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_2052 Putative glutathione transporter, ATP-binding component
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2052 Length = 345 Score = 172 bits (435), Expect = 1e-47 Identities = 91/243 (37%), Positives = 151/243 (62%), Gaps = 9/243 (3%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 + AV VSFE+++ + ++LVGESG GK+T A++++ L PT G + F+ +D K ++ Sbjct: 48 LHAVDGVSFEIEKGKTLALVGESGCGKSTVARLLVGLYEPTRGGLTFDNQDAHAAFKGKD 107 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAI---SLLENKPSNKKEALELIKESLFR 139 + RR++ +FQDP+AS NP + VE + + + L+ +K K EL+K Sbjct: 108 AQA-MRRRIQMIFQDPYASLNPRWLVEDIIGEPLREHGLITDKAELKARVGELLKS---- 162 Query: 140 VGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 VG+ P D++ KYPHQ SGGQ+QRI IAR P +V DEPTS +D S + ++ ++++ Sbjct: 163 VGLSPLDMV-KYPHQFSGGQRQRISIARALATEPEFLVCDEPTSALDVSVQAQVLNIMKD 221 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259 L+ E+ + +FI+H+L + +VSD + VM G +VE ++ P H YT++L+ +IP Sbjct: 222 LQRERQLTYLFISHNLAVVRHVSDQVGVMYLGRLVELADKHQLFNSPRHPYTRMLLDAIP 281 Query: 260 KLY 262 K++ Sbjct: 282 KMH 284 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: 237 Number of extensions: 9 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: 345 Length adjustment: 27 Effective length of query: 241 Effective length of database: 318 Effective search space: 76638 Effective search space used: 76638 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 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