Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate BPHYT_RS29180 BPHYT_RS29180 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS29180 Length = 306 Score = 273 bits (697), Expect = 4e-78 Identities = 136/280 (48%), Positives = 188/280 (67%), Gaps = 13/280 (4%) Query: 13 SRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDV--- 69 +R+ +YA LL AA +L+PL VML+TS K +IR GNLL++PT W AW Sbjct: 29 ARLGVYAFLLTAALFFLLPLYVMLVTSVKPMNEIRLGNLLAFPTHFTLSAWSAAWQSACT 88 Query: 70 --------VGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLP 121 VG FWNSV+I VP+ ++S IGA+NGY LS WR RG+ L FG+LL G F+P Sbjct: 89 GLDCNGIQVG--FWNSVRIVVPSTILSIAIGAVNGYALSFWRPRGAGLLFGVLLMGAFIP 146 Query: 122 FQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGA 181 Q ++ P L L ++ G+V++H ++G+ TL FRNYYVSIP L KAAR+DG Sbjct: 147 VQVMVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYVSIPQELFKAARIDGG 206 Query: 182 GFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTG 241 GF+ IF++++LPMS PI++V +I Q T IWNDF+ G+VFA P+TV LNN++NT+TG Sbjct: 207 GFWRIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNNIINTTTG 266 Query: 242 AKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 + YNV+MAA ++ + L VY +G++F+RG+ SGAVKG Sbjct: 267 ERLYNVNMAATILTSMVPLAVYFVSGRWFVRGIASGAVKG 306 Lambda K H 0.329 0.143 0.447 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: 264 Number of extensions: 11 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: 281 Length of database: 306 Length adjustment: 26 Effective length of query: 255 Effective length of database: 280 Effective search space: 71400 Effective search space used: 71400 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