Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 130 bits (327), Expect = 4e-35 Identities = 79/246 (32%), Positives = 139/246 (56%), Gaps = 17/246 (6%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 AL+D SL + +G ++ ++GESG+GK++L R+I GL+ ++G V I +K+ Sbjct: 19 ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVPG 78 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146 Y ++QLI Q+ Y P N TVEE + P+L ++K + E ++ LL L F Sbjct: 79 Y-DEIQLIHQE-YKLYP-NSTVEENIARPLLLYDKAYQKERTAEILELLSL------RAF 129 Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206 K P QLSGGQ+Q+++I R+LS+ P +++ DEP + +DA + ++ L EI + L +T Sbjct: 130 KDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVT 189 Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDL---IKLTP 263 ++F+THD+ A L +++ G+++++ ++ E+ + P Y L + L P Sbjct: 190 VIFVTHDVDDA-----LLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGYLNLIP 244 Query: 264 SIDNLY 269 + Y Sbjct: 245 GAEEAY 250 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: 244 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: 318 Length adjustment: 28 Effective length of query: 296 Effective length of database: 290 Effective search space: 85840 Effective search space used: 85840 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: 48 (23.1 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