Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate CCNA_02173 CCNA_02173 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Caulo:CCNA_02173 Length = 249 Score = 106 bits (265), Expect = 4e-28 Identities = 76/240 (31%), Positives = 125/240 (52%), Gaps = 15/240 (6%) Query: 4 LVVKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT 63 L + L K F G + IE +K + F+ K ++ ++G SGSGK+T + LL P Sbjct: 14 LEARGLVKRFKTG---RSYIEVLKGIDFDAKHGDVTMVMGPSGSGKSTLVAALSGLLKPD 70 Query: 64 SGEIY-FEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENK 122 G++ E KD+W + ++ R H F F +N F P Q ++ L+ + Sbjct: 71 EGKVSALEAKDLWSLPTGK---IDKFRLDHCGFI--FQGFNLF-PALTAKQQVMTALKYQ 124 Query: 123 PSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPT 182 ++ E + +L VG+ P+ + + P ++SGG+KQR+ IAR P LI ADEPT Sbjct: 125 GASPGEQARRAQAALESVGLGPR--VNQRPSELSGGEKQRVAIARALAKNPNLIFADEPT 182 Query: 183 SMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVE--RGHPD 240 S +D + +I+LL E +G ++I +THD L Y +D + +++G I++ R PD Sbjct: 183 SALDGENGQIVIRLLREAASVRGAAVICVTHDPRLEAY-ADRVIHIEDGRILDDVRRTPD 241 Lambda K H 0.319 0.139 0.397 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: 163 Number of extensions: 12 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: 268 Length of database: 249 Length adjustment: 24 Effective length of query: 244 Effective length of database: 225 Effective search space: 54900 Effective search space used: 54900 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 (21.7 bits) S2: 47 (22.7 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