Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 208 bits (529), Expect = 2e-58 Identities = 122/321 (38%), Positives = 193/321 (60%), Gaps = 11/321 (3%) Query: 2 ASKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVII 61 A F ++L +L+ L VF + +P F+ N+ + + A+ G+LAI TFVII Sbjct: 21 ARVFTPTALQKLLAFGSLILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVII 80 Query: 62 SGGGAIDLSPGSMVALTGVMVAWLMTHG-VPVWISVILILLFSIGAGAWHGLFVTKLRVP 120 +GG IDLS G+++ T V+ +T+ +P+W V+ + G G K+++P Sbjct: 81 TGG--IDLSVGTLMTFTAVICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIP 138 Query: 121 AFIITLGTLTIARGMAAVITKGWPIIGLPS-SFLKIGQGEFL-----KIPIP--VWILLA 172 FI TLG + + +G++ V++ PI + +F I Q + +P+P V IL Sbjct: 139 PFIATLGMMMLLKGLSLVVSADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLILFF 198 Query: 173 VALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAAR 232 +A+V+ L +T G++ A G NE A R SGVNVDR ++ + +SG + G+ G++IA+R Sbjct: 199 LAVVSSITLNRTALGRYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASR 258 Query: 233 LSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYW 292 L+ QP +G YEL AIA+ VIGGTSL+GG G++LG I+GA I+S+L N L +++V+ W Sbjct: 259 LNSAQPALGQGYELEAIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEW 318 Query: 293 HNVVIGIVIVVAVTLDILRRR 313 VV G++I++AV DILRR+ Sbjct: 319 QIVVTGLIIILAVYGDILRRK 339 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: 317 Number of extensions: 19 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: 341 Length adjustment: 28 Effective length of query: 289 Effective length of database: 313 Effective search space: 90457 Effective search space used: 90457 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