Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_086510333.1 BZY95_RS12915 glutamine ABC transporter permease GlnP
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_002151265.1:WP_086510333.1 Length = 218 Score = 154 bits (388), Expect = 2e-42 Identities = 83/217 (38%), Positives = 137/217 (63%), Gaps = 2/217 (0%) Query: 1 MELDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYV 60 M D+S + +PQLL GA +T+ IT L G V+G + GI R + Y Y+ Sbjct: 1 MNTDWSVIVTFMPQLLKGAQMTIFITVVGLCGGMVVGAIAGIMRAYGNWLLNYT-AMVYI 59 Query: 61 AAIRGTPLLVQLFILFFGLPQFG-ILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQ 119 IRGTP++VQ+ L+F LP I + +I + I +GAY++E+VRG++QSI +G Sbjct: 60 EVIRGTPIVVQVMFLYFALPVLASIRIDPLSAAMIAIVINAGAYIAEIVRGSLQSISRGL 119 Query: 120 MEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKI 179 EA ++G+ + +V P A R+IPPLGN+FI +K+++L ++ + +L GQ+I Sbjct: 120 AEAGLALGLPRWKVLLYIVGPLAFRRLIPPLGNQFIISLKDTSLFIVIGVGELTRTGQEI 179 Query: 180 ISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLR 216 ++ ++R++E++ AIA++Y I+TG+ TL+LR IE R++ Sbjct: 180 MAANFRAVEIWSAIAIMYLIMTGSLTLMLRFIERRMK 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: 154 Number of extensions: 10 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 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