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_109737982.1 C1634_RS05005 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_002899945.2:WP_109737982.1 Length = 306 Score = 117 bits (294), Expect = 2e-31 Identities = 71/229 (31%), Positives = 133/229 (58%), Gaps = 11/229 (4%) Query: 24 EAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRES 83 +AV ++SF+ ++EI+ L+G SG GKTTT KMI RL+ +G I+ +GK+I +D+++ Sbjct: 15 KAVDHISFQAFDQEILVLLGTSGCGKTTTLKMINRLIEADAGNIFIDGKNI----RDQKA 70 Query: 84 LVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGID 143 E R + V Q + P Y +++ + LL+ +KK+ E L ++ + Sbjct: 71 -EELRMGIGFVMQH--SGLFPHYTIQQNIAVVPELLK---WDKKKTERRTHELLAKLHLS 124 Query: 144 PKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREE 203 ++VL ++PH++SGGQ+QR+ IAR I +++ DEP +D ++ I + L + Sbjct: 125 -EEVLSRFPHELSGGQQQRVGIARALIADSPVLLMDEPFGALDNITKADIHSEFKSLEDL 183 Query: 204 QGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTK 252 + +I+ +THD+ A+ + I +M G+IV+ G P +++ P++ + + Sbjct: 184 KNKTIVLVTHDVQEAFDLGHRICLMDQGKIVQTGTPKEILYHPSNHFVR 232 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: 196 Number of extensions: 8 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: 306 Length adjustment: 26 Effective length of query: 242 Effective length of database: 280 Effective search space: 67760 Effective search space used: 67760 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 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