Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate AO353_01535 AO353_01535 amino acid ABC transporter permease
Query= reanno::BFirm:BPHYT_RS07675 (229 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01535 Length = 242 Score = 296 bits (757), Expect = 3e-85 Identities = 150/225 (66%), Positives = 185/225 (82%) Query: 3 LYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPD 62 L GFGP+LL G+ T++LS+LSL +VLLGL GA+AKLS + LR A YTTLIR VPD Sbjct: 16 LKGFGPLLLEGSWMTVKLSILSLLLSVLLGLIGASAKLSSVKLLRIPAQLYTTLIRGVPD 75 Query: 63 LVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPR 122 LVLMLL+FYS+Q + + T+AL +I+PF AG++TLGFIYGAYFTETFRGA LAVPR Sbjct: 76 LVLMLLIFYSLQTWLTSFTEALGWEYIEINPFAAGIITLGFIYGAYFTETFRGAILAVPR 135 Query: 123 GQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQ 182 GQ+EA +AYG+S A+ F ++FPQMMRFALPGIGNNW V++KATALVSIIGLAD+VKAAQ Sbjct: 136 GQMEAATAYGLSRAQRFRFVVFPQMMRFALPGIGNNWMVILKATALVSIIGLADLVKAAQ 195 Query: 183 DAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVRHA 227 DAGKS++ +FFF+++AALIYL IT+ASN VL WLE+ Y+ G R A Sbjct: 196 DAGKSSYQLFFFLVLAALIYLVITSASNYVLRWLERHYAAGSREA 240 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: 202 Number of extensions: 3 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: 242 Length adjustment: 23 Effective length of query: 206 Effective length of database: 219 Effective search space: 45114 Effective search space used: 45114 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 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