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 PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 195 bits (495), Expect = 1e-54 Identities = 108/297 (36%), Positives = 171/297 (57%), Gaps = 3/297 (1%) Query: 15 LILIAIVVFLGVTTR--EFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILG 72 ++L A+ +F+ T FL+ N+ + L +S I + M + + DLSVGS++ Sbjct: 27 MLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 86 Query: 73 AASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGL 132 A VV ++M + S FL V L +G+ GL NG++I K R+ I+TL + + RGL Sbjct: 87 CAGVVAAVVMRDTN-SVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 145 Query: 133 AYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGG 192 AY+ + G + ESF V G G + VPVP++ V + L YT GR AIGG Sbjct: 146 AYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGG 205 Query: 193 NMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIG 252 N EA+ L G+ DR I+++ ++G + A AG +L + + QP GQG+EL VI+A V+G Sbjct: 206 NQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLG 265 Query: 253 GTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRR 309 G SLSGG G I G +I+ ++ N M L + +F+Q V+ G ++++A+ ID++++ Sbjct: 266 GVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQ 322 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: 294 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 313 Length of database: 323 Length adjustment: 27 Effective length of query: 286 Effective length of database: 296 Effective search space: 84656 Effective search space used: 84656 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