Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 185 bits (469), Expect = 2e-51 Identities = 104/289 (35%), Positives = 165/289 (57%), Gaps = 1/289 (0%) Query: 47 GLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVL 106 G+ + S S+FAS +N +NI RQ++ +++A G T V+ DLS+G++ ++ VL Sbjct: 27 GIIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVL 86 Query: 107 GMQVSLGAAPG-WAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLAD 165 ++ P + + + I G V+G NGA+V + +FV TL T G + L Sbjct: 87 SALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTG 146 Query: 166 GTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAA 225 G TV N F+++G +P L + +V++ W I+ +T LG +YAIGGN +A+ Sbjct: 147 GATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKAS 206 Query: 226 RLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLM 285 ++GI + +++ G+ + GA+ ASRL A+ G G+ L+A AAV LG T + Sbjct: 207 EVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVK 266 Query: 286 GGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDK 334 GV +I GT+ GA IIG+M NGLTIL + SF Q + GA+I++A+I K Sbjct: 267 NGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALISQK 315 Lambda K H 0.324 0.138 0.417 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: 312 Number of extensions: 22 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: 344 Length of database: 321 Length adjustment: 28 Effective length of query: 316 Effective length of database: 293 Effective search space: 92588 Effective search space used: 92588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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