Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BPHYT_RS18670 BPHYT_RS18670 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS18670 Length = 339 Score = 195 bits (495), Expect = 2e-54 Identities = 107/313 (34%), Positives = 182/313 (58%), Gaps = 13/313 (4%) Query: 16 KVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYN 75 K G+F AL VS ++ +G L V+GESG GK+TL R + ++ P++G ++ DG + Sbjct: 31 KRGMFASGTVKALNGVSFALERGKTLAVVGESGCGKSTLARQLTMIEAPSAGRLLIDGED 90 Query: 76 IWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLL 135 + R+ VQ++ Q+P+++L KTVE+ L P+ +++ E +R+ ++ Sbjct: 91 VAGADHAKIAALRRRVQMVFQNPFASLNPRKTVEQTLGEPLAINTQLSATERAERIAQMM 150 Query: 136 ELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNT 195 V L P E +YPH SGGQ+QR++IAR++ ++P+I+VADEPV+ +D S++ ILN Sbjct: 151 RTVGLRP--EHAKRYPHMFSGGQRQRVAIARAMILDPQIVVADEPVSALDVSIQAQILNL 208 Query: 196 LAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYT 255 +++ + + VFI+H++ + H+ D + +VM+ G + E D + I +P HPYT Sbjct: 209 FMDLQEQFKTSYVFISHNLSVVE---HIAD--DVMVMYFGGVAELGDKKRIFSNPRHPYT 263 Query: 256 NDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKY-S 309 L+ TPSI + I +K+ E GC + RCP+ +D C++EEPKL + Sbjct: 264 RALMSATPSIFEADRTIKIKLQGEMPSPLNPPSGCTFHQRCPYVIDRCRSEEPKLREVDG 323 Query: 310 HEVACFLYGKVGE 322 +V+C +VG+ Sbjct: 324 RQVSCHRAEEVGD 336 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: 269 Number of extensions: 9 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: 339 Length adjustment: 28 Effective length of query: 296 Effective length of database: 311 Effective search space: 92056 Effective search space used: 92056 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