GapMind for catabolism of small carbon sources

 

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

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate AO356_18730 AO356_18730 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18730
          Length = 339

 Score =  571 bits (1472), Expect = e-168
 Identities = 288/339 (84%), Positives = 312/339 (92%), Gaps = 1/339 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           MLVMRPAQ ADL +VQRLAADSP+GVTSLPDD ERL DKI ASEASFAAEVS+NGEESYF
Sbjct: 1   MLVMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYF 60

Query: 61  FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120
           FVLED+A+G+L GCSAIVASAG+SEPFYSFRNETFVHASR L IHNKIHVLS CHDLTGN
Sbjct: 61  FVLEDTATGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGN 120

Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180
           SLLTSFYV  +LV S ++ELNSRGRLLF+ASHPERFAD+VV EIVGYSDE G+SPFW+A+
Sbjct: 121 SLLTSFYVVPELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAI 180

Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240
           GRNFFDLNY  AE+L GLKSRTFLAELMPHYPIYVPLLPDAAQE+MGQVHPRAQITFDIL
Sbjct: 181 GRNFFDLNYAAAERLCGLKSRTFLAELMPHYPIYVPLLPDAAQEAMGQVHPRAQITFDIL 240

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPK-SGRPYLVTNGQLQD 299
           MREGFETD+YIDIFDGGPTLHAR SGIRSIAQSRVVPVKIGE  K +GR YLV N QLQD
Sbjct: 241 MREGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEPVKGAGRQYLVANAQLQD 300

Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
           +RAV+L+LD+APGKPV L +EAAEALGVGEGASVRLVAV
Sbjct: 301 YRAVLLELDYAPGKPVTLDMEAAEALGVGEGASVRLVAV 339


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: 445
Number of extensions: 9
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