GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Sphingomonas koreensis DSMZ 15582

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate Ga0059261_4188 Ga0059261_4188 pyridoxal-dependent decarboxylase, exosortase A system-associated

Query= curated2:O29458
         (419 letters)



>FitnessBrowser__Korea:Ga0059261_4188
          Length = 407

 Score =  142 bits (359), Expect = 1e-38
 Identities = 122/377 (32%), Positives = 174/377 (46%), Gaps = 15/377 (3%)

Query: 7   GILTVEGVKVTEIVRETGTPVYVTSRALLERNLEAYKKAFSNE-GLLYAVKANNNLALMR 65
           G LT+ G    + V E G+P++V    ++   L   + A  +   + +A+KAN     + 
Sbjct: 15  GELTIAGRAAADWVAEAGSPLFVYDMGIVHERLRGLRAALPDACEIHFAIKANPLPEFIA 74

Query: 66  IIASHGFGADVFSDGELYLASLAGFRKDM--VLFNGNSKSRKEIEMGVTAGVKFSVDSLD 123
            +A    G DV S GEL  A      KD   + F G  K   E+E  + AG   +++S  
Sbjct: 75  AVAPLVGGLDVASGGELAKALKV---KDAAHISFAGPGKRDAELEAAIVAGATLNLESEG 131

Query: 124 ELRTISKIAKEVGKEVEIAFRVNPDVDPKTHPKIATGLRESKFGIPHEMVREAYEMALKL 183
           E      I + +G    +A RVNPD + +    +  G R S FG+    V  A    L  
Sbjct: 132 EAERALTIGRVLGTTPRLAVRVNPDFELRGSG-MKMGGRASPFGVDAARV-PALVNRLIA 189

Query: 184 DGVVPVGIHCHIGSQILDLSPFVHALNKVMDIAVDI-EKLGVELSFVDMGGGLGIDYEGK 242
            G    G H   GSQ LD +  +      + +A  + ++ GV    V++GGG GI Y   
Sbjct: 190 AGADWRGFHIFAGSQSLDTAAIIETQAATVALAARLAQEAGVSPPLVNLGGGFGIPYFSG 249

Query: 243 GAPTPKDLASAILPEFEGRKADLTSDPQLWLEPGRSIVGNTTVLITRVNAVK-KGYKNFV 301
             P   D   A L +    + ++ +     +E GR I G   V + RV   K  G + F+
Sbjct: 250 DMPIDIDAVGAALGKTLESRQEILAQSGFAIELGRWIAGECGVYLMRVIDRKISGDETFL 309

Query: 302 AVDAGFN-VLIRPAMYGSYHR----VAVANKMDAEPEEVYTVVGPICESGDVLARDRKLP 356
             D G +  L     +G+  R    VAVA KMDAEP E  +VVGP+C   D LA    LP
Sbjct: 310 ICDGGLHHQLAASGNFGTVVRRNYPVAVAEKMDAEPVETVSVVGPLCTPLDRLADRVALP 369

Query: 357 KVEVGDLIAVFDAGAYG 373
           + E GD+IAVF AGAYG
Sbjct: 370 RTEPGDVIAVFLAGAYG 386


Lambda     K      H
   0.318    0.137    0.395 

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: 390
Number of extensions: 18
Number of successful extensions: 5
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: 419
Length of database: 407
Length adjustment: 31
Effective length of query: 388
Effective length of database: 376
Effective search space:   145888
Effective search space used:   145888
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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