GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF1617
          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.

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