Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate BPHYT_RS29180 BPHYT_RS29180 sugar ABC transporter permease
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__BFirm:BPHYT_RS29180 Length = 306 Score = 376 bits (966), Expect = e-109 Identities = 178/296 (60%), Positives = 228/296 (77%) Query: 10 GGPMAGPRGRKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAP 69 G P + R R+ R + + VY L+ AL++LLPLYVM+VTS+K M EIR+GN+ A Sbjct: 11 GTPPSRARPRRRRTAFTPARLGVYAFLLTAALFFLLPLYVMLVTSVKPMNEIRLGNLLAF 70 Query: 70 PLEITFEPWVKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFK 129 P T W AW ACTGL+C+G+ GFWNSVRI VPS I+SIAI +VNGYAL+ WR + Sbjct: 71 PTHFTLSAWSAAWQSACTGLDCNGIQVGFWNSVRIVVPSTILSIAIGAVNGYALSFWRPR 130 Query: 130 GADLFFTILIVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYF 189 GA L F +L++GAFIP QVM+YP+V VL + ++ +L G++++HTIFGMP++TLLFRNY+ Sbjct: 131 GAGLLFGVLLMGAFIPVQVMVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYY 190 Query: 190 AGLPEELFKAARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEY 249 +P+ELFKAAR+DG GFW I+ ++MLPMS PI VVA+I+QVTGIWNDF+ G+VF + Sbjct: 191 VSIPQELFKAARIDGGGFWRIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKN 250 Query: 250 YPMTVQLNNIVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 PMTVQLNNI+N+ G + YNVNMAATILT +VPL VYFVSGR FVRGIA+GAVKG Sbjct: 251 LPMTVQLNNIINTTTGERLYNVNMAATILTSMVPLAVYFVSGRWFVRGIASGAVKG 306 Lambda K H 0.329 0.145 0.450 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: 357 Number of extensions: 8 Number of successful extensions: 1 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: 305 Length of database: 306 Length adjustment: 27 Effective length of query: 278 Effective length of database: 279 Effective search space: 77562 Effective search space used: 77562 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 (21.8 bits) S2: 48 (23.1 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