GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Sphingomonas koreensis DSMZ 15582

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)

Query= curated2:Q8ZU99
         (261 letters)



>FitnessBrowser__Korea:Ga0059261_2530
          Length = 299

 Score =  107 bits (268), Expect = 2e-28
 Identities = 79/246 (32%), Positives = 126/246 (51%), Gaps = 16/246 (6%)

Query: 3   VVKIGGSVV-----CKDASKVIQNLPKYADRAVVIHGGGCLVNELLKRMGIEPKFLTHPG 57
           VVK GG  +      +D ++ +  L       VV+HGGG  + ++LKR+G+E +F+   G
Sbjct: 33  VVKYGGHAMGDPELARDFAEDVVLLKAVGINPVVVHGGGPQIGQMLKRLGVESEFV---G 89

Query: 58  GLVSRYTDWETLKVFVMAM-GWINKYIVASLHGLGVQALGLTGADLGVVVAKRKERVLVI 116
           GL  R TD ET ++  M + G INK IV+ +   G +A+G++G D G+V A++  R    
Sbjct: 90  GL--RVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLVTARKVTRSEAD 147

Query: 117 DERGRQRVVDGGYVGKIAEIRVDKLTPPP----LKVLAPVAVSEKGELLNIDGDQLAFDV 172
             +G +R VD G+VG+   +    LT       + V+AP+A+   G   NI+ D +A  +
Sbjct: 148 PLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADGHTYNINADTMAGAI 207

Query: 173 AREAKAERLILLSDVEGLILGGK-VVPRLTPEEAEKLVKSEEVRGGMKRKLLMASEAAKL 231
           A    A R  LL+DV G++   K ++  L P     L     + GGM  K+     A   
Sbjct: 208 AGALGASRFFLLTDVPGVLSKDKQLLSDLDPGRIAALKADGTISGGMIPKVETCVAAVDA 267

Query: 232 GIEVVI 237
           G++  +
Sbjct: 268 GVDAAV 273


Lambda     K      H
   0.319    0.139    0.393 

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: 217
Number of extensions: 15
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: 261
Length of database: 299
Length adjustment: 26
Effective length of query: 235
Effective length of database: 273
Effective search space:    64155
Effective search space used:    64155
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 (21.7 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