Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 129 bits (324), Expect = 1e-34 Identities = 89/243 (36%), Positives = 138/243 (56%), Gaps = 14/243 (5%) Query: 11 VIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVV 70 + F+D + + AL VSLS+ G++ V+G SGAGK+TL R+I GL+ P++G+V+ Sbjct: 2 ITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVI 61 Query: 71 YDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKR 130 DG ++ + R+ V +I Q + L KTV + + P L+ E++ R Sbjct: 62 VDGDDVAALGVAGLRALRRRVGMIFQ--HFNLLSGKTVAQNVAFP-LKLAGRPAAEVKAR 118 Query: 131 LINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRI 190 LLE V L+ GKYP QLSGGQKQR+ IAR+L+ NP++++ DE + +D Sbjct: 119 TAELLERVGLSA---HAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTE 175 Query: 191 GILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDP 250 IL+ +A + L LT+V ITH++ + R + D+ V+ AGR+VE +EE+ Sbjct: 176 QILDLIAGLNRELGLTIVLITHEMDVVR---RVCDR--VAVLDAGRVVEEGAVEEVF--- 227 Query: 251 LHP 253 LHP Sbjct: 228 LHP 230 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: 260 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: 324 Length of database: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 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: 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