Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_004124583.1 RHSP_RS24175 ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_000359745.1:WP_004124583.1 Length = 323 Score = 227 bits (578), Expect = 3e-64 Identities = 124/313 (39%), Positives = 194/313 (61%), Gaps = 2/313 (0%) Query: 1 MASKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVI 60 +A + K L ++ L++L + +F T N+ L RQ ++ +LA+G+TFVI Sbjct: 11 VAPRRKMNILFSLTLILLLLALWIVLGFWTDKFWTPLNITNLMRQGSMTAILALGQTFVI 70 Query: 61 ISGGGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVP 120 I+ G IDLS G++V V++AWL+ G PVW ++++ LLF + GA+HG + ++ +P Sbjct: 71 ITAG--IDLSVGAIVGFCTVIIAWLLHAGFPVWAAILITLLFGVLIGAFHGFGIVRMGLP 128 Query: 121 AFIITLGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFF 180 FIITL TLT RG+ +IT G I + F +FL IP W+++ VA+ A F Sbjct: 129 PFIITLATLTSLRGIGLLITNGSTINIVNDDFTNFSVSDFLGIPSLFWMVILVAIPAVVF 188 Query: 181 LRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGV 240 L + +G++L A G N AAR SGVNV+ + +A+++SG A VG+++A+R++ G Sbjct: 189 LHLSRWGRYLFAVGSNREAARLSGVNVNWMIYLAYILSGTCAAFVGVLLASRIAIGNATQ 248 Query: 241 GSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIV 300 +EL AIAS+VIGGTSL G GSV G ++GA I++ + N LLN++++W ++ G++ Sbjct: 249 ADGWELQAIASSVIGGTSLFGAVGSVYGPLIGAFILATINNGANLLNLNSFWQRIITGVL 308 Query: 301 IVVAVTLDILRRR 313 I+V V D LRRR Sbjct: 309 IIVIVYFDQLRRR 321 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: 347 Number of extensions: 21 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: 323 Length adjustment: 28 Effective length of query: 289 Effective length of database: 295 Effective search space: 85255 Effective search space used: 85255 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 24 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