Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 154 bits (390), Expect = 1e-42 Identities = 88/251 (35%), Positives = 138/251 (54%), Gaps = 20/251 (7%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L G+ KRF Q + D +I+ G+V GL+GPNGAGKTT F ++ GL DAGT +L Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 +H AK GI Q +F +T +N+M +R Sbjct: 61 DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLELR---------------- 104 Query: 129 AEEAAIAKRAQEL---LDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185 E + +RA EL LD + I AD + +LS G++RR+EIARALA +P+ + LDEP Sbjct: 105 -ENLSAKQRAGELESLLDELKIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPF 163 Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245 AG++ +++ ++ ++ +L+ +H+V+ +G+CDR +L+ G+ ++ G PA + Sbjct: 164 AGVDPISVGEIQRIVRHLKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHIL 223 Query: 246 KNEKVIEAYLG 256 +EKV E YLG Sbjct: 224 ADEKVREVYLG 234 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: 173 Number of extensions: 9 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: 260 Length of database: 239 Length adjustment: 24 Effective length of query: 236 Effective length of database: 215 Effective search space: 50740 Effective search space used: 50740 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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