Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 192 bits (489), Expect = 7e-54 Identities = 116/298 (38%), Positives = 169/298 (56%), Gaps = 2/298 (0%) Query: 16 LVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPGSMV 75 L AL L + A+ + FLT N+ + RQ ++ LLA G T VI++GG +DLS G+ V Sbjct: 21 LFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGG--LDLSVGANV 78 Query: 76 ALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTIARGM 135 A++ + A +M + V L G +GL V LR+P FI T G L + G+ Sbjct: 79 AMSACVAATVMKATGSTMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVLHGV 138 Query: 136 AAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLRASGG 195 G I G P +F IG G +PIPV+++L + +KT YG+ + A G Sbjct: 139 TYWFMAGETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEIYAIGA 198 Query: 196 NEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIASTVIG 255 N VAAR SGV V R ++ ++VSG +AG+ ++ ARL+ + +G L AIA+ +IG Sbjct: 199 NPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIAAVLIG 258 Query: 256 GTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILRRR 313 GTSL GG G V G +VGA I++L+ N + LL VS W +V G+++V+AV LD L R+ Sbjct: 259 GTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLDTLSRK 316 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: 330 Number of extensions: 19 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 289 Effective length of database: 294 Effective search space: 84966 Effective search space used: 84966 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