Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_01222 H281DRAFT_01222 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Burk376:H281DRAFT_01222 Length = 353 Score = 175 bits (443), Expect = 2e-48 Identities = 118/319 (36%), Positives = 165/319 (51%), Gaps = 11/319 (3%) Query: 24 PASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLA 83 PA+ G A + LA+ RE L L LLIV A P FL NL VL + ++L+ Sbjct: 22 PATAGGFA-ANLAKSRETTLFVVLILLIVGTALARPQFLNLQNLRDVLLNVSIISLLTAG 80 Query: 84 ESLIVLTGKFDLSLESTVGI-APAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGF 142 ++++L DLS+ STVGI A AVG++ V Q P L A + +G V G Sbjct: 81 MTVVILMRHIDLSVGSTVGISAYAVGSLYVAYP-------QMPVVVALAAGLGIGLVAGG 133 Query: 143 INGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTL--FDMPTSFFALATTIVLGLPLS 200 IN LV R+ + + TL+ L + RG GG + +P +F LAT G+P Sbjct: 134 INALLVAVGRVPSLVATLSTLYIFRGADYAWVHGGQINATSLPDAFSRLATGTFFGIPTL 193 Query: 201 VWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGG 260 +A A L+ R GR YAIG NPEAAR AG+ VER F+L +A G Sbjct: 194 ALIALVVLLALAIYLKQFRGGREHYAIGSNPEAARLAGVNVERRVMAGFLLSGAIAGFAG 253 Query: 261 LIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLA 320 + G ++A+ G+ V AAAV+G +++ GG GT+ GA G L+LGV+ L + Sbjct: 254 ALWLARFGTVDASTAKGIELQVVAAAVVGSVAITGGVGTILGATLGALVLGVISIALVVL 313 Query: 321 QVPSFWIQAIYGAIILGSL 339 V FW QAI GA+I+ ++ Sbjct: 314 HVSPFWEQAIEGALIVAAI 332 Lambda K H 0.326 0.140 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: 292 Number of extensions: 13 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: 351 Length of database: 353 Length adjustment: 29 Effective length of query: 322 Effective length of database: 324 Effective search space: 104328 Effective search space used: 104328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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