GapMind for catabolism of small carbon sources

 

Alignments for a candidate for orr in Marivita geojedonensis DPG-138

Align Ornithine racemase; OR; EC 5.1.1.12 (characterized)
to candidate WP_158090989.1 MGEO_RS07780 alanine/ornithine racemase family PLP-dependent enzyme

Query= SwissProt::C1FW08
         (353 letters)



>NCBI__GCF_002115805.1:WP_158090989.1
          Length = 379

 Score =  225 bits (574), Expect = 1e-63
 Identities = 137/348 (39%), Positives = 196/348 (56%), Gaps = 4/348 (1%)

Query: 3   PKITIDINKLRDNATFIKNLCEKGGCKTALVVKSMCANHDIVKELDSVEVDYFADSRIQN 62
           P++  D + L+ N   +  LC   G   + V K++  N DI + +    +   AD+R+ N
Sbjct: 10  PRVEFDTDALQQNFAHLAKLCAAHGIAVSGVTKAIGGNPDIARLMLDNGIRTLADARLDN 69

Query: 63  LKKLK--DLKTKKMLLRIPMLCEVEDVVKYADISMNSELDTLKALNKAAKTLNKVHSVII 120
           + +L+   +    MLLR P + EV +  + ADI + SE++T++AL  A   L K   V++
Sbjct: 70  IARLRAGGIDVPVMLLRAPAMVEVAEAARLADIFLLSEIETIRALATAKAELGKCCQVVL 129

Query: 121 MVDLGDLREGYFEAEDLKENIKEIIKLENIEIKGIGVNLTCYGAVIPKNDNLSRLCDIAD 180
           MVDLGDLREG    EDL    + ++  EN  I GIG NL C   V+P   N++ L  +A+
Sbjct: 130 MVDLGDLREGV-PPEDLPSLGRAVMATENANIIGIGTNLACNLGVLPDQSNMAELVALAN 188

Query: 181 ELRTEFNLELPIVSGGNSSSIYLIDKGELPEGITNLRVGESMLLGRETAYGEDIIGMNND 240
           +L       L  VS GNSS+I L+    LP  I +LR+GES+LLGRETAYG  +  M+ D
Sbjct: 189 QLEATIGHPLRYVSAGNSSAISLMLNQGLPSKINHLRLGESLLLGRETAYGHPLARMSGD 248

Query: 241 VFELKCQIVELKEKPSLPIGEIGVDAFGNKPYYEDKGIRKRAILAIGQQDTDISSLMPID 300
            F+L  QI+E K K   P    G +AFG +   E    R+  +L +G  D +I  L P+ 
Sbjct: 249 CFDLVAQIIEHKLKAPRPYAARGRNAFGQQVDVELTEPRRLGVLNVGAVDCEIGGLCPLI 308

Query: 301 DKLEILGASSDHLIVDVSDSNTSYKVGDIITFRMGYGALLKGFTSEYI 348
           + + I+G SSDHLIVD + S+TS  VGD I FR+ Y AL    TS Y+
Sbjct: 309 NGVSIVGYSSDHLIVDTT-SSTSLAVGDEIRFRVDYHALATAMTSPYL 355


Lambda     K      H
   0.317    0.138    0.384 

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: 262
Number of extensions: 12
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: 353
Length of database: 379
Length adjustment: 30
Effective length of query: 323
Effective length of database: 349
Effective search space:   112727
Effective search space used:   112727
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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