GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21715 in Cupriavidus basilensis 4G11

Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein

Query= reanno::pseudo5_N2C3_1:AO356_00475
         (220 letters)



>FitnessBrowser__Cup4G11:RR42_RS16450
          Length = 211

 Score =  148 bits (373), Expect = 9e-41
 Identities = 79/209 (37%), Positives = 122/209 (58%)

Query: 5   LNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVI 64
           ++F  V      LL    L + LA+V+   G V GL +A    S+H VLR  A +Y+ + 
Sbjct: 3   IDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIF 62

Query: 65  RNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAG 124
           R TP+L+ +  +Y+A P  G+RL+ LP+ +I LS+ + AY  E+ R G+ ++H+GQREA 
Sbjct: 63  RGTPVLLHLFFVYYAAPMFGLRLEALPAAIIALSMSSAAYNAEIIRAGIRAVHRGQREAA 122

Query: 125 LAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVES 184
            A+G+   ++  +V +P   R VLP    NFIS  K TSLA+ I VPEL   A+ I   +
Sbjct: 123 QAVGMTNPRILRHVILPQATRIVLPPYMGNFISHTKSTSLASVITVPELMLSAQTIYSST 182

Query: 185 YRVIETWLVTTALYVAACYLIAMVLRYFE 213
           YR +E   +  A+Y+A   ++ +V  +FE
Sbjct: 183 YRAVEVLTIAGAIYLALTTVLTLVQLHFE 211


Lambda     K      H
   0.329    0.142    0.414 

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: 131
Number of extensions: 3
Number of successful extensions: 1
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: 220
Length of database: 211
Length adjustment: 22
Effective length of query: 198
Effective length of database: 189
Effective search space:    37422
Effective search space used:    37422
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 (21.8 bits)
S2: 45 (21.9 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