Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_086508346.1 BZY95_RS02050 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_002151265.1:WP_086508346.1 Length = 243 Score = 127 bits (318), Expect = 2e-34 Identities = 73/209 (34%), Positives = 118/209 (56%), Gaps = 10/209 (4%) Query: 18 GALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFILFF 77 G ++T ++ SL+ G V+ + + IGR + +R + + Y RGTPLL+QL+I+++ Sbjct: 28 GLVLTTQLVFLSLVAGLVLAIPLAIGRSSGRRWISLPIYV-YTYVFRGTPLLIQLYIIYY 86 Query: 78 GLPQFG---------ILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGM 128 G+ F IL AF +I + + AY +E+ RGAI++ +G++EAAR+ GM Sbjct: 87 GVVFFDGIQQTFLWPILREAFYPALIAFTLNTAAYTTEIFRGAIKATPRGEIEAARAYGM 146 Query: 129 SSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLE 188 S GL MR +VLP A R +P GNE I ++ SA+ S++T+ D+ + + + Y E Sbjct: 147 SQGLMMRRIVLPSAFRRALPAYGNEVIFMLHASAIASVVTLMDITGAARFVYARFYAPFE 206 Query: 189 VYLAIAVVYFILTGATTLVLRRIELRLRA 217 +L A +Y LT A R +E +L A Sbjct: 207 AFLFAAAIYLCLTFAILYFFRYLEKKLLA 235 Lambda K H 0.328 0.143 0.412 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: 141 Number of extensions: 7 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: 222 Length of database: 243 Length adjustment: 23 Effective length of query: 199 Effective length of database: 220 Effective search space: 43780 Effective search space used: 43780 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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