Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 231 bits (589), Expect = 2e-65 Identities = 127/304 (41%), Positives = 190/304 (62%), Gaps = 3/304 (0%) Query: 11 RELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLS 70 REL L L+ + + ++ +P FLT NL + R ++ L++IG VII+GG IDLS Sbjct: 26 RELNVLSVLLLVGLLISVFSPYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGG--IDLS 83 Query: 71 PGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLT 130 GS++ L+ ++ A + HG ++ L I GA++G +T +++P FI TLGTL+ Sbjct: 84 VGSVMGLSSLVTALVFQHGYNAPAAIGAGLAVGIAVGAFNGFMITWIQLPPFIATLGTLS 143 Query: 131 IARGMAAVITKGWPII-GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKH 189 I RG+ +ITKG P+ +P SF IGQG +P PV ILLA+ V +R+T +G++ Sbjct: 144 IGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVVMRQTRFGRY 203 Query: 190 LRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAI 249 + A+GGNEVAAR SGV RV+ +++SG +A + G+I +R +P G EL I Sbjct: 204 VYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPASGFGAELDVI 263 Query: 250 ASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDI 309 A+ IGG SL+GG GSV GAI+GA++ ++ N +VLLN+ TY + G VI++AV++DI Sbjct: 264 AAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCVILIAVSIDI 323 Query: 310 LRRR 313 R R Sbjct: 324 WRVR 327 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: 352 Number of extensions: 25 Number of successful extensions: 3 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: 331 Length adjustment: 28 Effective length of query: 289 Effective length of database: 303 Effective search space: 87567 Effective search space used: 87567 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