Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BWI76_RS26865 BWI76_RS26865 dipeptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Koxy:BWI76_RS26865 Length = 337 Score = 191 bits (485), Expect = 2e-53 Identities = 108/307 (35%), Positives = 179/307 (58%), Gaps = 14/307 (4%) Query: 16 KVGLFK-KRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGY 74 K GLF +R AL VS ++ +G L V+GESG GK+TLGR++ ++ PT GE+ Y G Sbjct: 25 KKGLFAPERLVKALDGVSFTLERGKTLAVVGESGCGKSTLGRLLTMIEIPTGGELYYQGQ 84 Query: 75 NIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINL 134 ++ K+ + K R+ +Q++ Q+PY +L K V +IL P+ ++K++ R++ + + Sbjct: 85 DLLKHDPQAQKLRRQKIQIVFQNPYGSLNPRKKVGQILEEPLQINTSLSKEQRREKALAM 144 Query: 135 LELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILN 194 + V L E +YPH SGGQ+QR++IAR L ++P +++ADEPV+ +D S+R +LN Sbjct: 145 MAKVGLKT--EHYDRYPHMFSGGQRQRIAIARGLMLDPDVVIADEPVSALDVSVRAQVLN 202 Query: 195 TLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPY 254 + +++ L L+ VFI+HD+ + H+ D+ +VM+ GR VE+ ++I +P HPY Sbjct: 203 LMMDLQQDLGLSYVFISHDLSVVE---HIADE--VMVMYLGRCVEKGSKDQIFNNPQHPY 257 Query: 255 TNDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKYS 309 T L+ TP ++ + +K+ E GC + RC C +P+L Y Sbjct: 258 TQALLSATPRLNPDDRRERIKLTGELPSPLNPPPGCAFNARCRRRFGPCTQLQPQLKDYG 317 Query: 310 HE-VACF 315 + VACF Sbjct: 318 GQLVACF 324 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: 320 Number of extensions: 16 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: 337 Length adjustment: 28 Effective length of query: 296 Effective length of database: 309 Effective search space: 91464 Effective search space used: 91464 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