Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 214 bits (545), Expect = 2e-60 Identities = 112/299 (37%), Positives = 185/299 (61%), Gaps = 2/299 (0%) Query: 15 PLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSM 74 P + L+ + + + FL+ N++ + RQ++I ++A+G T VI++GG IDLS GS+ Sbjct: 39 PFIGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGG--IDLSVGSV 96 Query: 75 VALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARG 134 +AL G + A LM G+ ++ + + +G GA +G FV +P I+TL T+ IARG Sbjct: 97 MALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARG 156 Query: 135 MAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASG 194 +A + T G+PI GLP G G+ L + PV I+ + ++A L + +G+++ A G Sbjct: 157 LALIYTGGYPIDGLPDWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIG 216 Query: 195 GNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVI 254 GNE A R SGV V RV++I + ++G + I++ ARL GQP G +EL AIA+ V+ Sbjct: 217 GNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGFELDAIAAVVM 276 Query: 255 GGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313 GGTS++GG GS++G ++GA ++ +L N L ++ V+ Y NV+ G +I++A+ + RR+ Sbjct: 277 GGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDRRK 335 Lambda K H 0.328 0.143 0.424 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: 326 Number of extensions: 27 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: 317 Length of database: 335 Length adjustment: 28 Effective length of query: 289 Effective length of database: 307 Effective search space: 88723 Effective search space used: 88723 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 (21.7 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