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 Ac3H11_4824 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4824 Length = 295 Score = 172 bits (436), Expect = 7e-48 Identities = 97/262 (37%), Positives = 156/262 (59%), Gaps = 9/262 (3%) Query: 4 LVVKNLTKIFSLG----FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRL 59 L VK+L + ++L F ++A+ VSF + + +VGESGSGK+T A++++ L Sbjct: 14 LQVKDLVREYTLPREHLFRPPGTVQALNGVSFSIAAGRSLGVVGESGSGKSTLARLVMAL 73 Query: 60 LPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLL 119 PT+G + G+++ + E L + RR VFQDP+ S +P VER + + + Sbjct: 74 DAPTAGTVELLGRNLHQ--LPAEQLRQARRDFQMVFQDPYGSLDPRQTVERIVTEPLQA- 130 Query: 120 ENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVAD 179 + + E E + L +VG+ D LGKYPH+ SGGQ+QRI IAR I RP LIVAD Sbjct: 131 -QGQTTRAEQREQAAQVLSQVGLRTND-LGKYPHEFSGGQRQRIAIARALITRPRLIVAD 188 Query: 180 EPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHP 239 EP S +D S + ++ L+++L+++ G + + I+HDL + ++ D + V+ G IVERG P Sbjct: 189 EPVSALDVSVQAQVLNLMQDLQQQFGITYMLISHDLAVVNHLCDEVVVLYQGRIVERGSP 248 Query: 240 DKVVLEPTHEYTKLLVGSIPKL 261 ++ H YT+ LVG++P++ Sbjct: 249 GELFRNAQHPYTQSLVGAVPQV 270 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: 181 Number of extensions: 4 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: 295 Length adjustment: 26 Effective length of query: 242 Effective length of database: 269 Effective search space: 65098 Effective search space used: 65098 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 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