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_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 211 bits (538), Expect = 1e-59 Identities = 126/308 (40%), Positives = 183/308 (59%), Gaps = 6/308 (1%) Query: 5 FKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGG 64 F K E L+AL+ L + ++P F T NL + +Q ++ ++A+G T VI++ G Sbjct: 12 FTKAWLMEQKSLIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSG 71 Query: 65 GAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFII 124 IDLS GS++ALTG + A ++ V ++V L GA G+ V K RV AFI Sbjct: 72 --IDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIA 129 Query: 125 TLGTLTIARGMAAVITKGWPI-IGLPSS---FLKIGQGEFLKIPIPVWILLAVALVADFF 180 TL + + RG+ V T G P+ G + F G G L IP PVWI+ V L A + Sbjct: 130 TLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMAIVFLAAWYM 189 Query: 181 LRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGV 240 L T G+++ A GGNE A R SG++V++V++I + + G LA + GII ARLS QP Sbjct: 190 LHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTA 249 Query: 241 GSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIV 300 G+ YEL AIA+ V+GGTSL GG+G ++G ++GA I+ L N L LL VS+Y+ +V +V Sbjct: 250 GTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVV 309 Query: 301 IVVAVTLD 308 I++AV +D Sbjct: 310 ILLAVLVD 317 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: 294 Number of extensions: 19 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: 321 Length adjustment: 28 Effective length of query: 289 Effective length of database: 293 Effective search space: 84677 Effective search space used: 84677 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 Apr 09 2024. 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