Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__azobra:AZOBR_RS25585 Length = 301 Score = 139 bits (349), Expect = 1e-37 Identities = 87/267 (32%), Positives = 136/267 (50%), Gaps = 1/267 (0%) Query: 8 APTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSLWVFIGFRNYVNVLTNAEFWV 67 A L LLP IVLA PL +++ SFT L + + +G NY+ ++ + +W Sbjct: 17 AAWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLATLEG-FQGVGLDNYLWLMRDPVWWR 75 Query: 68 AFGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRALRTAMMFPMMFSPVLVGFQFKFLF 127 A T++ V++ E LGLG+AL++N G+ LR A++ P V+ + ++F Sbjct: 76 AVWNTLVFTVVSVGIETALGLGIALILNAHLPGRGLLRAAVLIPWAIPTVVSAQMWGWMF 135 Query: 128 NDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAMPKD 187 +D G VN L LGL W D +LAL +I +VW ST A+LILA L +P+D Sbjct: 136 HDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILAALQMLPRD 195 Query: 188 PVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKRTEL 247 EAA VDG P + F +T P + P +A+ R+LD R +D++ ++T + + Sbjct: 196 LYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDLMYVLTGNSRSTMSMS 255 Query: 248 LWTLIGRTAYGDARMGMANAMAYVAIL 274 ++ + D G A A V +L Sbjct: 256 VYARQYLIDFQDVGYGSAAATLLVLVL 282 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: 280 Number of extensions: 19 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: 298 Length of database: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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: 48 (23.1 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