Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 120 bits (302), Expect = 4e-32 Identities = 75/235 (31%), Positives = 139/235 (59%), Gaps = 12/235 (5%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWK-NKRKIFK 85 A+KD +LS+N+G++ +++G SG+GK+TL R I L +PTSGEV+ +G +I K + +++ + Sbjct: 42 AVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQ 101 Query: 86 KYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEE 145 RK++ ++ Q+ + LP + I L + + K E ++ + ++LV L E Sbjct: 102 IRRKELAMVFQN-FGLLPHRSVLHNIAFG--LELQGVKKGEREQKAMESMQLVGLKGYE- 157 Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205 + +LSGG +QR+ +AR+L+ NP +++ DE + +D +R+ + + L +++++ Sbjct: 158 --NQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKK 215 Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIK 260 T+VFITHD+ A L D+ +M G IV+ EEIL +P + Y ++ Sbjct: 216 TIVFITHDLSEA---IKLGDR--IAIMKDGEIVQIGTSEEILTEPANAYVERFVE 265 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: 294 Number of extensions: 16 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: 408 Length adjustment: 29 Effective length of query: 295 Effective length of database: 379 Effective search space: 111805 Effective search space used: 111805 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: 49 (23.5 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