GapMind for catabolism of small carbon sources

 

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

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_011383245.1 AMB_RS04100 2-oxo-hepta-3-ene-1,7-dioic acid hydratase

Query= BRENDA::B0VXM8
         (267 letters)



>NCBI__GCF_000009985.1:WP_011383245.1
          Length = 268

 Score =  172 bits (435), Expect = 9e-48
 Identities = 99/255 (38%), Positives = 145/255 (56%), Gaps = 8/255 (3%)

Query: 14  AELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGPKMGLTSQAKM 73
           A  L+ AE+ + +  +I+ + P++   +AY +Q+  ++ K N G +++G K+GLTS+A  
Sbjct: 12  AARLHRAEQTRHQCGQISLDHPEMGMADAYAVQKAWVETKINEGRKVVGHKIGLTSRAMQ 71

Query: 74  AQMKVKEPIYGYLFDYMFVPSGGAIHMSELIHPKVEVEIAFILGEDLEGPHVTSTQVLSA 133
              ++ EP YG L D M    G  I M+  I P VEVE+AFIL + LEGP VT TQVLSA
Sbjct: 72  QSSQIDEPDYGTLLDDMVFGEGTDIPMARFIVPMVEVELAFILKDRLEGPDVTLTQVLSA 131

Query: 134 TKYVAPALEIIDSRYQ--DFTFTLP----DVIADNASSSRVVIGNTMTPIHSLKTDLDLI 187
           T YV PALEIID+R    D     P    D I+DNA+++ +V+G    P+  +  DL  +
Sbjct: 132 TDYVIPALEIIDARCHRLDPETKRPRKVFDTISDNAANAGIVMGG--RPVRPMDVDLRWV 189

Query: 188 GAALYINGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGITEAIQLSA 247
            A +Y NG ++  G  A V NHPA+ ++ LA   A     L+ G ++L G  T  +   A
Sbjct: 190 AAIMYRNGVIEETGVAAGVLNHPAHGISWLARKFAPHSIALEPGQVVLAGSFTRPVPARA 249

Query: 248 GDTVIGQLDQLGDVS 262
           GDT       LG ++
Sbjct: 250 GDTFHVDYGPLGAIA 264


Lambda     K      H
   0.316    0.134    0.364 

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: 172
Number of extensions: 8
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: 267
Length of database: 268
Length adjustment: 25
Effective length of query: 242
Effective length of database: 243
Effective search space:    58806
Effective search space used:    58806
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 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 (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