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 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 139 bits (349), Expect = 1e-37 Identities = 90/270 (33%), Positives = 149/270 (55%), Gaps = 2/270 (0%) Query: 41 ILNVSF-IAIMSFGMTMVIITSGIDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAV 99 ILN S +A++S GM++VI T GIDLSVG+++ A V L+ +S + GL V Sbjct: 100 ILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIV 159 Query: 100 GVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGP 159 G+ G NG L++ + P ++TL ++ GRG+A +++ G I+ F G G Sbjct: 160 GLLAGCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLG 219 Query: 160 VPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLA 219 +P+PV + + + + L+ T G I A+G N +AS+ +GI I + Y I G A Sbjct: 220 LPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCA 279 Query: 220 AFAGFLLTAWL-GVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRN 278 A AG + TA + G NAG ELD + A VIGG +L+GG +++ + +GA+I+ L Sbjct: 280 ALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLAT 339 Query: 279 GMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308 +I+ G+ + + ++ IVI+ + + + Sbjct: 340 TIIVSGLPAKFNLLIKAIVILTVLLLQSAK 369 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: 285 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: 405 Length adjustment: 29 Effective length of query: 284 Effective length of database: 376 Effective search space: 106784 Effective search space used: 106784 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: 49 (23.5 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