Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 193 bits (491), Expect = 5e-54 Identities = 108/279 (38%), Positives = 167/279 (59%), Gaps = 6/279 (2%) Query: 60 FASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWA 119 F + N ++ + ++LA G VILT IDLSV + LA++ ++ V++ AAPG Sbjct: 31 FIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANLALTGMVVSMVNV-AAPGLP 89 Query: 120 IPMF----IFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDI- 174 I + I G ++GM NG +V L I VVTLGTMT FRG +L++DG V ++++ Sbjct: 90 IVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFRGIIFLISDGKWVNSHEMS 149 Query: 175 PSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGL 234 P+F+ + L +P L W+A+ V+L +++ +T LG YA GGN AA GI VG Sbjct: 150 PAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRAFYAAGGNPHAATYAGIDVGK 209 Query: 235 VLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGT 294 + ++ISG +GL G + SR + + G+ELD +AA V+GG S+MGGVG++ G Sbjct: 210 TQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVVAACVIGGVSIMGGVGTVGGA 269 Query: 295 VVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILD 333 ++GAL +G++ N L ++ +S FWQ G I++AV L+ Sbjct: 270 LLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALN 308 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: 296 Number of extensions: 18 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: 327 Length adjustment: 28 Effective length of query: 316 Effective length of database: 299 Effective search space: 94484 Effective search space used: 94484 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 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