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 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Dino:3606962
          Length = 357

 Score =  187 bits (476), Expect = 2e-52
 Identities = 109/302 (36%), Positives = 173/302 (57%), Gaps = 8/302 (2%)

Query: 13  IFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILG 72
           + +++ AI VF  +   +F +   +  ++  V  + I++   ++VI+T+GIDLSVG+I+ 
Sbjct: 49  LIVLVAAIAVFGLLLGSKFFSPFALTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAIMV 108

Query: 73  AASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGL 132
            +SVVMG      GL   ++V  GL  G   G  NG L+ K +L PFI TLGM  +    
Sbjct: 109 MSSVVMGQFTFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQIVLAA 168

Query: 133 AYVMSGGWPI--------SPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTG 184
            ++ S    I        +P  + F    +     +   VI+M ++ ++    L++T  G
Sbjct: 169 NFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARLTYGVIFMVLLVIVLAYALRHTAWG 228

Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELD 244
           R +YA+G + EA++L G++  R LI VY ++G + AFAG+ L   +G   P +GQ   ++
Sbjct: 229 RHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPTSGQLANIE 288

Query: 245 VIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAI 304
            I A VIGG SL GG G+ILGAF GA+I+GV   G+ LLG  + W  ++IG++II A+A+
Sbjct: 289 SITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAV 348

Query: 305 DQ 306
           DQ
Sbjct: 349 DQ 350


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: 284
Number of extensions: 12
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: 357
Length adjustment: 28
Effective length of query: 285
Effective length of database: 329
Effective search space:    93765
Effective search space used:    93765
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