Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 142 bits (357), Expect = 2e-38 Identities = 90/305 (29%), Positives = 158/305 (51%), Gaps = 9/305 (2%) Query: 43 LLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVG 102 ++ L ++I+ SF + N I++ + L ++ L +L++ +FDLS +G Sbjct: 22 IIAGLGIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLS----IG 77 Query: 103 IAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAM 162 ++G +L A++G P LL ++VG V+GF NG +V + ++ +F+ TLAM Sbjct: 78 AMASLGGVLSALLAASGT----PIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAM 133 Query: 163 LIVLRGMLVGATKGGTLFD-MPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLG 221 V+ G+ T G T+F+ +P F L + + LP + I +++ LG Sbjct: 134 GTVIGGVTFWLTGGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLG 193 Query: 222 RALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFT 281 R LYAIGGN +A+ +GI + R F L +LA+ G ++ +G+ + G+G Sbjct: 194 RRLYAIGGNEKASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLN 253 Query: 282 VFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMV 341 +AA +G + G + G L G ++G++ N LT+ +VPSF I GAII+ +L+ Sbjct: 254 AYAAVFLGMTIVKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALIS 313 Query: 342 ARLAS 346 ++ S Sbjct: 314 QKIGS 318 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: 282 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: 321 Length adjustment: 28 Effective length of query: 323 Effective length of database: 293 Effective search space: 94639 Effective search space used: 94639 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