Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 166 bits (421), Expect = 6e-46 Identities = 94/292 (32%), Positives = 162/292 (55%), Gaps = 9/292 (3%) Query: 46 MILFFSFASPN-FMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMA 104 +I+ FS SP+ F DN ++I + + ++A+ T V+ DLS+G M + V++ Sbjct: 28 IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87 Query: 105 GVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISG 164 ++ + G P+ + I G + G+ +G ++ K KV F+ TL M ++ G++ ++G Sbjct: 88 ALLAAS-GTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTG 146 Query: 165 TRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFAL 224 ++ N EGF + Q L +P+L + I+F++ I I+++T GR +A+ Sbjct: 147 GATVFENIPEGFKFLGQSKLA--FLPTLSV-----IMFVLVIIFWYIMSQTSLGRRLYAI 199 Query: 225 GSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVV 284 G NE+A +SG+ + +K + G + G ++ASRL SA P G G+ L+A AAV Sbjct: 200 GGNEKASEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVF 259 Query: 285 IGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAV 336 +G T + G ILGT+ GA I+ ++ NGL I+ V Q ++TG III+A+ Sbjct: 260 LGMTIVKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIAL 311 Lambda K H 0.326 0.139 0.398 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: 236 Number of extensions: 8 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: 347 Length of database: 321 Length adjustment: 28 Effective length of query: 319 Effective length of database: 293 Effective search space: 93467 Effective search space used: 93467 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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