Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 192 bits (487), Expect = 1e-53 Identities = 111/304 (36%), Positives = 171/304 (56%), Gaps = 13/304 (4%) Query: 13 LGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPG 72 LGP++ LV L + +LN F T N+ + + A G++A+G FVIISGG IDLS G Sbjct: 41 LGPVIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGG--IDLSVG 98 Query: 73 SMVALTGVMVAWLMTHGVPVW------ISVILILLFSIGA--GAWHGLFVTKLRVPAFII 124 SM AL V M PV + V ++L +GA G HGL +TK R+ FI+ Sbjct: 99 SMAALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIV 158 Query: 125 TLGTLTIARGMAAVITKGWPII---GLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFL 181 TLGTL I R + G I L + + L +PIPVWI L VA+V L Sbjct: 159 TLGTLGIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVIL 218 Query: 182 RKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVG 241 +T YG++++A G NE A+++ V+V +++++ +M+ G G+ ++ RL P G Sbjct: 219 NRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTG 278 Query: 242 SMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVI 301 ++EL AIA+ ++GGT L GG GS+ G +VGA ++S++ N L L ++ + + N + + Sbjct: 279 LLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFV 338 Query: 302 VVAV 305 ++AV Sbjct: 339 IIAV 342 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: 372 Number of extensions: 29 Number of successful extensions: 5 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: 350 Length adjustment: 28 Effective length of query: 289 Effective length of database: 322 Effective search space: 93058 Effective search space used: 93058 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