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_03379 H281DRAFT_03379 monosaccharide ABC transporter membrane protein, CUT2 family

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Burk376:H281DRAFT_03379
          Length = 343

 Score =  233 bits (594), Expect = 5e-66
 Identities = 131/311 (42%), Positives = 185/311 (59%), Gaps = 17/311 (5%)

Query: 17  LIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASV 76
           L+ ++V   +T+  F +V N+ TV L V+ IA +    T VIIT GIDLSVGS+L  A V
Sbjct: 33  LVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGIDLSVGSVLALAGV 92

Query: 77  VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVM 136
              LL+ + G+   +++  G+ VG   G  NG+ +T+  L PFI+TLGM+ V RGLA  +
Sbjct: 93  AAALLV-KAGVPVPVAMAGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLVARGLALQI 151

Query: 137 SGGWPISPFPESFTVHGQGMVGPV----------------PVPVIYMAVIGVIAHIFLKY 180
           +G  P+S   ++F   G G +  V                P PV+ M ++ V   + L  
Sbjct: 152 TGARPVSGLGDAFGELGNGALFKVSHIGADGFPDTVFPGIPYPVVIMVILFVAVSVLLSR 211

Query: 181 TVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQG 240
           T  GR IYA+G N EA++L G+    + +  Y ++G LA   G +L + L  AQPN G  
Sbjct: 212 TSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVM 271

Query: 241 YELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIII 300
           YELD IA+ VIGGTSL GG GTI G  +GA ++GVLRNG+ + GVSSF QQ++IG+VI+ 
Sbjct: 272 YELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILG 331

Query: 301 AIAIDQIRRAK 311
            + IDQ+R  K
Sbjct: 332 TVWIDQLRNRK 342


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: 332
Number of extensions: 20
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: 343
Length adjustment: 28
Effective length of query: 285
Effective length of database: 315
Effective search space:    89775
Effective search space used:    89775
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.

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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