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 PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 164 bits (414), Expect = 3e-45 Identities = 103/297 (34%), Positives = 154/297 (51%), Gaps = 1/297 (0%) Query: 12 GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71 G+ L+A++V + F + T+ + + +++ GMT V+I GIDLSVGS+L Sbjct: 28 GLAGALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVL 87 Query: 72 GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131 A+ + + + G S ++G+AV G G + R+ FI +LG+L + RG Sbjct: 88 ALAASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARG 147 Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191 LAY + G P +I + VI V+A + L TV GR + IG Sbjct: 148 LAYQFTDSRTAYIGDAYAWFSNPVAFGVSPAFIIALLVI-VLAQLVLTRTVFGRYLIGIG 206 Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251 N EA +L GI +LV+ + G LA A + L A PNAG G EL VIAA VI Sbjct: 207 TNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVI 266 Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308 GGTSL GG G+++ F G +I+ VL G+ +G S ++++ G VI+IA+ +D R Sbjct: 267 GGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYR 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: 292 Number of extensions: 15 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: 331 Length adjustment: 28 Effective length of query: 285 Effective length of database: 303 Effective search space: 86355 Effective search space used: 86355 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