Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 123 bits (309), Expect = 6e-33 Identities = 79/233 (33%), Positives = 128/233 (54%), Gaps = 10/233 (4%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 AL+ SL + G++ ++G SGAGK+TL R+I L++P+ G ++ DG + + Sbjct: 20 ALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRA 79 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 R+ + +I Q + L ++TV + + P+ + + +++ R+ LL V L E Sbjct: 80 QRRRIGMIFQ--HFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGL---EAH 134 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 KYP QLSGGQKQR+ IAR+L+ P I++ DE + +D +L LAEI L LT Sbjct: 135 ASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLT 194 Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 +V ITH++ + R + D+ V+ AGRIVE + ++ P HP T + Sbjct: 195 IVLITHEMDVVR---RVCDR--VAVLDAGRIVEHGAVADVFLHPRHPTTRRFV 242 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: 269 Number of extensions: 15 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: 336 Length adjustment: 28 Effective length of query: 296 Effective length of database: 308 Effective search space: 91168 Effective search space used: 91168 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