GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Pseudomonas fluorescens GW456-L13

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate PfGW456L13_1973 Arginine N-succinyltransferase (EC 2.3.1.109)

Query= CharProtDB::CH_107315
         (338 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973
          Length = 341

 Score =  229 bits (583), Expect = 1e-64
 Identities = 121/337 (35%), Positives = 194/337 (57%), Gaps = 3/337 (0%)

Query: 2   LVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFF 61
           +++RP +++DLP +  LA  +  G+T+LP + ERL  ++  +E +F  E    G+  Y F
Sbjct: 1   MIVRPVRSSDLPALIDLARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAG-RGDADYLF 59

Query: 62  VLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNS 121
           VLED   G +VG SAI  + G  EP+Y+FR    V AS+ L+I+ +I  L L +DLTGNS
Sbjct: 60  VLEDD-DGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNS 118

Query: 122 LLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVG 181
            L S ++  D    +   + S+ R+LF+A  P+ F + ++ E+ G SDE G SPFW ++G
Sbjct: 119 ELCSLFLHADYRSGLNGRMLSKARMLFIAEFPQLFGNKIIAEMRGVSDEAGRSPFWESLG 178

Query: 182 RNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILM 241
           R+FF + + +A+ L+G+ ++ F+AELMP +P+Y   L   A+  +GQVHP  +    +L 
Sbjct: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSPDARNVIGQVHPDTEPALAMLK 238

Query: 242 REGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDFR 301
            EGF    Y+DIFD GP +   T  IR++  S+ + + +G       P+++ N + +D R
Sbjct: 239 SEGFSYQGYVDIFDAGPAIECETGKIRAVRDSQALVLAVGTPGDDATPFIIHNRKREDCR 298

Query: 302 AVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
                   A G  + +    A+ L +  G  VR VA+
Sbjct: 299 ITAAPARLAAG-TLVVDPLTAKRLQLNAGDQVRAVAL 334


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: 275
Number of extensions: 15
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: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
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