Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF186 PS417_00935 sulfate ABC transporter permease
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__WCS417:GFF186 Length = 272 Score = 61.2 bits (147), Expect = 2e-14 Identities = 53/165 (32%), Positives = 78/165 (47%), Gaps = 16/165 (9%) Query: 51 TLENYRQVIGSPEVLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLS 110 T + + +I +P VL L S A L+ +G A+V+ RY PG++ I ++ Sbjct: 42 TWDQFWNIISAPRVLAALQLSFSTALYAALINGVIGTLLAWVLVRYTFPGRKIID-AMID 100 Query: 111 LRFLPPVAVA-IPLIAIWVDLGLY-----DTRFSMIVTYLLTTLSTITWLSI-------- 156 L F P AVA I L A++ GL D F + T L TL+ +T++++ Sbjct: 101 LPFALPTAVAGIALTALYTPNGLVGQFAADLGFKIAYTPLGITLA-LTFVTLPFVVRTVQ 159 Query: 157 PVFQRMPREIEEAATLDGYGPYAVFWKIALPNCATTLLGGIIFSF 201 PV +PRE+EEAA G P VF I +P L G +F Sbjct: 160 PVLADIPREVEEAAACLGAKPLQVFRHILVPALLPAWLTGFALAF 204 Lambda K H 0.327 0.142 0.434 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: 187 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 270 Length of database: 272 Length adjustment: 25 Effective length of query: 245 Effective length of database: 247 Effective search space: 60515 Effective search space used: 60515 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 (21.7 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