GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Caulobacter crescentus NA1000

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate CCNA_00285 CCNA_00285 acetylglutamate kinase

Query= curated2:A0RWW1
         (266 letters)



>FitnessBrowser__Caulo:CCNA_00285
          Length = 304

 Score =  112 bits (280), Expect = 9e-30
 Identities = 84/276 (30%), Positives = 137/276 (49%), Gaps = 30/276 (10%)

Query: 2   ITIKIGGSIVDSLHPSAIPDIKKAAAGGVVL----------VHGGGKEVTKVCEQLGKEP 51
           + IK GG      H     D+ K  A   VL          VHGGG +++++ ++ G + 
Sbjct: 31  VVIKYGG------HAMGQEDVAKVFAADAVLLKLLGVHPVVVHGGGPQISRMLDKAGVKS 84

Query: 52  RFVTSPGNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNA----VGLSGIDGGLI 107
            FV        R TD+ T E+  MV+SG INK I   +   G  A    VGLSG D  LI
Sbjct: 85  TFVDG-----LRVTDEATMEVAEMVLSGAINKEIANWITLAGAEADVRGVGLSGKDARLI 139

Query: 108 RAERKSRLVIVNERGRKQAIEGGYTGRITSVNSELLETLLGK--GIVPVVSPIAMGNEYE 165
            AE+ +R     +   +QA++ G+ G  T V+ +L+E LL      +PVV+PI +  + +
Sbjct: 140 TAEKVTRTKKDPDSNIEQAVDLGFVGEPTKVDPQLIEALLTSEHDYIPVVAPIGVSPDGD 199

Query: 166 LLNVDGDRAAANIAGATKSERILFVTDVDGLM-MDEKLVSRLSAAEAEEI--RPKIGPGM 222
             N++ D  A  +AGA K++R+L +TD+ G++  + +L+  ++  +A  +        GM
Sbjct: 200 TFNINADTVAGALAGALKAKRMLMLTDIKGVLDGNGELIREMTIEQARALIDTGVATGGM 259

Query: 223 EKKVLAATEALKMGVREAIIARGSRENPVSAAIAHE 258
             K+  A  A++ GV   +I  G R + +   +  E
Sbjct: 260 IPKLENAIHAIESGVEAVVILDGRRPHAMLVELFSE 295


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: 180
Number of extensions: 5
Number of successful extensions: 3
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: 304
Length adjustment: 26
Effective length of query: 240
Effective length of database: 278
Effective search space:    66720
Effective search space used:    66720
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: 47 (22.7 bits)

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