Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate Pf1N1B4_4792 Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
Query= reanno::BFirm:BPHYT_RS07675 (229 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4792 Length = 371 Score = 276 bits (706), Expect = 4e-79 Identities = 144/223 (64%), Positives = 181/223 (81%) Query: 3 LYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPD 62 L G+GP+LL GT T++LS LSL ++ LGL GAAAKLS + L AT YTTLIR VPD Sbjct: 15 LQGYGPLLLHGTWVTLKLSALSLLVSMALGLLGAAAKLSPLKLLNLPATFYTTLIRGVPD 74 Query: 63 LVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPR 122 LVLMLL+FYS+Q +++LT+A++ P +IDPFVAGV+TLGFIYGAYFTETFRGA L+VPR Sbjct: 75 LVLMLLIFYSLQGWLSSLTEAMDWPYMEIDPFVAGVVTLGFIYGAYFTETFRGAILSVPR 134 Query: 123 GQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQ 182 GQ EA +++G++ + F ++FPQMMRFALP +GNNW VL+KATALVSIIGL+D+VK AQ Sbjct: 135 GQQEAAASFGLNRWQRFRFVVFPQMMRFALPSLGNNWLVLLKATALVSIIGLSDLVKVAQ 194 Query: 183 DAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVR 225 +AGKSTFNM F+L+A +YL IT+ASN VL LE+RY+ GVR Sbjct: 195 EAGKSTFNMLDFLLLAGALYLLITSASNYVLRVLERRYNQGVR 237 Lambda K H 0.329 0.142 0.411 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: 249 Number of extensions: 9 Number of successful extensions: 1 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: 229 Length of database: 371 Length adjustment: 26 Effective length of query: 203 Effective length of database: 345 Effective search space: 70035 Effective search space used: 70035 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: 48 (23.1 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