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_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 201 bits (512), Expect = 2e-56 Identities = 127/304 (41%), Positives = 179/304 (58%), Gaps = 3/304 (0%) Query: 11 RELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLS 70 R LG L LV L + ++L F NL + +Q +I +LA G TFVI++GG IDLS Sbjct: 27 RALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGG--IDLS 84 Query: 71 PGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLT 130 GS+++++ V+ + +SV LL + G +G V +++P FI+TLGTLT Sbjct: 85 VGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLT 144 Query: 131 IARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHL 190 RG+A ++ I F IG GE L +P V I AV V+ F LR+TV G + Sbjct: 145 AVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQI 204 Query: 191 RASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARL-SQGQPGVGSMYELYAI 249 A GGN AAR SG+ V V + + VSG LAG+ G++ +ARL + +G YEL AI Sbjct: 205 YAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAI 264 Query: 250 ASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDI 309 A+ ++GGTS GG GS++G +VGA II++L N LVLL VS W ++ G+VI+ AV LD Sbjct: 265 AAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDS 324 Query: 310 LRRR 313 RR+ Sbjct: 325 YRRK 328 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: 340 Number of extensions: 23 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: 333 Length adjustment: 28 Effective length of query: 289 Effective length of database: 305 Effective search space: 88145 Effective search space used: 88145 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