Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 7025500 Shewana3_2654 ABC transporter related (RefSeq)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__ANA3:7025500 Length = 261 Score = 150 bits (379), Expect = 3e-41 Identities = 87/234 (37%), Positives = 148/234 (63%), Gaps = 10/234 (4%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 AL VS +N+G+ L ++GE+G+GK+TL R++VG + + GE+ ++G + + R I ++ Sbjct: 29 ALAPVSFELNRGETLAIVGEAGSGKSTLARILVGAEPRSGGEIYFEGEAL--DSRNIKQR 86 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 R +++I QDP ++L T+ ++L P+ +++ E ++I+ L V L P E Sbjct: 87 CRL-IRMIFQDPNTSLNPRLTIGQLLDEPLRFNTELSAKERSGQVIDTLRKVGLLP--EH 143 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 YPH +S GQKQR+++AR+L +NP+II+ADE +T +D S+R ILN L +++ L L+ Sbjct: 144 ADFYPHMISEGQKQRVAVARALMLNPKIIIADEALTALDLSVRSQILNLLLKLQKDLGLS 203 Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIK 260 +F++H++ I R H+ DK +V+ G +VE+A E+I P H YT LI+ Sbjct: 204 YIFVSHNLNIIR---HVSDK--IMVLHKGVMVEKAPTEQIFNSPQHEYTQRLIQ 252 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: 226 Number of extensions: 9 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: 261 Length adjustment: 26 Effective length of query: 298 Effective length of database: 235 Effective search space: 70030 Effective search space used: 70030 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 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