Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_083875558.1 J416_RS08065 ribose ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >NCBI__GCF_000359605.1:WP_083875558.1 Length = 316 Score = 258 bits (660), Expect = 1e-73 Identities = 135/300 (45%), Positives = 191/300 (63%) Query: 3 KKLFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSG 62 + LFK E L + + + + EFLT NI ++ VS I++ GMT VI+TSG Sbjct: 8 RDLFKNPEILTLLGFLVLCFIFSIISSEFLTATNITNILRQVSINGILAVGMTFVILTSG 67 Query: 63 IDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFIST 122 IDLSVGS++ +M LM GL P L+++ G+ +G G NG + A++ I T Sbjct: 68 IDLSVGSVMAFTGTIMAGLMINNGLPPILAIIAGILLGALLGYINGSFVAYAKIPAIIVT 127 Query: 123 LGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTV 182 L M+ RGLA + +GG+P+S P+SFT G+G V +P+PVI M + +IA++ L + Sbjct: 128 LAMMETARGLALLYTGGYPLSGVPDSFTFIGRGYVLGIPMPVIIMIAVYLIAYLMLNHLP 187 Query: 183 TGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYE 242 GR IYAIGGN EA +L GIK RI LVY I+G A+ +G ++T+ L QP AG YE Sbjct: 188 LGRYIYAIGGNEEAVRLSGIKVKRIKSLVYLISGVTASISGLIMTSRLASGQPTAGVTYE 247 Query: 243 LDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302 LD IAA V+GGT++SGG G I G FLGA+++GVL NG+ L+GVS + Q+V+ G++I+ AI Sbjct: 248 LDAIAAVVLGGTAISGGRGHIFGTFLGALLLGVLSNGLNLIGVSPYLQRVLKGVIIVGAI 307 Lambda K H 0.328 0.145 0.421 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: 315 Number of extensions: 16 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: 313 Length of database: 316 Length adjustment: 27 Effective length of query: 286 Effective length of database: 289 Effective search space: 82654 Effective search space used: 82654 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