Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 204 bits (518), Expect = 3e-57 Identities = 117/314 (37%), Positives = 182/314 (57%), Gaps = 2/314 (0%) Query: 4 KFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISG 63 +F R E+G LV + L + ++ P F++ N + R A G+ A T +IISG Sbjct: 18 QFVSRHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISG 77 Query: 64 GGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFI 123 ID+S G MVA V +A+L+ VP+ ++ +L+LL G G+ VP+F+ Sbjct: 78 --EIDVSVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFV 135 Query: 124 ITLGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRK 183 TLG + RGM +T P+ + L G+FL +P+ I++ + + F RK Sbjct: 136 ATLGLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRK 195 Query: 184 TVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSM 243 T +G+ + A GGN AA+ G+NV RVR++ F +SG LA V GI++AARL G G + Sbjct: 196 TAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANG 255 Query: 244 YELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVV 303 E IA+ V+GGT+L+GG GS+ G ++G +I+L+ N LVLL +++++ VV G++IVV Sbjct: 256 LEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVV 315 Query: 304 AVTLDILRRRLASK 317 AV +IL + +SK Sbjct: 316 AVLANILLTQRSSK 329 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: 328 Number of extensions: 20 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: 332 Length adjustment: 28 Effective length of query: 289 Effective length of database: 304 Effective search space: 87856 Effective search space used: 87856 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