Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate Pf6N2E2_2052 amino acid ABC transporter, permease protein
Query= reanno::WCS417:GFF4244 (229 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2052 Length = 220 Score = 120 bits (300), Expect = 3e-32 Identities = 78/214 (36%), Positives = 117/214 (54%), Gaps = 12/214 (5%) Query: 9 ILDGAWLTLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLVLILLI 68 +L G L L LAL S+A+ V+GL LS R L L +Y TVIR P LVLILLI Sbjct: 17 LLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLILLI 76 Query: 69 FYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAG 128 ++ P LG I L+ L + + TL GAYL+E FRG ++I KGQ EAG Sbjct: 77 YFA--------LPSLG----IRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAG 124 Query: 129 LAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADAT 188 LA G+ +QV V VP M+R +P +NN++ L K T+L + + + ++ + A++ + Sbjct: 125 LAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVES 184 Query: 189 REPFTFFLAVAAMYLVITSVSLLALRHLEKRYSV 222 +L A+Y+ + + LR+ E+R ++ Sbjct: 185 YRVIETWLVTTALYVAACYLIAMLLRYFEQRLAI 218 Lambda K H 0.329 0.143 0.424 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: 139 Number of extensions: 11 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: 220 Length adjustment: 22 Effective length of query: 207 Effective length of database: 198 Effective search space: 40986 Effective search space used: 40986 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