GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ocd in Phaeobacter inhibens BS107

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate GFF1617 PGA1_c16390 ornithine cyclodeaminase ArcB

Query= SwissProt::Q59701
         (356 letters)



>lcl|FitnessBrowser__Phaeo:GFF1617 PGA1_c16390 ornithine
           cyclodeaminase ArcB
          Length = 348

 Score =  468 bits (1205), Expect = e-137
 Identities = 224/339 (66%), Positives = 279/339 (82%)

Query: 9   VVPFISVDHMMKLVLKVGIDTFLTELAAEIEKDFRRWPIFDKKPRVGSHSQDGVIELMPT 68
           +VPF+SVD+MM+L+  VGIDT + +LA  IE+DF+RW +FDK PRV SHS  GVIELMPT
Sbjct: 9   LVPFVSVDNMMRLIHHVGIDTVMKDLATYIEEDFKRWELFDKTPRVASHSDVGVIELMPT 68

Query: 69  SDGSLYGFKYVNGHPKNTHQGRQTVTAFGVLSDVGNGYPLLLSEMTILTALRTAATSALA 128
           SDG  YGFKYVNGHPKNT +G QTVTAFG+L+DV  GYP+LL+EMTILTALRTAATSA+ 
Sbjct: 69  SDGEAYGFKYVNGHPKNTSEGLQTVTAFGLLADVYTGYPVLLTEMTILTALRTAATSAMV 128

Query: 129 AKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQKLRLFDIDTSATRKCARNLTGPGFD 188
           AK+LA   + TMA+IGNGAQSEFQ+ A +AI G++ +RL+D+D +AT KCA NL G G  
Sbjct: 129 AKHLAPKGATTMAMIGNGAQSEFQSLAMQAICGLKSVRLYDVDPAATAKCAANLAGTGLA 188

Query: 189 IVECGSVAEAVEGADVITTVTADKQFATILSDNHVGPGVHINAVGGDCPGKTEISMEVLL 248
           +V C +  EA+EGA ++TT TADKQ+ATIL+DN VG GVHINA+GGDCPGKTE++  +L 
Sbjct: 189 VVSCKTPEEAIEGAQILTTCTADKQYATILTDNMVGSGVHINAIGGDCPGKTELAPGILS 248

Query: 249 RSDIFVEYPPQTWIEGDIQQLPRTHPVTELWQVMTGEKTGRVGDRQITMFDSVGFAIEDF 308
           RSD+FVE+PPQT +EG+IQQ+P    VTELWQV+ G+K GR  D+QIT+FDSVGFAIEDF
Sbjct: 249 RSDVFVEFPPQTRVEGEIQQMPEDFEVTELWQVILGQKPGRRDDKQITLFDSVGFAIEDF 308

Query: 309 SALRYVRAKITDFEMFTELDLLADPDEPRDLYGMLLRCE 347
           SALRY+R +I D + F ELD+LADPD+PRDL+GM+ R +
Sbjct: 309 SALRYIRDRIKDTDFFLELDMLADPDDPRDLFGMVQRAK 347


Lambda     K      H
   0.320    0.137    0.405 

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: 403
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: 356
Length of database: 348
Length adjustment: 29
Effective length of query: 327
Effective length of database: 319
Effective search space:   104313
Effective search space used:   104313
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 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, the preprint on GapMind for carbon sources, 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