Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 186 bits (471), Expect = 9e-52 Identities = 97/285 (34%), Positives = 167/285 (58%), Gaps = 1/285 (0%) Query: 33 LLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLCS 92 ++ + S F ++ N+++I RQ S I+A+G T V+ K DLS+G++ + G+ S Sbjct: 28 IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87 Query: 93 AMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDG 152 A++A G ++ + + G ++G NG +V + FV TL M ++ G+TF L G Sbjct: 88 ALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTGG 147 Query: 153 SPITD-LPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSAR 211 + + + +P+ + LG K+ + +I V+ +IFW ++ T+ GR +YA+GGNEK++ Sbjct: 148 ATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKASE 207 Query: 212 TSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSG 271 SGI + + + + G+LA G +L++R SA P G + L+A AAV +G T + Sbjct: 208 VSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVKN 267 Query: 272 GTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVL 316 G +I+GTLFGA +IG++ NGL +L V S+ Q + G II+ A++ Sbjct: 268 GVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALI 312 Lambda K H 0.326 0.141 0.412 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: 221 Number of extensions: 16 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: 325 Length of database: 321 Length adjustment: 28 Effective length of query: 297 Effective length of database: 293 Effective search space: 87021 Effective search space used: 87021 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 (21.6 bits) S2: 48 (23.1 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