Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011020340.1 MA_RS01500 ATP-binding cassette domain-containing protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000007345.1:WP_011020340.1 Length = 348 Score = 204 bits (519), Expect = 3e-57 Identities = 118/315 (37%), Positives = 188/315 (59%), Gaps = 29/315 (9%) Query: 9 VSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRL 68 + + +K K +LDN+++ +E+GE F ILGP+GAGKT F+ +IAG VP +G + D + Sbjct: 4 IESLSRKWKNFSLDNLSLKVESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKD 63 Query: 69 VASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKIL 128 V + PE I V+Q ++L+P++ +N+ F M+M K + KRV + A+ L Sbjct: 64 VTD-----LSPEKHDIAFVYQNYSLFPHMNVKKNLEF---GMRMKKIKDPKRVLDTARDL 115 Query: 129 DIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS 188 I H+L+ P LSGG+QQRVALARALV +P +LLLDEP S LD R +++AR ++ + Sbjct: 116 KIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLHK 175 Query: 189 RLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELE 248 + +T+L ++HD + +ADR+ V++ GKL+QVGKPE++++ PV +VAS +G N L+ Sbjct: 176 KNKLTVLHITHDQTEARIMADRIAVVMDGKLIQVGKPEEIFEKPVEGRVASFVGFENVLK 235 Query: 249 GKVTNE---------GVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKD--------- 290 G+V + G V+ + V D+ +RPE++ LSK + Sbjct: 236 GRVISAEQGLLRIRVGEVVIDAAGDMEV-GDQVYAFLRPENIALSKSSTQSSIRNSLQGR 294 Query: 291 --DSWILVGKGKVKV 303 ++W+L +VKV Sbjct: 295 VTEAWVLGALVRVKV 309 Lambda K H 0.319 0.139 0.390 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: 325 Number of extensions: 18 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: 353 Length of database: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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