Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS10275 BPHYT_RS10275 ABC transporter substrate-binding protein
Query= reanno::BFirm:BPHYT_RS07735 (264 letters) >FitnessBrowser__BFirm:BPHYT_RS10275 Length = 262 Score = 290 bits (743), Expect = 2e-83 Identities = 142/257 (55%), Positives = 183/257 (71%), Gaps = 2/257 (0%) Query: 10 ALALFAAAS--ATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKL 67 +L++F AA+ + GT +A + FG+EA+Y PFESKSP+G+L+GFD+DVGNAVCAK+ Sbjct: 6 SLSVFVAAALLGSVGTVSAETQNTLRFGIEAAYPPFESKSPTGQLEGFDVDVGNAVCAKM 65 Query: 68 KAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSG 127 KC WVEN+FDGLIPALQARKF+AINS M ITD+R+Q + FT PIY +P M+AK+ SG Sbjct: 66 GVKCEWVENAFDGLIPALQARKFDAINSAMNITDKRKQTIAFTRPIYVVPIVMVAKRSSG 125 Query: 128 LLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQD 187 LLP SL+GK VGVLQ + QE + K WA AGV +V Y QDQ+YADL +GRLDAA Q+ Sbjct: 126 LLPDVKSLQGKRVGVLQASSQEDFLKRHWANAGVSIVSYADQDQVYADLVAGRLDAAVQE 185 Query: 188 AEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQALKELKADG 247 A+ GFL KP G + AG ++D LG G GFG+RKGD+AL ++ AL LK DG Sbjct: 186 AQTVQDGFLNKPAGHDYAIAGQPLSDPATLGEGTGFGLRKGDRALAGKIDAALDALKKDG 245 Query: 248 TIDRFAAKYFDVKVVLK 264 T+ + KYF ++ K Sbjct: 246 TLSALSQKYFKRDIIAK 262 Lambda K H 0.317 0.133 0.383 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: 240 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: 264 Length of database: 262 Length adjustment: 25 Effective length of query: 239 Effective length of database: 237 Effective search space: 56643 Effective search space used: 56643 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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