Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate AO356_00960 AO356_00960 ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00960 Length = 325 Score = 115 bits (288), Expect = 2e-30 Identities = 91/302 (30%), Positives = 149/302 (49%), Gaps = 10/302 (3%) Query: 41 LALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLEST 100 L L AL ++ + + +S FL+ ++ L ++ + + I++ G DLS+ S Sbjct: 21 LGLAGALLAMVALFSTLSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGIDLSVGSV 80 Query: 101 VGIAPAVGAMLVMPAASAGFGMQ-WPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVT 159 + +A + ++ V+ G+G WP+A L + V A+ G + G + V R+ +FIV+ Sbjct: 81 LALAASTVSVAVL-----GWGWSVWPSA---LLGMAVAALAGTVTGSITVAWRIPSFIVS 132 Query: 160 LAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHR 219 L +L + RG+ T T + + SF L+ I G+ S +A IA +L Sbjct: 133 LGVLEMARGLAYQMTGSRTAY-IGDSFAWLSNPIAFGISPSFIIALLVIFIAQAVLTRTV 191 Query: 220 LGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMI 279 GR L IG N EA R AGI + VF L +LA V L + A + N G+G+ Sbjct: 192 FGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSGLE 251 Query: 280 FTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSL 339 V AA VIGG SL GG+G++ GVL++ V+ L + I GA+I+ ++ Sbjct: 252 LQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAV 311 Query: 340 MV 341 ++ Sbjct: 312 VL 313 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: 261 Number of extensions: 20 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: 325 Length adjustment: 28 Effective length of query: 323 Effective length of database: 297 Effective search space: 95931 Effective search space used: 95931 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