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 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 164 bits (414), Expect = 3e-45 Identities = 99/277 (35%), Positives = 154/277 (55%), Gaps = 13/277 (4%) Query: 45 SFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFG 104 +F+ I + GMT+VII+ GIDLSVG+++ + VV LL+ E P L+ V+ L +G FG Sbjct: 44 AFLLITALGMTLVIISGGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFG 103 Query: 105 LANGLLITKARLAPFISTLGMLSVGRGLAYVMSGGWPISPFP-------ESFTVHGQGMV 157 G +I +L PFI TL + + RGLA +S P S + G G + Sbjct: 104 ALMGTIIHVYKLQPFIVTLAGMFLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGAL 163 Query: 158 GPVP-VPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTING 216 + +++ +I V+ H YT G +YAIGGN +++L+GI + I +Y I+ Sbjct: 164 DLSSLIFILFFVIIAVVMH----YTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISS 219 Query: 217 FLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVL 276 FLA AG + T + G ELD IAA VIGGT L+GG G +LG LG ++MGV+ Sbjct: 220 FLATLAGIVFTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVI 279 Query: 277 RNGMILLG-VSSFWQQVVIGIVIIIAIAIDQIRRAKE 312 + + G +SS+W ++VIG+++ I + ++ ++ Sbjct: 280 QTYITFDGSLSSWWTKIVIGLLLFFFILLQKLLNGRK 316 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: 304 Number of extensions: 23 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: 320 Length adjustment: 27 Effective length of query: 286 Effective length of database: 293 Effective search space: 83798 Effective search space used: 83798 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