Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079 Length = 241 Score = 140 bits (352), Expect = 3e-38 Identities = 82/247 (33%), Positives = 134/247 (54%), Gaps = 14/247 (5%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 LK ++K + Q + DV ++I GQ+ GL+GPNGAGKTT F +I GL D G + Sbjct: 4 LKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLID 63 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 +H AKAGI Q +F +++ +N+M A+ T+ + Sbjct: 64 DLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIM-------------AILETRK-EL 109 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 ++A + + LL I D +LS G++RR+EIARALAT+P+ I LDEP AG++ Sbjct: 110 DQAGRRQELESLLQEFHIHHIRDNLGMSLSGGERRRVEIARALATNPKFILLDEPFAGVD 169 Query: 190 ATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEK 249 ++++I ++ +L+ +H+V+ + +C+ +++ G+ IAEG+ A + NE Sbjct: 170 PISVGDIKQIIHHLKAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDSATILANEL 229 Query: 250 VIEAYLG 256 V E YLG Sbjct: 230 VKEVYLG 236 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: 153 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: 241 Length adjustment: 24 Effective length of query: 236 Effective length of database: 217 Effective search space: 51212 Effective search space used: 51212 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