GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruG in Pseudomonas fluorescens GW456-L13

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate PfGW456L13_1972 Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109)

Query= BRENDA::P80358
         (340 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1972 Arginine
           N-succinyltransferase, alpha subunit (EC 2.3.1.109)
          Length = 339

 Score =  229 bits (583), Expect = 1e-64
 Identities = 128/336 (38%), Positives = 195/336 (58%), Gaps = 4/336 (1%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAE-RGDADYLF 59
           +++RP   ADL  +  LA  +  G+T+LP + +RL  +++ +E +F  E    G+  Y F
Sbjct: 2   LVMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYFF 61

Query: 60  VLEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118
           VLED A GK+VG SAI  + G  EP+Y++R    V AS+EL IH +I  L   +DLTGNS
Sbjct: 62  VLEDSATGKLVGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGNS 121

Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178
            L S ++  +       +L SR R LF+A     F D ++ E+ G SDE G SPFW+++G
Sbjct: 122 LLTSFYVQRELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAIG 181

Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238
           R+FF + +++A+ L G+ ++ F+AELMP +P+Y   L + A+  +G+VHP  +    +L 
Sbjct: 182 RNFFDLNYAEAERLCGLKSRTFLAELMPHYPIYVPLLPDSAQEAMGQVHPRAQITFDILM 241

Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDD-AEPYLIHNRKREDC 297
            EGF    Y+DIFD GP + A    IR+IA+S+ + + +G P       YL+ N + +D 
Sbjct: 242 REGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEPVKGVGRQYLVANAQLQDY 301

Query: 298 RITAAPARAAAG-TLVVDPLTAKRLRLSAGASVRAV 332
           R        A G  + +D   A+ L +  GASVR V
Sbjct: 302 RAVMLELDYAPGKPVTLDLEAAEALGVGEGASVRLV 337


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: 303
Number of extensions: 19
Number of successful extensions: 3
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: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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