Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate HSERO_RS17545 HSERO_RS17545 glutamine ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__HerbieS:HSERO_RS17545 Length = 218 Score = 151 bits (381), Expect = 1e-41 Identities = 78/217 (35%), Positives = 135/217 (62%), Gaps = 2/217 (0%) Query: 1 MELDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYV 60 ++ DFS + +P LL GA VTV ITAA L+ G ++GLL G+ R ++ + YV Sbjct: 1 VDFDFSVITDSLPALLEGAKVTVLITAAGLVGGTLVGLLAGLMRAYGNT-LLKGIGFGYV 59 Query: 61 AAIRGTPLLVQLFILFFGLPQF-GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQ 119 +RGTP++VQ+ ++F LP GI + V + + SGAY++E+VRGA S+ +G Sbjct: 60 EFVRGTPIVVQVMFIYFALPVLLGIRVDPMTAAVTSIVVNSGAYIAEIVRGAFLSVPRGL 119 Query: 120 MEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKI 179 EA ++G+ + V+ P A+ RM+P +GN+FI +K+++L ++ + +L +GQ+I Sbjct: 120 REAGLALGLPVWRVLAFVIGPVAIRRMVPAMGNQFIVSLKDTSLFIVIGVGELTRQGQEI 179 Query: 180 ISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLR 216 ++ ++R++E+++A+A +Y + G T LR E R+R Sbjct: 180 MAANFRAVEIWIAVAAIYLCMIGVMTYALRTFEKRMR 216 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: 158 Number of extensions: 11 Number of successful extensions: 3 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: 218 Length adjustment: 22 Effective length of query: 200 Effective length of database: 196 Effective search space: 39200 Effective search space used: 39200 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: 45 (21.9 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