Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate GFF3089 HP15_3032 amino acid ABC transporter, inner membrane subunit
Query= reanno::BFirm:BPHYT_RS07675 (229 letters) >FitnessBrowser__Marino:GFF3089 Length = 247 Score = 248 bits (633), Expect = 8e-71 Identities = 129/227 (56%), Positives = 163/227 (71%), Gaps = 5/227 (2%) Query: 3 LYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPD 62 L G+GP L+ G I TIEL+ LSLA +V LGL GA+AKLS +R + IAT YTTLIR VPD Sbjct: 17 LKGYGPALMDGAIVTIELAFLSLALSVALGLIGASAKLSQSRVAKGIATTYTTLIRGVPD 76 Query: 63 LVLMLLLFYSIQIAVNNLTDALNLPQ-----FDIDPFVAGVLTLGFIYGAYFTETFRGAF 117 LV+MLL +Y Q+AVN L+D + F DPF++GV+T+G I+GAY TETFRGAF Sbjct: 77 LVMMLLFYYGGQVAVNMLSDYIWEAYEIDFFFQFDPFISGVVTIGLIFGAYMTETFRGAF 136 Query: 118 LAVPRGQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADV 177 LAV GQ+EA AYG + F RI+ PQMMR ALPG+GNNWQVL+K TALVSIIGL D+ Sbjct: 137 LAVETGQIEAARAYGFTRFHTFRRIMLPQMMRHALPGLGNNWQVLLKTTALVSIIGLTDM 196 Query: 178 VKAAQDAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGV 224 V+ A++A K+ F F + A +YLA+T S L + WL+KR ++GV Sbjct: 197 VRVAEEAAKAERMPFHFFIPVAFVYLALTAGSELFIKWLDKRANVGV 243 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: 191 Number of extensions: 8 Number of successful extensions: 2 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: 247 Length adjustment: 23 Effective length of query: 206 Effective length of database: 224 Effective search space: 46144 Effective search space used: 46144 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