Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate WP_084684831.1 H035_RS0104695 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >NCBI__GCF_000421465.1:WP_084684831.1 Length = 270 Score = 134 bits (336), Expect = 3e-36 Identities = 79/243 (32%), Positives = 129/243 (53%), Gaps = 9/243 (3%) Query: 27 PLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWVAFGRTVLLLTVALNAEMFL 86 PL ++ + S + L P+ F+G NY +VLT+ +W A TVL+ ++ E+ L Sbjct: 8 PLAYAFWLSLYRYDLRFPEQR-AFVGGANYASVLTSEVWWQALANTVLITAGSVMMELML 66 Query: 87 GLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLFNDNIGFVNNALQSLGLTDR 146 G LALL+++ + +R +RTA++ P V+ +KF F+ GF+N L + Sbjct: 67 GFALALLMHRTLFARRTVRTAILVPYGIITVVAALAWKFAFDPTTGFIN------ALLNL 120 Query: 147 AIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKDPVEAAHVDGCTPWQTFRYV 206 PWL + A II EVW +T A+L++AGL +P+D ++AA VDG + Q F + Sbjct: 121 DQPWLNERWSAFCVIIATEVWKTTPFMALLLMAGLTLVPQDLLQAARVDGASRIQRFFQI 180 Query: 207 TWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTELLWTLIGRTAYGDARMGMAN 266 T P + P +A+ R+LD R +D V + T G A TE + + T +G+ + Sbjct: 181 TLPLMKPAVAVALLFRTLDAFRIFDTVFVQTRG--AHGTETVSIVAYHTLIARLNLGLGS 238 Query: 267 AMA 269 A++ Sbjct: 239 AVS 241 Lambda K H 0.331 0.142 0.441 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: 218 Number of extensions: 15 Number of successful extensions: 3 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: 298 Length of database: 270 Length adjustment: 26 Effective length of query: 272 Effective length of database: 244 Effective search space: 66368 Effective search space used: 66368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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