GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PCBD in Magnetospirillum magneticum AMB-1

Align Pterin-4-alpha-carbinolamine dehydratase 2; PHS 2; 4-alpha-hydroxy-tetrahydropterin dehydratase 2; DcoH-like protein DCoHm; Dimerization cofactor of hepatocyte nuclear factor 1 from muscle; HNF-1-alpha dimerization cofactor; EC 4.2.1.96 (characterized)
to candidate WP_011383005.1 AMB_RS02910 4a-hydroxytetrahydrobiopterin dehydratase

Query= SwissProt::Q9CZL5
         (136 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383005.1 AMB_RS02910
           4a-hydroxytetrahydrobiopterin dehydratase
          Length = 132

 Score =  111 bits (277), Expect = 4e-30
 Identities = 53/116 (45%), Positives = 79/116 (68%), Gaps = 5/116 (4%)

Query: 22  AALRSPGASRAAMSSDAQW---LTAEERDQLIPGLKAAGWSELSERDAIYKEFSFKNFNQ 78
           A  R P +  +    D +    L+  ER   + GL  AGW+E+  RDAI +   F +F++
Sbjct: 14  AGTRGPHSFDSTRQGDGKMIARLSGSERTSALAGL--AGWTEVEGRDAISRSLRFADFSE 71

Query: 79  AFGFMSRVALQAEKMNHHPEWFNVYNKVQITLTSHDCGGLTKRDVKLAQFIEKAAA 134
           AF FM+R+A+ AE+MNHHPEWFNV+N+V ITL++HD GG+T++D+ LA+ I+ AA+
Sbjct: 72  AFAFMTRIAMAAERMNHHPEWFNVWNRVDITLSTHDVGGVTQKDISLARAIDAAAS 127


Lambda     K      H
   0.318    0.127    0.375 

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: 52
Number of extensions: 1
Number of successful extensions: 1
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: 136
Length of database: 132
Length adjustment: 15
Effective length of query: 121
Effective length of database: 117
Effective search space:    14157
Effective search space used:    14157
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: 42 (20.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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