Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 189 bits (479), Expect = 1e-52 Identities = 102/249 (40%), Positives = 154/249 (61%), Gaps = 11/249 (4%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I + N+SK F G+ AL +N++I+ GE G+LGPSG+GKTT +RIIAGL+ +G+++ Sbjct: 3 IRLTNISKKF--GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLT----NMKMSKEEIRK 119 F +R V V DR++G VFQ +AL+ ++T +N+AF L + SK EI+K Sbjct: 61 FGNRDVTQ-----VHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQK 115 Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179 RV + +++ + H+ +P +LSGGQ+QR+ALARAL P +LLLDEPF LDA++R Sbjct: 116 RVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKEL 175 Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239 R ++ + L T + V+HD + ++DRV V+ G + QV P +LY P S V Sbjct: 176 RRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFD 235 Query: 240 LIGEINELE 248 +G +N E Sbjct: 236 FLGNVNRFE 244 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: 324 Number of extensions: 16 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: 353 Length of database: 376 Length adjustment: 29 Effective length of query: 324 Effective length of database: 347 Effective search space: 112428 Effective search space used: 112428 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