GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Chromobacterium vaccinii MWU205

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate WP_046157873.1 VL52_RS15520 arginine/ornithine succinyltransferase subunit alpha

Query= BRENDA::P80358
         (340 letters)



>NCBI__GCF_000971335.1:WP_046157873.1
          Length = 339

 Score =  232 bits (592), Expect = 9e-66
 Identities = 129/336 (38%), Positives = 198/336 (58%), Gaps = 7/336 (2%)

Query: 3   VRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDAD---YLF 59
           VRPV ++DLPA+  LA+++G G+T+LP+N ++L  R+  +  AF  EA  G+A    Y+F
Sbjct: 4   VRPVRTSDLPAIERLAQASGIGVTSLPSNREKLFERIQQSVSAFEHEAT-GEASRDYYMF 62

Query: 60  VLEDDAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119
            LE   G VVG ++I  + G  EP+Y+YR    V AS+ L ++  +  L + +DLTG  +
Sbjct: 63  ALEQ-GGAVVGTASICASAGFDEPFYSYRSETAVHASRALKVNNRVHVLNICHDLTGTVQ 121

Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179
           LC  F+ +     + G+L+SRAR LFIA  R  FG ++IAEM+G+ D+ G+SPFW ++GR
Sbjct: 122 LCGFFVDSG-LDAIAGELMSRARLLFIAGERERFGRRIIAEMQGVHDDAGQSPFWNAIGR 180

Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239
            FF ++F Q +      +K FIAELMP +P+Y   L +EA+  IG++HP+ E    +L  
Sbjct: 181 RFFNLDFLQVEQAFVSHSKTFIAELMPSYPIYVPLLPDEAQQAIGQIHPHFERVCQLLCK 240

Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAV-GTPGDDAEPYLIHNRKREDCR 298
           EGF    Y+DIFD G  + AE D+++ +  S+   + +  +    A   L+ N++     
Sbjct: 241 EGFEADNYLDIFDGGAVLTAELDRLKTVEHSRAYPVEIQASLPAQASLQLVSNQRLAGFA 300

Query: 299 ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPL 334
            TAA      G   ++P  AK L +S+G  VR   L
Sbjct: 301 ATAARVAVVDGVAFINPDAAKALGVSSGDRVRVAGL 336


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: 270
Number of extensions: 13
Number of successful extensions: 4
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 24 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 (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