GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Sphingomonas koreensis DSMZ 15582

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Ga0059261_3619 Ga0059261_3619 Predicted sugar kinase

Query= BRENDA::A3DDM2
         (289 letters)



>FitnessBrowser__Korea:Ga0059261_3619
          Length = 257

 Score = 70.9 bits (172), Expect = 3e-17
 Identities = 51/156 (32%), Positives = 85/156 (54%), Gaps = 10/156 (6%)

Query: 57  DMSDVMVCLGGDGTFLKAARMTVVKGK--PLLGVNLGKLGFLADVDKNDIENAVKRLVED 114
           D ++++V LGGDG  L+   M + K +  P+ G+NLG +GFL +  + D  +A  RL   
Sbjct: 33  DEAEMIVALGGDGFMLQTLHMLLEKHRNLPVFGMNLGTIGFLMNEWRPDGLDA--RLARA 90

Query: 115 K-FTVDERMMLDTVIVRDGKIIAEDIVLNDVVISRGAISRILHLKTYINDAF-MDLYPGD 172
           + F V   +M  T +  D  ++     +N+V + R    +   L+  +ND   +     D
Sbjct: 91  RPFRVTPLVMTATTVEGDTHVLP---AINEVSLLRET-RQTAKLEVTVNDRIVLPELVCD 146

Query: 173 GLIISTPTGSTAYSLSAGGPLVEPDVDLIICTPICP 208
           G++++TP GSTAY+LSA GP++     ++  TPI P
Sbjct: 147 GILVATPAGSTAYNLSAHGPILPLGSQMLALTPISP 182


Lambda     K      H
   0.320    0.140    0.398 

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: 146
Number of extensions: 10
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: 289
Length of database: 257
Length adjustment: 25
Effective length of query: 264
Effective length of database: 232
Effective search space:    61248
Effective search space used:    61248
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: 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