GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd-S-ferredoxin in Clostridium kluyveri DSM 555

Align Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component) (characterized)
to candidate WP_011988737.1 CKL_RS00685 [Fe-Fe] hydrogenase large subunit C-terminal domain-containing protein

Query= reanno::Miya:8499492
         (147 letters)



>NCBI__GCF_000016505.1:WP_011988737.1
          Length = 447

 Score = 42.4 bits (98), Expect = 9e-09
 Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 78  VTDVSQRISRDEDSCMHCGMCTAICPTSALAMDIEARVVVFDKDRCTACGLCTRVCPVGA 137
           VT+ SQ   RD D  +    C   CP  A+ +  E      DKD+CT CG C   CP G+
Sbjct: 78  VTNCSQEC-RDGDKTL----CEKSCPFDAIFIHKEKNHPFIDKDKCTDCGFCVDACPNGS 132

Query: 138 M 138
           +
Sbjct: 133 I 133


Lambda     K      H
   0.321    0.137    0.414 

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: 170
Number of extensions: 12
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: 147
Length of database: 447
Length adjustment: 24
Effective length of query: 123
Effective length of database: 423
Effective search space:    52029
Effective search space used:    52029
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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