GapMind for Amino acid biosynthesis

 

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

Align Predicted asd-S-ferredoxin by GapMind curators (no experimental data)
to candidate WP_011989405.1 CKL_RS04110 2Fe-2S iron-sulfur cluster-binding protein

Query= predicted:A6UQ02
         (132 letters)



>NCBI__GCF_000016505.1:WP_011989405.1
          Length = 253

 Score = 43.5 bits (101), Expect = 2e-09
 Identities = 26/59 (44%), Positives = 32/59 (54%), Gaps = 9/59 (15%)

Query: 82  CIDCGSCVVHCP---VGALSVDSD--YKILLDEDE----CIGCKNCAKVCPVNAIKVFE 131
           C  CG CV  C    VG LS+ +   YK L   D+    CIGC +CA VCP NAI + +
Sbjct: 129 CALCGLCVKACKAVGVGVLSLVNKGIYKKLDTSDKSTQKCIGCGSCANVCPTNAIDIID 187



 Score = 29.3 bits (64), Expect = 4e-05
 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 77  KDDNLCIDCGSCVVHCPVGALSV---DSDYKILLDEDECIGCKNCAK 120
           K    CI CGSC   CP  A+ +   D   +I  ++ + + C  C +
Sbjct: 163 KSTQKCIGCGSCANVCPTNAIDIIDKDGKREIWGNKFKMVKCDCCGE 209


Lambda     K      H
   0.321    0.140    0.421 

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: 101
Number of extensions: 6
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: 132
Length of database: 253
Length adjustment: 19
Effective length of query: 113
Effective length of database: 234
Effective search space:    26442
Effective search space used:    26442
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: 44 (21.6 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