GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Desulfovibrio vulgaris Miyazaki F

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate 8499536 DvMF_0306 acetylglutamate kinase (RefSeq)

Query= curated2:A0RWW1
         (266 letters)



>FitnessBrowser__Miya:8499536
          Length = 320

 Score =  128 bits (321), Expect = 2e-34
 Identities = 88/255 (34%), Positives = 138/255 (54%), Gaps = 13/255 (5%)

Query: 2   ITIKIGGSIV--DSLHPSAIPDIKKAAAGGV--VLVHGGGKEVTKVCEQLGKEPRFVTSP 57
           + IK GG  +  ++L  +   +I      G+  V+VHGGG ++ ++ EQL  + +F    
Sbjct: 40  VVIKYGGHAMKDEALKKAFALNIALLKQVGINPVVVHGGGPQIGRMLEQLHIQSQFREG- 98

Query: 58  GNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLVI 117
                R TD  T ++  MV+ G++NK IV +L   GV AVGLSG DG LIRA RK  +++
Sbjct: 99  ----LRVTDDATMDVVEMVLVGKVNKEIVNLLNLSGVKAVGLSGKDGQLIRA-RKMEMIV 153

Query: 118 VNERGRKQAIEGGYTGRITSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGDRAAAN 177
                  + I+ G  G +  V + LL +L     VPV++P+ +    E  N++ D  A  
Sbjct: 154 NGGNHAPEIIDLGKVGEVMRVETTLLRSLERDNFVPVIAPVGVDENGETYNINADAVAGA 213

Query: 178 IAGATKSERILFVTDVDGLMMDEK-LVSRLSAAEAEEI--RPKIGPGMEKKVLAATEALK 234
           +A A +++R+L +TDV G++  +K L+  L+  EA E+     +  GM  KV    EAL+
Sbjct: 214 VAAALRAKRLLLLTDVAGILDKQKELIRSLTTREAVELFTDGTLTGGMIPKVKCCLEALE 273

Query: 235 MGVREAIIARGSREN 249
            GV +A+I  G  EN
Sbjct: 274 EGVEKAMIVDGRVEN 288


Lambda     K      H
   0.316    0.135    0.370 

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: 207
Number of extensions: 13
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: 266
Length of database: 320
Length adjustment: 26
Effective length of query: 240
Effective length of database: 294
Effective search space:    70560
Effective search space used:    70560
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: 48 (23.1 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