Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 90.9 bits (224), Expect = 3e-23 Identities = 63/183 (34%), Positives = 96/183 (52%), Gaps = 5/183 (2%) Query: 31 VSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKD 90 VS+S+ G+L +V+G SG GK+TL ++ GL P GEV G I + K +R Sbjct: 31 VSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGEVDALGNPICRMKAGARDAFRLA 90 Query: 91 VQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEFLGKY 150 ++ FN E VA +L+ K+ E R+R LE V L P Sbjct: 91 NTGFVFQGFNL--FNALTAEEQVAYVLQCMKVKPAEARQRARAALEAVGLGPRMRLR--- 145 Query: 151 PHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFI 210 P +LSGG+KQR++IAR+L+ PRI+ ADEP + +D+ ++ L +I + ++ + Sbjct: 146 PFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHNQGAAVLCV 205 Query: 211 THD 213 THD Sbjct: 206 THD 208 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: 175 Number of extensions: 11 Number of successful extensions: 3 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: 243 Length adjustment: 26 Effective length of query: 298 Effective length of database: 217 Effective search space: 64666 Effective search space used: 64666 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: 47 (22.7 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