GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Pseudomonas fluorescens FW300-N2C3

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate AO356_01525 AO356_01525 arginine N-succinyltransferase

Query= BRENDA::P80358
         (340 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01525
          Length = 338

 Score =  219 bits (557), Expect = 1e-61
 Identities = 124/337 (36%), Positives = 188/337 (55%), Gaps = 3/337 (0%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAER-GDADYLF 59
           + +RPV  ADLP L  LAR +  G+T+LP + +RL+ ++  +  +F  +A+  G  +Y F
Sbjct: 2   LALRPVQLADLPQLQRLARDSLVGVTSLPDDTRRLEEKILDSCASFAADAQGPGAENYFF 61

Query: 60  VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118
           VL+D ++G++VG S I  + G  EP+Y+ R     S S+ELNI   +P L L  DL G +
Sbjct: 62  VLQDLESGRLVGCSEILSSTGCNEPFYSLRNRPFSSESRELNIQHGVPALSLCQDLNGQT 121

Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178
            L    + A        +LLSRAR +FIA     F + +I E+ G S E+G+SPFW+++G
Sbjct: 122 LLRGFHIDAGRVRTPESELLSRARLMFIAAHPQRFAESVITEIVGFSSEDGQSPFWDAIG 181

Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238
           +HFF + + +A+ L G+ ++ F+AELMP++P+Y   L   A+  IGRVHP+ + A  +L+
Sbjct: 182 QHFFDLPYVEAERLCGLQSRTFLAELMPQYPIYVPMLPPAAQACIGRVHPDGQEAFDILE 241

Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCR 298
            EGF    YVDIFD GP + A    IR+I +S+          D    YL+ N      R
Sbjct: 242 REGFETNSYVDIFDGGPTLHARIANIRSITQSRTTTARQSPQIDARGLYLVSNEHLASYR 301

Query: 299 ITAAPARAAA-GTLVVDPLTAKRLRLSAGASVRAVPL 334
              A     A G + + P     L +  GA +R + L
Sbjct: 302 AIVAELDVGADGPVALSPAMLTALDIQDGARIRVIAL 338


Lambda     K      H
   0.320    0.136    0.398 

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: 263
Number of extensions: 12
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: 340
Length of database: 338
Length adjustment: 28
Effective length of query: 312
Effective length of database: 310
Effective search space:    96720
Effective search space used:    96720
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