Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate BWI76_RS07245 BWI76_RS07245 ABC transporter
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Koxy:BWI76_RS07245 Length = 343 Score = 195 bits (496), Expect = 1e-54 Identities = 117/281 (41%), Positives = 171/281 (60%), Gaps = 19/281 (6%) Query: 45 QIAIFGLLAIGETFVIISGGGAIDLSPGSMVALTGVMVAWLMTHG---VPVWISVI-LIL 100 Q+AI G++A+G T VII+ G IDLS GS++AL V+ A L P++ S++ + Sbjct: 67 QVAIIGIIAVGVTQVIITTG--IDLSSGSVIALAAVVAASLAQTSDSLSPMFPSLVNMPA 124 Query: 101 LFSIGAGAWHGLF--------VTKLRVPAFIITLGTLTIARGMAAVITKGWPIIGLPSSF 152 + IGAG GL VT+ +P FI TLG + ARG+A T+G PI L SF Sbjct: 125 IIPIGAGIGVGLLCGLTNGFLVTRTGIPPFIATLGMMVSARGLAQYYTQGNPISFLSDSF 184 Query: 153 LKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRM 212 IGQG +PV I VA V L+ T YGK++ A GGN +A+ SG+NV++ + Sbjct: 185 TAIGQGA-----MPVIIFFVVAAVFHIALKHTRYGKYVYAIGGNMTSAKVSGINVNKYLV 239 Query: 213 IAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVG 272 I + ++G L+G+ G+++AAR+S GQ +G YEL AIA+ VIGG+SL GG G + G ++G Sbjct: 240 IVYAIAGALSGLAGVVLAARVSSGQSSMGMSYELDAIAAAVIGGSSLMGGVGRITGTLIG 299 Query: 273 ASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313 A I+ L+ + + V Y +++ GI+IV AVT+D+ R R Sbjct: 300 AMILGLIKSGFTFVGVDAYVQDIIKGIIIVAAVTIDMRRNR 340 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: 309 Number of extensions: 24 Number of successful extensions: 4 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: 343 Length adjustment: 28 Effective length of query: 289 Effective length of database: 315 Effective search space: 91035 Effective search space used: 91035 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: 49 (23.5 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