Align ATPase (characterized, see rationale)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_001013305.1:WP_047094318.1 Length = 240 Score = 144 bits (363), Expect = 2e-39 Identities = 92/221 (41%), Positives = 126/221 (57%), Gaps = 9/221 (4%) Query: 21 MIYAEGVEKWYGN---QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77 +I EG+ K +G FQAL GV + + RG+ V +MGPSGSGKST + L L+ G Sbjct: 6 LIELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLDVPTDG 65 Query: 78 EI---WIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQA 134 IE L+ D+R + R+ +G VFQ FNL T L+N+ L P+ R Q Sbjct: 66 IFRFRGIEVQALTRDQRSLLR-RRYLGFVFQGFNLLARTTALENVEL-PLLYRGETKKQR 123 Query: 135 EATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVR 194 A + L++V + A P +LSGGQQQRVAIARAL P +LL DEPT LD E Sbjct: 124 RIAAERSLDKVGLLPWASHTPAELSGGQQQRVAIARALVTDPDVLLADEPTGNLDTERSL 183 Query: 195 EVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQI 235 E+++++ DL+ G+T+L+ THE A E A +V DG + Sbjct: 184 EIMELLTDLSDTGITVLMVTHEEEMA-EYARTIVHFRDGLV 223 Lambda K H 0.321 0.134 0.387 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: 149 Number of extensions: 9 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: 261 Length of database: 240 Length adjustment: 24 Effective length of query: 237 Effective length of database: 216 Effective search space: 51192 Effective search space used: 51192 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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