GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Magnetospirillum magneticum AMB-1

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_011382609.1 AMB_RS00825 NAD(+) kinase

Query= BRENDA::A3DDM2
         (289 letters)



>NCBI__GCF_000009985.1:WP_011382609.1
          Length = 255

 Score = 66.2 bits (160), Expect = 7e-16
 Identities = 45/149 (30%), Positives = 78/149 (52%), Gaps = 6/149 (4%)

Query: 59  SDVMVCLGGDGTFLKAARMTVVKGKPLLGVNLGKLGFLADVDKNDIENAVKRLVEDKFTV 118
           +DV++ LGGDG  L+     V +  P+ G+N G +GFL +V +      ++RL + +  +
Sbjct: 35  ADVIIALGGDGFMLETLHRFVDRRVPIYGMNRGSVGFLMNVYRE--HGLIERLSKAEEVI 92

Query: 119 DERMMLDTVIVRDGKIIAEDIVLNDVVISRGAISRILHLKTYINDAF-MDLYPGDGLIIS 177
              + +        ++  E + +N+V + R    +   L+  I+    MD    DG+++S
Sbjct: 93  LHPLRMKARTASGEEV--EALAINEVSLLRET-RQAAKLRIRIDGKIRMDELICDGILLS 149

Query: 178 TPTGSTAYSLSAGGPLVEPDVDLIICTPI 206
           TP GSTAY+LSA GP++     +   TPI
Sbjct: 150 TPAGSTAYNLSAHGPIIPLGAGIAALTPI 178


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: 173
Number of extensions: 5
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: 255
Length adjustment: 25
Effective length of query: 264
Effective length of database: 230
Effective search space:    60720
Effective search space used:    60720
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