Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 201 bits (512), Expect = 2e-56 Identities = 116/327 (35%), Positives = 184/327 (56%), Gaps = 15/327 (4%) Query: 14 PPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQV 73 PP R + A + L +L VL+++ LL + Y F + N M + R Sbjct: 10 PPSGRAADWIRACLRIRELNVLSVLLLVGLLISVFSPY--------FLTTNNLMGVFRSF 61 Query: 74 AINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSGLVMGMV 133 ++ +++ GM VI+T GIDLSVGSV+ +S+++ +L G+ P I +GL +G+ Sbjct: 62 SLIALMSIGMMLVIITGGIDLSVGSVMGLSSLV---TALVFQHGYNAPAAIGAGLAVGIA 118 Query: 134 ----NGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVP 189 NG M+ + + F+ TLGT++ RG Y++ G V + SF +IG G VP Sbjct: 119 VGAFNGFMITWIQLPPFIATLGTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVP 178 Query: 190 WLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGL 249 + + + +A+ + V++R+T G ++YA GGN AARL+G+R V VY +SGL + + Sbjct: 179 FPVVILLAMTAVFSVVMRQTRFGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASM 238 Query: 250 AGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLT 309 AG ++ SR A G G ELD IAA +GG SL GG GS+ G ++GA + G++ NG+ Sbjct: 239 AGVIAFSRFVSAEPASGFGAELDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVV 298 Query: 310 ILGLSSFWQYVAKGAVIVLAVILDKWR 336 +L + ++ Q G VI++AV +D WR Sbjct: 299 LLNIDTYAQQAITGCVILIAVSIDIWR 325 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: 299 Number of extensions: 20 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: 331 Length adjustment: 28 Effective length of query: 316 Effective length of database: 303 Effective search space: 95748 Effective search space used: 95748 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