Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 95.5 bits (236), Expect = 1e-24 Identities = 70/225 (31%), Positives = 116/225 (51%), Gaps = 13/225 (5%) Query: 28 LKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKKY 87 L V L + +G+ ++VLG+SG GK+ L +++VGL G + G + K + Sbjct: 21 LMGVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQDEGTMNVLGKEVSNLGAKDLNEL 80 Query: 88 RKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK-INKDELRKRLINLLELVKLTPAEEF 146 R + Q S L + TV E L P++R K +++ E K + +LE V L+ + Sbjct: 81 RLKIGFSFQA--SALYDSMTVRENLEFPLVRNVKGLSRTEKDKMVEEVLEAVGLS---QT 135 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 + + P +LSGGQ++R+ IAR+L + P I++ DEP +D I N + E++ N + Sbjct: 136 INQMPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGLDPITCSDINNLINEVRENYNTS 195 Query: 207 MVFITHDIPIARYFYHLFDKGNTI-VMFAGRIVERADLEEILKDP 250 + ITHD+ AR D G+ + V+ G+ EE+ K P Sbjct: 196 SIIITHDLTCAR------DTGDRVAVLLDGQFGAEGKFEEVFKTP 234 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: 192 Number of extensions: 9 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: 249 Length adjustment: 26 Effective length of query: 298 Effective length of database: 223 Effective search space: 66454 Effective search space used: 66454 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