Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate GFF2275 PGA1_c23070 putative ribose transport system permease protein
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Phaeo:GFF2275 Length = 333 Score = 159 bits (401), Expect = 1e-43 Identities = 95/291 (32%), Positives = 154/291 (52%), Gaps = 9/291 (3%) Query: 25 FTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMVALTGVMV-- 82 F ++ + F+ N+ L +Q A G++A+G T V+++G IDLS G++ A+ +++ Sbjct: 32 FFSVSDKAFMDTDNMLLLLKQSAPIGIIAMGMTIVMVNGN--IDLSVGAIYAICAIILLD 89 Query: 83 --AWLMTHGVPVWISVI---LILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARGMAA 137 W M G+ W+ + L LL + GA +GL V K V AFI+TLG++ RG+ Sbjct: 90 SMTWTMFAGLGNWVIPVAWCLALLTGVVLGAINGLIVWKTGVDAFIVTLGSMLGYRGLVF 149 Query: 138 VITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASGGNE 197 + P L + + + +FL + W LL V + F + +TV+G++ A G N Sbjct: 150 MYNGEQPTSHLNWTLVDFAEAQFLGLHTATWFLLVVTVAIWFLMNRTVHGRNAYAIGNNR 209 Query: 198 VAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIGGT 257 AA +G+ V MI FM+ GFLA + ++ + P G +YEL+ I + V+GGT Sbjct: 210 EAAVNAGIRVGPHMMINFMIIGFLAALSAVVFYSESGSVNPNDGQLYELWVITAVVLGGT 269 Query: 258 SLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308 LTGG GS++ G I LL L + T N+VIG++++ + LD Sbjct: 270 KLTGGAGSIVSTFGGVIAIQLLRKGLAHIGADTSTVNLVIGLILIAVLFLD 320 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: 327 Number of extensions: 17 Number of successful extensions: 1 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: 333 Length adjustment: 28 Effective length of query: 289 Effective length of database: 305 Effective search space: 88145 Effective search space used: 88145 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