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_085638008.1 MGEO_RS12330 ATP-binding cassette domain-containing protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_002115805.1:WP_085638008.1 Length = 320 Score = 167 bits (424), Expect = 2e-46 Identities = 96/270 (35%), Positives = 155/270 (57%), Gaps = 17/270 (6%) Query: 1 MSRLVVKNLTKIFSLGF---------FSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTT 51 M+ + VKNL+++F + SK + AV V FEV+ + +LVGESGSGK+T Sbjct: 1 MALVRVKNLSRVFDVSKPWLNRVIERRSKAFLTAVSEVDFEVEPRSTYALVGESGSGKST 60 Query: 52 TAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERT 111 KM++ LL P+SG + EG D+ + D + R + +FQDP+AS NP + V Sbjct: 61 IGKMLVGLLKPSSGTVEIEGIDLASET-DAAKIDAIRSDIQMIFQDPYASLNPRWRVRDI 119 Query: 112 LWQAISLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWIL 171 + + ++ + E L L +VG+ +D GK+PH+ SGGQ+QRI IAR Sbjct: 120 IVEPVASRGGRTEGLAEKL------LEQVGLSVQDA-GKFPHEFSGGQRQRICIARALAS 172 Query: 172 RPLLIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNG 231 P LIV DEPTS +D S + ++ L+ +L+++ G + + I+HDL + +++D I V+ G Sbjct: 173 EPNLIVCDEPTSALDVSVQAQVLNLMSDLKDDFGLTYVLISHDLTVVRHMADKIGVLYLG 232 Query: 232 EIVERGHPDKVVLEPTHEYTKLLVGSIPKL 261 +VE P+ + P H YT++L+ + P++ Sbjct: 233 RLVEEASPNDLFETPKHPYTQMLLEAAPQM 262 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: 209 Number of extensions: 11 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: 268 Length of database: 320 Length adjustment: 26 Effective length of query: 242 Effective length of database: 294 Effective search space: 71148 Effective search space used: 71148 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: 48 (23.1 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