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_004129777.1 RHSP_RS32465 ribose ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_000359745.1:WP_004129777.1 Length = 320 Score = 217 bits (553), Expect = 3e-61 Identities = 123/304 (40%), Positives = 185/304 (60%), Gaps = 4/304 (1%) Query: 11 RELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLS 70 R+ ++ + F A N F+T N L RQ +I G+LAIG TFVI++ G IDLS Sbjct: 19 RQFSIVLVFFLIVAFFAFANQYFMTWLNWLNLVRQSSINGILAIGVTFVILTKG--IDLS 76 Query: 71 PGSMVALTGVMVAWLMTHGVPVWI--SVILILLFSIGAGAWHGLFVTKLRVPAFIITLGT 128 GS++AL G++ A L+T ++ + L G G +G+ V ++VP F++TLG Sbjct: 77 VGSVMALAGMIAASLVTETNEQFVLFGIFAGLAAGAGLGLVNGVLVAAVKVPPFVVTLGM 136 Query: 129 LTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGK 188 L++ARG+ + ++G PI L F IG G+ + IP+P+ IL V L+ L T +G+ Sbjct: 137 LSVARGLTLIFSEGRPIPNLSDPFKWIGSGQIMYIPVPIVILFVVFLIGWTVLNYTTFGR 196 Query: 189 HLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYA 248 ++ A GGNE AAR SG++ + +++SG LAG+ G+++ AR + P G YEL A Sbjct: 197 YVYAVGGNEKAARTSGISTKVIVGATYVISGLLAGLAGLVLTARTTAALPQAGIGYELDA 256 Query: 249 IASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308 IA+ VIGGTSL GG GS+LG ++GA II + N + L+ VS+Y+ V+ G +IVVAV D Sbjct: 257 IAAVVIGGTSLAGGRGSLLGTLIGALIIGTINNGMDLMGVSSYYQQVLKGTIIVVAVIAD 316 Query: 309 ILRR 312 +R+ Sbjct: 317 QIRK 320 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: 316 Number of extensions: 17 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: 320 Length adjustment: 27 Effective length of query: 290 Effective length of database: 293 Effective search space: 84970 Effective search space used: 84970 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