GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd-S-ferredoxin in Trichormus variabilis ATCC 29413

Align Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component) (characterized)
to candidate WP_011317224.1 AVA_RS01700 NIL domain-containing protein

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



>NCBI__GCF_000204075.1:WP_011317224.1
          Length = 134

 Score =  102 bits (255), Expect = 2e-27
 Identities = 46/133 (34%), Positives = 73/133 (54%)

Query: 10  RKNIHLTFPPEISGKPIVSDLVRRYDLTVNILKAQITPRKEGYLTLEISGGEDNCLKGIA 69
           +K + LTFP      P+   L + +++  NI++AQ+ P + G L +E+SG  D     I 
Sbjct: 2   KKRVTLTFPKRAIQMPVTYVLAKEFNVAANIIRAQVAPNQIGKLVVELSGDIDQLDAAIE 61

Query: 70  YLREQDVTVTDVSQRISRDEDSCMHCGMCTAICPTSALAMDIEARVVVFDKDRCTACGLC 129
           ++R + + V+     I  DED C+HCG+CT +CPT AL +  E   + F + RC  C  C
Sbjct: 62  WMRSRHINVSLTLGEIVVDEDICVHCGLCTGVCPTEALTLHPETYKLTFTRSRCIVCEQC 121

Query: 130 TRVCPVGAMNVEV 142
              CPV A++  +
Sbjct: 122 IPTCPVQAISTNL 134


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: 71
Number of extensions: 2
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 147
Length of database: 134
Length adjustment: 15
Effective length of query: 132
Effective length of database: 119
Effective search space:    15708
Effective search space used:    15708
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: 42 (20.8 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