Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 214 bits (545), Expect = 2e-60 Identities = 128/321 (39%), Positives = 194/321 (60%), Gaps = 11/321 (3%) Query: 2 ASKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVII 61 A F ++L +L+ + +F + +P F+ NL ++ + A+ G+LAI T+VII Sbjct: 26 ARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVII 85 Query: 62 SGGGAIDLSPGSMVALTGVMVAWLMTH-GVPVWISVILILLFSIGAGAWHGLFVTKLRVP 120 + G IDLS G+M+ VM ++T+ G+P+ + + + F +G G+ + KL+VP Sbjct: 86 TSG--IDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVP 143 Query: 121 AFIITLGTLTIARGMAAVITKGWPI-IGLPSSFLKIGQGEFL-----KIPIP--VWILLA 172 FI TLG + + +G++ VI+ PI F I Q + +PIP V IL Sbjct: 144 PFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFL 203 Query: 173 VALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAAR 232 VA+ A L KTV+G++ A G NE A R SGV VD ++ + SG + G+ G+IIA+R Sbjct: 204 VAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASR 263 Query: 233 LSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYW 292 L+ QP +G YEL AIA+ VIGGTSL+GG G++LG I+GA I+S+L N L +++V+ W Sbjct: 264 LNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEW 323 Query: 293 HNVVIGIVIVVAVTLDILRRR 313 VV G++I++AV LDILRRR Sbjct: 324 QTVVTGVIIILAVYLDILRRR 344 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: 312 Number of extensions: 21 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: 347 Length adjustment: 28 Effective length of query: 289 Effective length of database: 319 Effective search space: 92191 Effective search space used: 92191 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