Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate RR42_RS07935 RR42_RS07935 peptide ABC transporter ATPase
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS07935 Length = 361 Score = 184 bits (468), Expect = 2e-51 Identities = 110/297 (37%), Positives = 170/297 (57%), Gaps = 15/297 (5%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 A+ VS + +G+ L V+GESG GK+T R+++ L + SGE+++D + + + K+ Sbjct: 51 AVDGVSFEVRKGETLGVVGESGCGKSTTARLLMQLIEQNSGELIFDALGVGSAQLPM-KR 109 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 YR VQ++ QD YS+L T+EE +A R I+ E R LL+ V L P F Sbjct: 110 YRSQVQMVFQDSYSSLNPRLTIEES-IAFTARVHGIDAAEASARARALLDRVGLEPTR-F 167 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 G+YPH+LSGGQ+QR++IAR+L + PR+++ DE V+ +D S+ +LN L E+K +LT Sbjct: 168 AGRYPHELSGGQRQRVNIARALVLRPRLVILDEAVSALDKSVEAQVLNLLLELKAEFDLT 227 Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSID 266 VFI+HD+ + RY L D+ +VM+ G++VE D E + +P HPYT L+ P++D Sbjct: 228 YVFISHDLNVIRY---LCDR--VMVMYLGKVVEVGDTETLYANPAHPYTRALLASMPAMD 282 Query: 267 NLYKEINVKI-----NYERVEKGCPYRLRCPFAMDICKNEEPKLFK--YSHEVACFL 316 ++ + N GC + RC A D+C P+L H VAC + Sbjct: 283 PDHRTQVAPLAGDPPNPINPPSGCSFHPRCAMAQDVCSRRAPQLSDALAGHPVACLM 339 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: 278 Number of extensions: 11 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: 361 Length adjustment: 29 Effective length of query: 295 Effective length of database: 332 Effective search space: 97940 Effective search space used: 97940 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