYSIPHAAPVLQLLLTALPWTGLLILGAMPVFLIGGALAGIEAGQLPGGS 157 Query: 138 TDSVATVSLSILRSVPIYIYAVLLIYILAFIYHIFPTGGAYSIHVTPGFNLPFIASVLYH 197 D T +++L S+P + AVLL+ + ++ + PTGGA + L VL H Sbjct: 158 VDRWVTPVVTMLASLPPFTGAVLLLLVFGILWPVLPTGGAEPLFPAMD-QLGRAVGVLRH 216 Query: 198 AFLPILTLTIVNLVGWILQMRANTIYVLGEDFVNFAEISGVKKDIIEKKYIGKNAILPLY 257 A LP+L L + L + RA T+ + DF+ A G+ + YIG++ I Sbjct: 217 AILPMLALALHELARFYFLARAETLNLAQRDFIVNAGARGISPWRLRWAYIGRSLIPACL 276 Query: 258 TSLIISIGFSFSGSVFVEQTFSYPGVGNLLINSITSNDYPTEMGVFIIIIVAVIVGNLIA 317 + L ++ S FVE FSYPG G L+ ++I DY G + + V++ N + Sbjct: 277 SRLSDTLTGLVSAVFFVEIVFSYPGTGYLIYSAILDRDYDLLQGAVVFMAGVVLLMNWLV 336 Query: 318 D 318 D Sbjct: 337 D 337 Lambda K H 0.327 0.144 0.429 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: 225 Number of extensions: 10 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: 333 Length of database: 347 Length adjustment: 28 Effective length of query: 305 Effective length of database: 319 Effective search space: 97295 Effective search space used: 97295 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: 49 (23.5 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