Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BPHYT_RS22030 BPHYT_RS22030 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS22030 Length = 341 Score = 174 bits (442), Expect = 2e-48 Identities = 99/295 (33%), Positives = 168/295 (56%), Gaps = 22/295 (7%) Query: 22 KRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDG-YNIWKNK 80 K A+ VS ++ +G+ + ++GESG GK+TL R I+GL SG V + G + Sbjct: 36 KATLRAVDGVSFNVRRGETVGLVGESGCGKSTLARAIIGLAPVASGSVRWLGDETVLPGA 95 Query: 81 RKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPIL-RWEKINKDELRKRLINLLELVK 139 R+ + R+DVQ+I QDP ++L T+E+I+ P+ + + + ++++R++ +LE V Sbjct: 96 RRNTSRLRRDVQMIFQDPLASLDPRMTIEQIVSEPLTTHGQDVARADVQRRVLTMLERVG 155 Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199 L + L +YPH+ SGGQ QR+ IAR+L P++++ DEPV+ +D S++ I+N L ++ Sbjct: 156 LNA--QHLRRYPHEFSGGQCQRVGIARALIGEPQLVICDEPVSALDVSIQAQIVNLLRDL 213 Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 + L+L+++F+ HD+ + + H +VM+ GR++E D E+ P HPYT L+ Sbjct: 214 QRELSLSLLFVAHDLAVVKAISH-----RVLVMYLGRVMEFGDKREVYGTPRHPYTRALL 268 Query: 260 KLTPSIDNLYK----------EINVKINYERVEKGCPYRLRCPFAMDICKNEEPK 304 P D + + EI +N GC +R RCP A+D C E P+ Sbjct: 269 SAVPVPDPVVERARRHLLLRGEIASPLN---PPSGCAFRTRCPDAIDACAREIPQ 320 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: 291 Number of extensions: 16 Number of successful extensions: 5 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: 341 Length adjustment: 28 Effective length of query: 296 Effective length of database: 313 Effective search space: 92648 Effective search space used: 92648 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