Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_008484720.1 B3C1_RS10465 cell division ATP-binding protein FtsE
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_000299915.1:WP_008484720.1 Length = 225 Score = 103 bits (256), Expect = 5e-27 Identities = 71/199 (35%), Positives = 116/199 (58%), Gaps = 8/199 (4%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 AL++VS + +G++ + G SGAGK+TL R+I ++P++G+V +G++I + + Sbjct: 17 ALQNVSFHLGKGEMAFLTGHSGAGKSTLLRLITLQERPSAGKVSINGHDISRLRSAQIPL 76 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 R+D+ +I QD L +KTV E + P++ E+RKR+ L V L+ Sbjct: 77 VRRDIGIIFQD--HRLLMDKTVFENVALPLI-VVGFTAGEIRKRVQTALGWVGLSDKAHC 133 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 YP QLSGG++QR+ IAR++ P +++ADEP +D L + IL L E N L ++ Sbjct: 134 ---YPIQLSGGEQQRVGIARAVVNKPPLLLADEPTGNLDPKLSMDILR-LFEDLNSLGIS 189 Query: 207 MVFITHDIP-IARYFYHLF 224 ++ THD+ IAR +H F Sbjct: 190 VLVATHDLGLIARMRHHTF 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: 194 Number of extensions: 11 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: 225 Length adjustment: 25 Effective length of query: 299 Effective length of database: 200 Effective search space: 59800 Effective search space used: 59800 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 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