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 AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__azobra:AZOBR_RS27940 Length = 329 Score = 164 bits (415), Expect = 3e-45 Identities = 107/312 (34%), Positives = 167/312 (53%), Gaps = 11/312 (3%) Query: 6 FKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDL 65 F + G FL L A++V + FL+ NI V+ +FI I++ G T VI GIDL Sbjct: 12 FDLKLYGPFLALAALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDL 71 Query: 66 SVGSILGAASVVMGLLMDE------KGLSPFL-SVVIGLAVGVGFGLANGLLITKARLAP 118 SVGS+ AS VM ++M+ GL L V++ L +G+ GL NGLL+TK R+ Sbjct: 72 SVGSLAAFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEA 131 Query: 119 FISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQ---GMVGPVPVPVIYMAVIGVIAH 175 FI TLG + + R L ++ G +S E T++ G V + P++ AV+ +I Sbjct: 132 FIVTLGTMGIFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGA 191 Query: 176 IFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQP 235 + + T GR AIG + + ++ I DR+ +L + + G A A + LG A Sbjct: 192 LIMYRTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASA 251 Query: 236 NAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLG-VSSFWQQVVI 294 G +EL+ IAA +IGGT L GG G I G +GAV++ ++ N + L G +S + + Sbjct: 252 TTGLLWELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQ 311 Query: 295 GIVIIIAIAIDQ 306 G++II+A+ + + Sbjct: 312 GVIIIVAVLLQR 323 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: 317 Number of extensions: 24 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 285 Effective length of database: 301 Effective search space: 85785 Effective search space used: 85785 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