Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 192 bits (488), Expect = 1e-53 Identities = 105/308 (34%), Positives = 170/308 (55%), Gaps = 3/308 (0%) Query: 43 LLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVG 102 L AL ++ + + SP FLT + L +++ + + + + + +++T DLS+ S V Sbjct: 29 LFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVA 88 Query: 103 IAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAM 162 + V A ++ ++ G+ AGL A + VGA G +NG V LRL FIVTLAM Sbjct: 89 LTGMVAATVMAGSSPGAIGL---GIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAM 145 Query: 163 LIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGR 222 + + RG+ + + G T FD P +F A V GLP+ + + F I +LR G Sbjct: 146 MAMARGLTLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGH 205 Query: 223 ALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTV 282 ++A+GGN EAAR AGI V R+ + ++L + A++ G+++ G + + + NG+ V Sbjct: 206 QVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQV 265 Query: 283 FAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMVA 342 AA VIGG SL GG+G++ G GV+L+GV+ L+L V FW Q I G +I ++++ Sbjct: 266 IAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLD 325 Query: 343 RLASGEGQ 350 L+ Q Sbjct: 326 ALSQRRKQ 333 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: 295 Number of extensions: 17 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: 351 Length of database: 333 Length adjustment: 29 Effective length of query: 322 Effective length of database: 304 Effective search space: 97888 Effective search space used: 97888 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