Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_086510187.1 BZY95_RS12120 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_002151265.1:WP_086510187.1 Length = 367 Score = 182 bits (461), Expect = 1e-50 Identities = 103/311 (33%), Positives = 177/311 (56%), Gaps = 16/311 (5%) Query: 3 LMELKGVSVIFEDKVGLFKK--RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60 L+ +KG+ F K L + + +A+ + + +G+ L ++GESG GK+T R+++ Sbjct: 31 LLRVKGLRKHFVIKRDLLGRPLSRVHAVDGIDFEVRKGETLGIVGESGCGKSTTARLLMH 90 Query: 61 LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEE-ILVAPILRW 119 L +P GEV++DG + ++ R+ +Q++ Q+ Y++L T+EE I P + Sbjct: 91 LLQPDGGEVIFDGDPVGTRGGLSLREMRRQMQMVFQNSYASLNPRMTIEESIAFGPQVHG 150 Query: 120 EKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADE 179 + + E R+R LL+ V L P E F +YPH+LSGGQ+QR++IAR+L++ PR+++ DE Sbjct: 151 --VGRREARQRARRLLDQVGLLP-ERFAQRYPHELSGGQRQRVNIARALALEPRLLILDE 207 Query: 180 PVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVE 239 V+ +D S+ +LN L ++K LT +FI+HD+ + RY +VM+ G++ E Sbjct: 208 AVSALDKSVEAQVLNLLGDLKQEYGLTYLFISHDLNVVRYV-----SDRVMVMYLGKVAE 262 Query: 240 RADLEEILKDPLHPYTNDLIKLTPSIDNLYKEINVKI-----NYERVEKGCPYRLRCPFA 294 D E + + P HPYT L+ PS++ + + N + GC + RCP A Sbjct: 263 VGDSEALYRAPAHPYTRALMSAMPSLEPGRRTQTAPLAGDPPNPIDLPPGCRFCPRCPLA 322 Query: 295 MDICKNEEPKL 305 +D+C+ EP+L Sbjct: 323 VDLCRGTEPEL 333 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: 288 Number of extensions: 14 Number of successful extensions: 4 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: 367 Length adjustment: 29 Effective length of query: 295 Effective length of database: 338 Effective search space: 99710 Effective search space used: 99710 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 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