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_057507534.1 ABB28_RS04735 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_001431535.1:WP_057507534.1 Length = 229 Score = 100 bits (250), Expect = 2e-26 Identities = 72/236 (30%), Positives = 123/236 (52%), Gaps = 13/236 (5%) Query: 1 MSRLV-VKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL 59 MS LV ++++TK + G +++ + + +++ + V+L+G SGSGKTT +I L Sbjct: 1 MSTLVSLRSITKTYQRG---PEQVKVLHGIDLDIETGDFVALMGPSGSGKTTLLNLIGGL 57 Query: 60 LPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLL 119 P+ GEI EG+ I D L +R H F F + P ++ + + L Sbjct: 58 DSPSGGEITIEGERI--DQMGGGQLSTWRSH-HVGFVFQFYNLMPMLTAQKNVELPLLLT 114 Query: 120 ENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVAD 179 + ++ E+ +L VG+ D P+++SGGQ+QR+ IAR + P ++ D Sbjct: 115 HLGAAQRRRNAEI---ALTLVGL--ADRRSHRPNELSGGQQQRVAIARAIVSDPTFLICD 169 Query: 180 EPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVE 235 EPT +D S I++LL++L E G +II +THD A Y + + + K GE+ + Sbjct: 170 EPTGDLDRQSAEEILQLLQQLNREHGKTIIMVTHDPKAAEYATHTVHLDK-GELAD 224 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: 143 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: 229 Length adjustment: 24 Effective length of query: 244 Effective length of database: 205 Effective search space: 50020 Effective search space used: 50020 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 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