Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 199 bits (507), Expect = 7e-56 Identities = 98/223 (43%), Positives = 150/223 (67%), Gaps = 5/223 (2%) Query: 20 ALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPP 79 A+D +++ + E +LGPSG+GKTT +R+IAGL+ P++G++ R+V +PP Sbjct: 18 AVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDILVGGRVVTG-----LPP 72 Query: 80 EDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPR 139 + MVFQ++ALYP+L+ NIAFPL +M +E I ++V A + I H+L+ PR Sbjct: 73 RAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAALFGIGHLLSRKPR 132 Query: 140 ELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSH 199 +LSGG++QRVALARA+V++P LLDEP SNLDA++R SAR ++++Q RL T + V+H Sbjct: 133 QLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQRRLATTTIYVTH 192 Query: 200 DPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIG 242 D + A+ DRV +L G++ Q+G P+ +Y+ P VA+ IG Sbjct: 193 DQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIG 235 Lambda K H 0.319 0.139 0.390 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: 285 Number of extensions: 12 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: 353 Length of database: 351 Length adjustment: 29 Effective length of query: 324 Effective length of database: 322 Effective search space: 104328 Effective search space used: 104328 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: 49 (23.5 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