GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Burk376:H281DRAFT_02714
          Length = 331

 Score =  256 bits (653), Expect = 7e-73
 Identities = 134/309 (43%), Positives = 203/309 (65%), Gaps = 3/309 (0%)

Query: 7   KAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLS 66
           + RE  +  +L+ + + + V +  FLT  N+  V  + S IA+MS GM +VIIT GIDLS
Sbjct: 24  RIRELNVLSVLLLVGLLISVFSPYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGGIDLS 83

Query: 67  VGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGML 126
           VGS++G +S+V  L+  + G +   ++  GLAVG+  G  NG +IT  +L PFI+TLG L
Sbjct: 84  VGSVMGLSSLVTALVF-QHGYNAPAAIGAGLAVGIAVGAFNGFMITWIQLPPFIATLGTL 142

Query: 127 SVGRGLAYVMSGGWPISP-FPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGR 185
           S+GRGL Y+++ G P++P  P+SFT  GQG +G VP PV+ +  +  +  + ++ T  GR
Sbjct: 143 SIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVVMRQTRFGR 202

Query: 186 RIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDV 245
            +YA GGN  A++L G++T R+   VY ++G +A+ AG +  +    A+P +G G ELDV
Sbjct: 203 YVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPASGFGAELDV 262

Query: 246 IAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAID 305
           IAA  IGG SLSGG G++ GA +GA + G++ NG++LL + ++ QQ + G VI+IA++ID
Sbjct: 263 IAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCVILIAVSID 322

Query: 306 QIR-RAKER 313
             R R KER
Sbjct: 323 IWRVRRKER 331


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: 315
Number of extensions: 24
Number of successful extensions: 3
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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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