GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Dinoroseobacter shibae DFL-12

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 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Dino:3609042
          Length = 328

 Score =  184 bits (467), Expect = 2e-51
 Identities = 107/302 (35%), Positives = 170/302 (56%), Gaps = 2/302 (0%)

Query: 7   KAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLS 66
           K+ E  + L+ I I V     +  FL   N+     N +  A+++F M ++II+  IDLS
Sbjct: 21  KSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLS 80

Query: 67  VGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGML 126
           V SI+  AS  MG  +     +P L V+IGL VG+  G  NG+L+T+  L   + T+G +
Sbjct: 81  VASIIALASTAMGAAVQMGVGTPGL-VLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTM 139

Query: 127 SVGRGLAYVMSGGWPISPFPESFTVHGQGMVG-PVPVPVIYMAVIGVIAHIFLKYTVTGR 185
           S+ RG++Y++ G      +PESF+  GQG V   +   ++  A+I VI  + L  T  GR
Sbjct: 140 SLFRGISYIVLGDQAFRGYPESFSWFGQGYVWWVISFELVLFAIIAVIYAMLLHKTNFGR 199

Query: 186 RIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDV 245
            +YAIG N   +   GI+  R+  +++ + G ++  A   LTA LG  +P+   G+EL+V
Sbjct: 200 AVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWELEV 259

Query: 246 IAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAID 305
           +   V+GG S+ GG GTILG  + A +MG++  G+ LL V      +VIG ++I  IA+ 
Sbjct: 260 VTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIALP 319

Query: 306 QI 307
           ++
Sbjct: 320 RL 321


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: 344
Number of extensions: 21
Number of successful extensions: 4
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: 328
Length adjustment: 28
Effective length of query: 285
Effective length of database: 300
Effective search space:    85500
Effective search space used:    85500
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