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_086510990.1 BZY95_RS16560 L-arabinose ABC transporter permease AraH
Query= TCDB::Q9WXW7 (317 letters) >NCBI__GCF_002151265.1:WP_086510990.1 Length = 336 Score = 179 bits (455), Expect = 6e-50 Identities = 101/302 (33%), Positives = 172/302 (56%), Gaps = 3/302 (0%) Query: 8 RTFRELGPLVAL-VSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGA 66 RT + L+A+ V L V A+ P FLT N+ L I + G +A T +++ G Sbjct: 27 RTLLDTSGLIAIFVILFVALAVFIPGFLTGRNMVGLLLSITLIGTIAT--TMMMVLALGE 84 Query: 67 IDLSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITL 126 +DLS S+VA GV+ A + + V I V+ +L GA++G V K + + I TL Sbjct: 85 VDLSVASIVAFAGVVAAVVTSTSGSVAIGVLGGVLAGGAVGAFNGFVVAKFGINSLIATL 144 Query: 127 GTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVY 186 ++ RG+A + ++G ++ F +G FL + +PVW ++A ++ L T + Sbjct: 145 ASMEFVRGLAYITSRGDAVMITVPEFFDLGSASFLGLTLPVWTMIACFVIFGVLLNMTAF 204 Query: 187 GKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYEL 246 G+++ A+GGN AA +GVNV R+++I F + G +AG+ G+++A+R+ G P EL Sbjct: 205 GRNVLATGGNAEAAALAGVNVRRLKVIVFGLQGVVAGIAGVLLASRMGLGDPNTSMGLEL 264 Query: 247 YAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVT 306 I++ V+GG +L+GG ++ G +VG I+ + NA+ LLNV T++ +V G ++++AV Sbjct: 265 AVISACVLGGVALSGGVATITGVLVGVLIMGCVQNAMGLLNVPTFYQYLVRGAILLLAVM 324 Query: 307 LD 308 D Sbjct: 325 FD 326 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: 348 Number of extensions: 17 Number of successful extensions: 1 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: 336 Length adjustment: 28 Effective length of query: 289 Effective length of database: 308 Effective search space: 89012 Effective search space used: 89012 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