GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Halomonas xinjiangensis TRM 0175

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_043529622.1 JH15_RS09235 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>NCBI__GCF_000759345.1:WP_043529622.1
          Length = 354

 Score =  249 bits (636), Expect = 7e-71
 Identities = 127/335 (37%), Positives = 203/335 (60%), Gaps = 2/335 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           MLV+RPA+ ADLP ++RLA+ +   +T+LP   +RL ++I  S+ +F+ ++ + GEE+Y 
Sbjct: 1   MLVVRPARPADLPALERLASSATPRLTNLPAHRDRLEERIARSQRAFSHDIDFPGEENYT 60

Query: 61  FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120
           FV+ED    E+VG + I A AG  E +Y++R ET +HAS+ L++  ++  L+L H+++  
Sbjct: 61  FVIEDRERDEVVGTATIRALAGAHEAYYTYRQETLIHASQQLNVRREVQTLALSHEVSDA 120

Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180
           SLL +  +      +    L  R RL+F+A +PERF+  + V   GY D  GESPFWN+V
Sbjct: 121 SLLCALSLHPRYKDTSAESLLRRSRLMFIAQYPERFSQILAVAFPGYLDNDGESPFWNSV 180

Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240
           GR+FF   Y E   ++G++S++F+AE+MP +P+Y+PLL   A+ ++G+ HP  +   + +
Sbjct: 181 GRHFFVRGYQEMNHVAGVRSKSFIAEVMPQFPLYLPLLTPQARAAIGREHPAHERALEEM 240

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKI--GEAPKSGRPYLVTNGQLQ 298
           + EGF    ++DIFD GP +      + +   +   PV+I          P ++ N +L 
Sbjct: 241 LAEGFLRSRHVDIFDAGPVVKGERDRLATFRNAAWHPVRIRPQHTLPDAEPAMIANQKLG 300

Query: 299 DFRAVVLDLDWAPGKPVALSVEAAEALGVGEGASV 333
           DFR VV     +P   + LS E AE LGV EG +V
Sbjct: 301 DFRCVVARYALSPTGQLMLSPEHAEVLGVEEGRAV 335


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: 310
Number of extensions: 12
Number of successful extensions: 1
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: 354
Length adjustment: 29
Effective length of query: 309
Effective length of database: 325
Effective search space:   100425
Effective search space used:   100425
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 24 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