Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate SMa2079 SMa2079 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Smeli:SMa2079 Length = 314 Score = 194 bits (492), Expect = 3e-54 Identities = 113/322 (35%), Positives = 182/322 (56%), Gaps = 23/322 (7%) Query: 1 MGLMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60 M L+ + ++ + GL + ++ V L + +G+ + ++GESG GK+TLG+ ++ Sbjct: 1 MPLISASNLKTHYKTRDGLLR-----SVDGVDLVVERGETVGLVGESGCGKSTLGKTLLR 55 Query: 61 LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE 120 L PT+G + + G +I + + RK +Q+I QDP+++L T+ EIL AP++ + Sbjct: 56 LVDPTAGRIEFKGEDITALDQGRLRNVRKSIQMIFQDPFASLNPRHTIGEILEAPLIVHQ 115 Query: 121 KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEP 180 + E R + +++ V L PA+ + +YPH+ SGGQ+QR+ IAR+L +NP +IV DEP Sbjct: 116 AGSPPERRSTVASIVAKVGL-PADA-INRYPHEFSGGQRQRIGIARALLLNPELIVCDEP 173 Query: 181 VTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVER 240 V+ +D S++ ILN L E+K L+ +FI+HD+ + RYF +VM+ GR+VE Sbjct: 174 VSALDLSIQAQILNLLVEMKKEFGLSYLFISHDLSVVRYFC-----DRVLVMYLGRVVES 228 Query: 241 ADLEEILKDPLHPYTNDLIKLTPSIDN------LYKEINVKINYERVEKGCPYRLRCPFA 294 AD E + DP HPYT L+ P L E+ N + GC + RCP A Sbjct: 229 ADNETLWSDPRHPYTRALMAAVPDPSRPRQAAPLGGELPSPSN---IPPGCRFHTRCPLA 285 Query: 295 MDICKNEEPKL--FKYSHEVAC 314 ++C+ EP+ K H VAC Sbjct: 286 TELCRVAEPEFRSIKPGHRVAC 307 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: 12 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: 314 Length adjustment: 28 Effective length of query: 296 Effective length of database: 286 Effective search space: 84656 Effective search space used: 84656 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