Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_085638008.1 MGEO_RS12330 ATP-binding cassette domain-containing protein
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_002115805.1:WP_085638008.1 Length = 320 Score = 177 bits (450), Expect = 2e-49 Identities = 112/332 (33%), Positives = 183/332 (55%), Gaps = 30/332 (9%) Query: 1 MGLMELKGVSVIFE------DKVGLFKKRKFY-ALKDVSLSMNQGDLLIVLGESGAGKTT 53 M L+ +K +S +F+ ++V + + F A+ +V + ++GESG+GK+T Sbjct: 1 MALVRVKNLSRVFDVSKPWLNRVIERRSKAFLTAVSEVDFEVEPRSTYALVGESGSGKST 60 Query: 54 LGRVIVGLQKPTSGEVVYDGYNIWKNKRKI-FKKYRKDVQLIPQDPYSTLPFNKTVEEIL 112 +G+++VGL KP+SG V +G ++ R D+Q+I QDPY++L V +I+ Sbjct: 61 IGKMLVGLLKPSSGTVEIEGIDLASETDAAKIDAIRSDIQMIFQDPYASLNPRWRVRDII 120 Query: 113 VAPILRWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNP 172 V P+ + K LLE V L+ + GK+PH+ SGGQ+QR+ IAR+L+ P Sbjct: 121 VEPVASRGGRTEGLAEK----LLEQVGLSVQDA--GKFPHEFSGGQRQRICIARALASEP 174 Query: 173 RIIVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVM 232 +IV DEP + +D S++ +LN ++++K+ LT V I+HD+ + R H+ DK V+ Sbjct: 175 NLIVCDEPTSALDVSVQAQVLNLMSDLKDDFGLTYVLISHDLTVVR---HMADKIG--VL 229 Query: 233 FAGRIVERADLEEILKDPLHPYTNDLIKLTPSIDNLYKEINV-------KINYERVEKGC 285 + GR+VE A ++ + P HPYT L++ P +D +E+ IN GC Sbjct: 230 YLGRLVEEASPNDLFETPKHPYTQMLLEAAPQMDGFGREVQPPEGEIPDPIN---PPSGC 286 Query: 286 PYRLRCPFAMDICKNEEPKLFKYS-HEVACFL 316 + RCP A DICK + P++ + VAC L Sbjct: 287 AFHPRCPIAQDICKRQRPEMRSINGMRVACHL 318 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: 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: 320 Length adjustment: 28 Effective length of query: 296 Effective length of database: 292 Effective search space: 86432 Effective search space used: 86432 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 Sep 24 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