GapMind for catabolism of small carbon sources

 

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

Align Lysine racemase; Lys racemase; Ornithine racemase; EC 5.1.1.5; EC 5.1.1.12 (characterized)
to candidate WP_158090989.1 MGEO_RS07780 alanine/ornithine racemase family PLP-dependent enzyme

Query= SwissProt::Q9X1T3
         (354 letters)



>NCBI__GCF_002115805.1:WP_158090989.1
          Length = 379

 Score =  207 bits (528), Expect = 3e-58
 Identities = 115/349 (32%), Positives = 191/349 (54%), Gaps = 3/349 (0%)

Query: 4   PRLLINLKEIEENARKVVEMASRRGIEIVGVTKVTLGDPRFAETLRKAGIGILGESRIRN 63
           PR+  +   +++N   + ++ +  GI + GVTK   G+P  A  +   GI  L ++R+ N
Sbjct: 10  PRVEFDTDALQQNFAHLAKLCAAHGIAVSGVTKAIGGNPDIARLMLDNGIRTLADARLDN 69

Query: 64  VLRMKKAGIEGPFMLLRLPMMSELVEDVKHFDYIMVSDPDVAKKVDELSREMKRNVKIIY 123
           + R++  GI+ P MLLR P M E+ E  +  D  ++S+ +  + +     E+ +  +++ 
Sbjct: 70  IARLRAGGIDVPVMLLRAPAMVEVAEAARLADIFLLSEIETIRALATAKAELGKCCQVVL 129

Query: 124 MIDVGDLREGVWFEKAVE---EIAQCRGANIVGIGTNFGCYGGIIPTREKFEILLDIKEK 180
           M+D+GDLREGV  E        +     ANI+GIGTN  C  G++P +     L+ +  +
Sbjct: 130 MVDLGDLREGVPPEDLPSLGRAVMATENANIIGIGTNLACNLGVLPDQSNMAELVALANQ 189

Query: 181 LEKNHGFNIEIVSGGNTPALYALENGEIPEGINQLRIGEAIVLGRDITNNRVIDWLSQNT 240
           LE   G  +  VS GN+ A+  + N  +P  IN LR+GE+++LGR+      +  +S + 
Sbjct: 190 LEATIGHPLRYVSAGNSSAISLMLNQGLPSKINHLRLGESLLLGRETAYGHPLARMSGDC 249

Query: 241 FLIEAEVIEVKEKPSVPLGKRGLDVFGRKVDFVDRGIRKRAICALGEQDIDSRGLIPVDK 300
           F + A++IE K K   P   RG + FG++VD      R+  +  +G  D +  GL P+  
Sbjct: 250 FDLVAQIIEHKLKAPRPYAARGRNAFGQQVDVELTEPRRLGVLNVGAVDCEIGGLCPLIN 309

Query: 301 GVEVLHASSDHIVLDVTDFGDVKVGDVFRFRMTYSCLLKAMTSPFVEKV 349
           GV ++  SSDH+++D T    + VGD  RFR+ Y  L  AMTSP++ +V
Sbjct: 310 GVSIVGYSSDHLIVDTTSSTSLAVGDEIRFRVDYHALATAMTSPYLAQV 358


Lambda     K      H
   0.321    0.142    0.407 

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: 302
Number of extensions: 7
Number of successful extensions: 2
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: 354
Length of database: 379
Length adjustment: 30
Effective length of query: 324
Effective length of database: 349
Effective search space:   113076
Effective search space used:   113076
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.

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