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 N515DRAFT_2043 N515DRAFT_2043 putative ABC transport system ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Dyella79:N515DRAFT_2043 Length = 230 Score = 104 bits (259), Expect = 2e-27 Identities = 73/232 (31%), Positives = 125/232 (53%), Gaps = 14/232 (6%) Query: 6 VKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSG 65 V++L+K++ G K+++E + +++ + E + ++L+G SGSGKTT +I L PT G Sbjct: 9 VRDLSKVYERG---KQKVEVLHHINLNIAEGDFLALMGPSGSGKTTLLNLIGGLDSPTGG 65 Query: 66 EIYFEGKDIWKDIKDRESLVEFRR-KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPS 124 I G+ I D +L ++R V VFQ F + P +R + + L + + Sbjct: 66 SIGVGGQRI--DQLGAGALAKWRAANVGFVFQ--FYNLMPMLTAQRNVELPLLLTKLSAA 121 Query: 125 NKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSM 184 +++ + +L VG+D + P ++SGGQ+QR+ IAR + P L+V DEPT Sbjct: 122 QRRKNAAI---ALQLVGLDERS--SHKPSELSGGQQQRVAIARAIVSDPTLLVCDEPTGD 176 Query: 185 IDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 +D S ++ LL L E G +I+ +THD A Y + + + K G +VE+ Sbjct: 177 LDRQSAEDVLGLLRTLNREHGKTIVMVTHDPKAAEYANHTLHLDK-GTLVEQ 227 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: 230 Length adjustment: 24 Effective length of query: 244 Effective length of database: 206 Effective search space: 50264 Effective search space used: 50264 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 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