Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_013402767.1 CALHY_RS04220 amino acid ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_000166355.1:WP_013402767.1 Length = 220 Score = 171 bits (432), Expect = 1e-47 Identities = 91/205 (44%), Positives = 138/205 (67%), Gaps = 3/205 (1%) Query: 13 PQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQL 72 P LL ++VT+E+TA ++ +G V GL+ + R++ K +V+ + + YV RGTPLL+Q+ Sbjct: 11 PVLLKASVVTIELTAIAVTIGLVFGLVAALFRIS-KIKVLNYIGSFYVWLFRGTPLLLQI 69 Query: 73 FILFFGLPQF--GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSS 130 F +++GLP+ + LPAF+ G I L I SGAY +E++R AI SIDKGQ EAA+++GM+ Sbjct: 70 FFIYYGLPKIVPALTLPAFLAGAIALIINSGAYTAEIIRAAILSIDKGQYEAAKALGMTY 129 Query: 131 GLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVY 190 MR V++PQ R+IPP+GNEFIAL+K+S+LVS + + +LM Q S + R E+Y Sbjct: 130 LQTMRYVIVPQTYKRLIPPIGNEFIALLKDSSLVSTIGMVELMRAAQLKASATGRDAEIY 189 Query: 191 LAIAVVYFILTGATTLVLRRIELRL 215 +A V+Y LT + + +E RL Sbjct: 190 IAALVIYLALTTVFSTIFNWLEKRL 214 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: 144 Number of extensions: 9 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: 220 Length adjustment: 22 Effective length of query: 200 Effective length of database: 198 Effective search space: 39600 Effective search space used: 39600 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 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