GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Caulobacter crescentus NA1000

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 CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  233 bits (595), Expect = 4e-66
 Identities = 124/306 (40%), Positives = 189/306 (61%), Gaps = 4/306 (1%)

Query: 8   AREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSV 67
           AR+    L L+ +V   G     FLT  N   ++  VS   I++ GMT VI+  GID++V
Sbjct: 23  ARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAV 82

Query: 68  GSILGAASV----VMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTL 123
           GS+L  AS+    V+  ++ +   +  +++++   +G+  G   G  +T   +  FI TL
Sbjct: 83  GSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTL 142

Query: 124 GMLSVGRGLAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVT 183
           G ++V RG   +++ G PIS F +++   G G +  +PVPV+  A++    H+ L+YT  
Sbjct: 143 GGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRY 202

Query: 184 GRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYEL 243
           GR++YA+GGN EA++L G+  D I   VY I G LA  +GFLL+A LG A+  AG GYEL
Sbjct: 203 GRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYEL 262

Query: 244 DVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIA 303
            VIA+ VIGG SL+GG G + G  LGA+++GVL NG+++L V+S+ QQVVIG++I+ A+A
Sbjct: 263 RVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVA 322

Query: 304 IDQIRR 309
            D   R
Sbjct: 323 FDHYAR 328


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: 306
Number of extensions: 21
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: 332
Length adjustment: 28
Effective length of query: 285
Effective length of database: 304
Effective search space:    86640
Effective search space used:    86640
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.

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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