Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 169 bits (428), Expect = 9e-47 Identities = 109/330 (33%), Positives = 175/330 (53%), Gaps = 15/330 (4%) Query: 27 RGKRARSELARLRELAL---LPALALLIVIGA---FISPSFLTKANLISVLGASAALALV 80 R A E L++LA L L L +VIGA +SP FLT++N+ ++L S + ++ Sbjct: 14 RSAAAAGEGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGIL 73 Query: 81 VLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI 140 + + ++LTG DLS+ S G++ V + + +P +L V+ GA + Sbjct: 74 SIGMTFVILTGGIDLSVGSVAGLSGIVLGLALK---------DYPIPVAILLGVLTGAGV 124 Query: 141 GFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLS 200 G ++G L+ RL AF+VTL M+ + R + + + P+ ++ T V G+P + Sbjct: 125 GLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTN 184 Query: 201 VWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGG 260 V A+ +A L Y + GR +YAIG N EAARAAG+ V + +V+ LA+V Sbjct: 185 VLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAI 244 Query: 261 LIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLA 320 + +++ GNGM AA VIGG SL GG+G++ G L GVL++ +++N L L Sbjct: 245 TFSVAQILSVDPLTGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLL 304 Query: 321 QVPSFWIQAIYGAIILGSLMVARLASGEGQ 350 V FW + G+II+ +L+V RL + Sbjct: 305 GVSPFWQGSAIGSIIIMALLVERLVRARSE 334 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: 296 Number of extensions: 23 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: 335 Length adjustment: 29 Effective length of query: 322 Effective length of database: 306 Effective search space: 98532 Effective search space used: 98532 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 Apr 09 2024. 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