Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__HerbieS:HSERO_RS22745 Length = 300 Score = 124 bits (310), Expect = 4e-33 Identities = 75/235 (31%), Positives = 130/235 (55%), Gaps = 8/235 (3%) Query: 145 TPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPG-RAVL 203 T T + +VL+ F NSL V V + + +L A AA+AL F G RA+ Sbjct: 73 TAETLTFAGFQKVLAGTHFLLYFGNSLAVTVAALFLIVLFGAMAAWALTEYRFFGNRALN 132 Query: 204 LAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYM 263 + +G+++ P+++ + +LQL V A ++ +T + L +T GLPLA+ +L +M Sbjct: 133 FFIAIGIMI-PIRLGTVSILQL---VVALDLINTRT--ALVLVYTAQGLPLAVMILSEFM 186 Query: 264 AGLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGD 323 +P E+ ++AR DG + IF ++ILPL PA+A+ A+F + WNDL ++ L G+ Sbjct: 187 RQIPGELKDAARCDGVGELSIFFRVILPLLRPAIATVAVFTMIPAWNDLWFPLI-LAPGE 245 Query: 324 DKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVK 378 D +T + +G +W + A+ + ++ L+++ A R L+RGL +G+VK Sbjct: 246 DTRTVTLGVQQFIGQYATDWNSVLAALSMAVIPVLLLYMAFSRQLIRGLTSGAVK 300 Lambda K H 0.324 0.139 0.418 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: 224 Number of extensions: 8 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: 380 Length of database: 300 Length adjustment: 28 Effective length of query: 352 Effective length of database: 272 Effective search space: 95744 Effective search space used: 95744 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 (21.5 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