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 WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 113 bits (282), Expect = 4e-30 Identities = 73/229 (31%), Positives = 125/229 (54%), Gaps = 12/229 (5%) Query: 7 KNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGE 66 KN+ KI+ G + + ++ ++ ++KE E V+++G SG GK+T ++ L P G Sbjct: 21 KNIWKIYGGG---EAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGM 77 Query: 67 IYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNK 126 +Y +GK ++ ++ FRRK+ F N +E + +NK Sbjct: 78 VYIKGKKTTMFSENDRAV--FRRKISGFIFQQFNLINTLTALENVELPLVLDEKNKNYRI 135 Query: 127 KEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMID 186 K+A +L+K + + ++ YP+Q+SGGQ+QR+ IAR P +I ADEPT +D Sbjct: 136 KKAKKLLKI----INLGHRE--NYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLD 189 Query: 187 ASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVE 235 + + ++ +L+EL E++G ++I +TH+ A Y S I MK+GEIVE Sbjct: 190 SKNSREVMDILKELNEKEGITVIMVTHEPEFAKYAS-RIINMKDGEIVE 237 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: 177 Number of extensions: 9 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: 238 Length adjustment: 24 Effective length of query: 244 Effective length of database: 214 Effective search space: 52216 Effective search space used: 52216 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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