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_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 177 bits (449), Expect = 8e-49 Identities = 104/312 (33%), Positives = 162/312 (51%), Gaps = 21/312 (6%) Query: 12 GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71 G+ +L +V + F + E T+ + +A+M+ GMT V+I +GIDLSVGS++ Sbjct: 591 GLLAVLAGMVALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVM 650 Query: 72 GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131 A+ + + G + + + LA G+ G G + RL FI +LGML RG Sbjct: 651 ALAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRG 710 Query: 132 LAYVMSGG----------WPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYT 181 AYV++ W +PF G + + V+ V+A + L T Sbjct: 711 SAYVVTDSRTQYVGDAISWLSAPF-----------FGGISFAFLLAVVLVVVAQLVLSRT 759 Query: 182 VTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGY 241 V GR + IG N EA +L G+ I ++V+ + G LA AG + +A L A PNAG G Sbjct: 760 VFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGM 819 Query: 242 ELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIA 301 EL VIAA VIGGTSL GG G+++ G +I+ VL G+ +G S ++++ G VI+ A Sbjct: 820 ELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAA 879 Query: 302 IAIDQIRRAKER 313 + +D +R+ + + Sbjct: 880 VIVDTLRQRRAK 891 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: 522 Number of extensions: 25 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: 892 Length adjustment: 35 Effective length of query: 278 Effective length of database: 857 Effective search space: 238246 Effective search space used: 238246 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: 52 (24.6 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