Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 244 bits (623), Expect = 2e-69 Identities = 144/314 (45%), Positives = 207/314 (65%), Gaps = 16/314 (5%) Query: 22 LDRFGLPLVFILLCVVMAFSSEY--------FMTWRNWMDILRQTSINGILAVGMTYVIL 73 L R G+ V ++L ++ + Y F + N M+ILRQ +IN +LA GMT+VIL Sbjct: 24 LHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVIL 83 Query: 74 TKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFV 133 T GIDLSVGS+LA + + V+ G A+ +F+G ++G+VNG MVA L+I FV Sbjct: 84 TAGIDLSVGSVLAVSAVLGMQVSL-GAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFV 142 Query: 134 ATLGMLSIARGMTFILNDGSPI--TDLPDAYLALGIGKIGPIGVPIIIFAVVALIF--WM 189 TLG ++ RG ++L DG+ + D+P ++ +G G + VP +I+ VA++ W+ Sbjct: 143 VTLGTMTAFRGAAYLLADGTTVLNNDIP-SFEWIGNGDF--LHVPWLIWVAVAVVLLSWV 199 Query: 190 VLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQ 249 +LR T G ++YA+GGN ++AR +GI V V+ VY +SGL +GLAG + ++R A Sbjct: 200 ILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGN 259 Query: 250 AGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGL 309 G YELDAIAAVV+GGTSL GG GSI GT+ GAL+IGV+NNGL +LG+SS++Q VAKG Sbjct: 260 WGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGA 319 Query: 310 IIVFAVLIDVWRKK 323 +IV AV++D WR+K Sbjct: 320 VIVLAVILDKWRQK 333 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: 282 Number of extensions: 13 Number of successful extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 297 Effective length of database: 311 Effective search space: 92367 Effective search space used: 92367 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: 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