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 H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 239 bits (609), Expect = 9e-68 Identities = 129/307 (42%), Positives = 184/307 (59%), Gaps = 8/307 (2%) Query: 13 IFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILG 72 +F L+ I + L + + EFLT + +++ VS + I + G T VIITSGIDLSVGS++ Sbjct: 29 LFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVA 88 Query: 73 AASVVMGLLMDEKGLSP------FLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGML 126 +V +M G SP + LAVG G NGL + RL PFI TL M+ Sbjct: 89 LTGMVAATVM--AGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMM 146 Query: 127 SVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRR 186 ++ RGL +S G FP +FT G V +P+P+I M VI VI H+ L+ T G + Sbjct: 147 AMARGLTLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQ 206 Query: 187 IYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVI 246 ++A+GGN EA++L GI R++ L Y + G AA AG +L L A P+A G EL VI Sbjct: 207 VFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVI 266 Query: 247 AATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQ 306 AA VIGGTSL+GG G+I+G F+G V++GV+ G+ LLGV+ FW Q + G VI A+ +D Sbjct: 267 AAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLDA 326 Query: 307 IRRAKER 313 + + +++ Sbjct: 327 LSQRRKQ 333 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: 302 Number of extensions: 18 Number of successful extensions: 2 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: 333 Length adjustment: 28 Effective length of query: 285 Effective length of database: 305 Effective search space: 86925 Effective search space used: 86925 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