GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Marinobacter adhaerens HP15

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate GFF3098 HP15_3041 arginine N-succinyltransferase, alpha chain

Query= CharProtDB::CH_107315
         (338 letters)



>FitnessBrowser__Marino:GFF3098
          Length = 339

 Score =  227 bits (578), Expect = 4e-64
 Identities = 131/337 (38%), Positives = 193/337 (57%), Gaps = 3/337 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTS-LPDDAERLRDKILASEASFAAEVSYNGEESY 59
           M ++RPA+  DL Q+  +A      ++S LP   + L  KI  S ASFA  +S   +   
Sbjct: 1   MWLVRPAEPDDLDQILAIAGTQCARLSSTLPKQGDALAYKIEQSLASFAGRISAEDDPPR 60

Query: 60  F-FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLT 118
           F FVLED+ +G++ G + I A AG  +PFYS+R +  +HAS  L +  ++ VL   H LT
Sbjct: 61  FLFVLEDTETGDIAGTAGIDAHAGNGQPFYSYRRDALIHASHELGVSRRVEVLYPSHSLT 120

Query: 119 GNSLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWN 178
             SLL SF ++ +L  +   EL SR R+LF+A H E F   + VEI G   E G  PFW+
Sbjct: 121 DVSLLCSFSIRPELQGTDAFELLSRARILFIADHREWFTQRMAVEIQGVQLEDGSVPFWD 180

Query: 179 AVGRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFD 238
           ++GR+FFD+++  A++ SG  S+TF+AELMP  PIYV LL +AAQ++MGQ H      F+
Sbjct: 181 SLGRHFFDMDFETADQYSGQLSKTFIAELMPPNPIYVTLLSEAAQKAMGQPHQITVPNFE 240

Query: 239 ILMREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQ 298
           +L REGF+  NY+DIFD GP L ART  ++++  S    +  G    +G   L+  G+ +
Sbjct: 241 LLQREGFQPGNYLDIFDAGPVLEARTDSLKTLVTSHPKELH-GTNEDTGETCLIAAGEGE 299

Query: 299 DFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRL 335
            FR  +  +  +    + + V     L    G  VR+
Sbjct: 300 QFRCTLTPVAESLDDKLKVPVSTWNTLNRTAGDRVRI 336


Lambda     K      H
   0.319    0.135    0.387 

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: 290
Number of extensions: 11
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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