Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_000017185.1:WP_011972867.1 Length = 281 Score = 98.6 bits (244), Expect = 2e-25 Identities = 72/224 (32%), Positives = 121/224 (54%), Gaps = 14/224 (6%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 AL ++S+ +GD++ +LG +GAGK+TL G+ KP SG+++ G I K K + Sbjct: 19 ALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGKILLKGAPI-KYDAKSLME 77 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 RK V ++ Q+ L +++ P+ K ++E+ KR+ L+ V + E F Sbjct: 78 VRKTVGIVFQNSDDQLFAPTVKQDVAFGPLNLGLK--EEEVEKRVKEALKEVGM---EGF 132 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 K PH LSGGQK+R++IA L+++P I+V DEP +D I+ L ++ N+ +T Sbjct: 133 ENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDEPTAGLDPMGASKIMKLLYKL-NKEGIT 191 Query: 207 MVFITHDIPIAR-YFYHLFDKGNTIVMFAGRIVERADLEEILKD 249 ++ THD+ + Y +F G T +IV+ +EE+ D Sbjct: 192 IIISTHDVDLVPIYANKIFVMGKT------KIVKSGTVEEVFSD 229 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: 225 Number of extensions: 6 Number of successful extensions: 2 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: 281 Length adjustment: 27 Effective length of query: 297 Effective length of database: 254 Effective search space: 75438 Effective search space used: 75438 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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