Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028313407.1 G491_RS0102100 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000429905.1:WP_028313407.1 Length = 259 Score = 241 bits (616), Expect = 8e-69 Identities = 127/254 (50%), Positives = 174/254 (68%), Gaps = 1/254 (0%) Query: 5 SNE-VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 SNE +L++ S FGG++A+ DV +++G + LIGPNGAGKTT FN+ITG++ D+ Sbjct: 6 SNENSLLRIENASISFGGVKAVRDVSFEVQKGAIQALIGPNGAGKTTLFNLITGVFPLDS 65 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123 G G+ + GIARTFQN+ LF MT LENVMVG+H+RT +G GA+ R Sbjct: 66 GHIFFQGQDTAKRKNFQRVSMGIARTFQNVELFTGMTVLENVMVGQHVRTKTGFLGAIAR 125 Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183 + EEA I ++A L++VG+ AD KA L++G QR +EIARALA++PQL+ LDE Sbjct: 126 LPKTRREEAEIREKAMHWLEFVGLDHEADSKAGDLAFGWQRSVEIARALASEPQLLLLDE 185 Query: 184 PAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243 PAAG+NA E QL +L+ +IR+ T+LL+EHD+ L M + DR+ VLD G +++EG P E Sbjct: 186 PAAGLNANETGQLGDLMRQIRDLGVTLLLVEHDMSLTMEISDRIVVLDQGAKLSEGAPRE 245 Query: 244 VQKNEKVIEAYLGT 257 VQ +EKVI AYLGT Sbjct: 246 VQADEKVIAAYLGT 259 Lambda K H 0.319 0.137 0.384 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: 202 Number of extensions: 6 Number of successful extensions: 1 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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: 47 (22.7 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