Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084934314.1 HA51_RS09630 LPS export ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_002095475.1:WP_084934314.1 Length = 241 Score = 144 bits (364), Expect = 1e-39 Identities = 78/242 (32%), Positives = 133/242 (54%), Gaps = 14/242 (5%) Query: 15 ISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYE 74 ++K + G + + DV + +K G++ GL+GPNGAGKTT F ++ G+ DAG + + Sbjct: 9 LAKAYKGRRVVEDVSLQVKSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGRIVIDDEDIS 68 Query: 75 PTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAI 134 +H A+ GI Q +F ++ +N+M AV + + EE Sbjct: 69 ILPLHARARRGIGYLPQEASIFRRLSVFDNLM-------------AVLQIRDDLTEEQR- 114 Query: 135 AKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKV 194 RA EL++ I D + LS G++RR+EIARALA +P+ I LDEP AG++ + Sbjct: 115 QDRANELMEEFHIEHLRDSMGQALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVI 174 Query: 195 QLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEAY 254 ++++I+ +R+ +L+ +H+V+ + +C+R ++ G IA G P E+ +E+V Y Sbjct: 175 DIKKIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPDEILADEQVKRVY 234 Query: 255 LG 256 LG Sbjct: 235 LG 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: 157 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 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