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 Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 226 bits (577), Expect = 4e-64 Identities = 120/301 (39%), Positives = 179/301 (59%), Gaps = 3/301 (0%) Query: 12 GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71 G F+ LI F + FL+ +N ++ V +A+++ G T+VI+T+GIDLS G ++ Sbjct: 15 GPFIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVM 74 Query: 72 GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131 +VM + + GLS +++ G+AV + FGL NGLL+TK +L PFI TLG L++ Sbjct: 75 ALGGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFA 134 Query: 132 LAYVMSGGWPISPFPESFTVHGQGM-VGPVPVP--VIYMAVIGVIAHIFLKYTVTGRRIY 188 + SG I+ P T G +G + + M + ++ L+ T GR +Y Sbjct: 135 ATQLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVTWFALRETAPGRHVY 194 Query: 189 AIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAA 248 A+G + EA++L GI TD++L+ VY + G A L A G PNAGQ LD I+A Sbjct: 195 AVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDAISA 254 Query: 249 TVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308 V+GGTSL GG G ILG +GA+I+GV RNG+ L+GVSS +Q +V GI++I+A+A DQ+ Sbjct: 255 VVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATDQLS 314 Query: 309 R 309 R Sbjct: 315 R 315 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: 263 Number of extensions: 10 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: 319 Length adjustment: 27 Effective length of query: 286 Effective length of database: 292 Effective search space: 83512 Effective search space used: 83512 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