Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 6937060 Sama_1231 peptide ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__SB2B:6937060 Length = 261 Score = 142 bits (358), Expect = 9e-39 Identities = 76/240 (31%), Positives = 150/240 (62%), Gaps = 10/240 (4%) Query: 20 FKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKN 79 FK++ AL +S + +G+ L ++GE+G+GK+TL R++VG ++ +SG++ ++G ++ Sbjct: 22 FKRQYNEALAPISFELGRGETLAIVGEAGSGKSTLARILVGAEQRSSGDIQFEGESL--- 78 Query: 80 KRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVK 139 + + K+ + +++I QDP ++L ++ E+L P+ ++ E ++ L V Sbjct: 79 ESRNLKQRCRLIRMIFQDPNTSLNPRLSIGELLEEPLRFNTGMSAHERSVQVTETLRKVG 138 Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199 L P E YPH +S GQKQR+++AR+L ++P++I+ADE +T +D S+R ILN L + Sbjct: 139 LLP--EHADFYPHMISEGQKQRVAVARALMLSPKVIIADEALTALDLSVRSQILNLLLHL 196 Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 + + L+ +F++H++ + R H+ DK +V+ G+++E+ ++++ + P H YT LI Sbjct: 197 QKEMGLSYIFVSHNLNLVR---HVSDK--IMVLHKGQLIEKGPVQKVFESPEHEYTARLI 251 Lambda K H 0.321 0.141 0.410 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: 14 Number of successful extensions: 4 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: 324 Length of database: 261 Length adjustment: 26 Effective length of query: 298 Effective length of database: 235 Effective search space: 70030 Effective search space used: 70030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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