GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Marinobacter adhaerens HP15

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF2696 HP15_2640 arginine/ornithine succinyltransferase

Query= BRENDA::P80358
         (340 letters)



>FitnessBrowser__Marino:GFF2696
          Length = 379

 Score =  195 bits (496), Expect = 1e-54
 Identities = 105/272 (38%), Positives = 155/272 (56%), Gaps = 2/272 (0%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAF-RGEAERGDADYLF 59
           MI+RP+T  DL AL+++A  +G G T+L  +   L  ++  + ++F R     GD  YLF
Sbjct: 7   MIIRPITPKDLDALMQIAVESGPGFTSLMPDRDALSRKIDHSVESFARTVTTPGDEHYLF 66

Query: 60  VLEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118
           VLED A G+++G + I  A GL  P  ++R    +   ++        +L      TG +
Sbjct: 67  VLEDSATGQIMGTTGIEAAAGLSRPLVHFRRNAVIHHEEDPRKRHAEESLTRCQHYTGCT 126

Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178
           E+CSL+L    R    GKLLSR RFLF+A     F D +IAEMRG+SD  GRSPFW+ L 
Sbjct: 127 EVCSLYLRPGFRRANAGKLLSRVRFLFMALHPERFADTVIAEMRGVSDHAGRSPFWDWLK 186

Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238
            H   ++F  A  L   G   F+   +P  PL+T  +++ AR VIG+VH +T PA  ML+
Sbjct: 187 HHVADLDFMSATQLACCGQSGFVERFIPATPLFTRQMTDAARAVIGQVHEDTRPARHMLE 246

Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAES 270
            EGF ++G+VD+ D GP +E     I ++ ++
Sbjct: 247 REGFRHRGFVDLLDGGPTLECARSDIASVRDT 278


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: 315
Number of extensions: 6
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: 379
Length adjustment: 29
Effective length of query: 311
Effective length of database: 350
Effective search space:   108850
Effective search space used:   108850
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