GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Shewanella halifaxensis HAW-EB4

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_012278670.1 SHAL_RS18650 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>NCBI__GCF_000019185.1:WP_012278670.1
          Length = 339

 Score =  246 bits (627), Expect = 8e-70
 Identities = 126/337 (37%), Positives = 197/337 (58%), Gaps = 1/337 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           MLV+RP ++ D   + ++A +S  G TSLP + + LR KI   E SF  ++    +E Y 
Sbjct: 1   MLVIRPIRSTDFKALYQIAEESGHGFTSLPVNEDLLRSKIARVEESFTKQIDKPFDEGYL 60

Query: 61  FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120
            VLED+ +GE+VG   I A+ G  + FY +R  T V+ S  + + N++  L+LCHD TG 
Sbjct: 61  MVLEDTETGEVVGTCGIEAAVGMVDAFYHYRLGTEVYHSEQIGVRNEVETLTLCHDYTGA 120

Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180
           + L + +++    ++    + SR R LF+A H ERF + V+ E+ G SD  G SPF+  +
Sbjct: 121 AELCTLFLRGHYRKNNNGRMLSRSRFLFLAQHAERFGETVIAEMRGESDADGNSPFYGWL 180

Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240
             +F  +++++A+ LSGL  + F+AE+MP   +YV LLP  AQ+ +G+VH   +   ++L
Sbjct: 181 QEHFLGIDFVQADYLSGLSQKAFMAEMMPKNAVYVCLLPKEAQKVIGEVHANTRPALNLL 240

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKSGRPYLVTNGQLQDF 300
             EGF    Y+DIFDGGPT+      IRS+ +SR++ + IG  P     Y+V+N QL D+
Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECHLHDIRSVRESRLLTITIGATPSDAESYIVSNTQLADY 300

Query: 301 RAVVLDLDWAPG-KPVALSVEAAEALGVGEGASVRLV 336
           RA   +L        V L  + A AL V +G  +R++
Sbjct: 301 RATTANLAVVDDCDDVILDAQTAAALMVADGEQIRVL 337


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: 277
Number of extensions: 10
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: 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 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