GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-small in Methylocapsa aurea KYG

Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate WP_036260175.1 DL86_RS08520 (2Fe-2S)-binding protein

Query= metacyc::MONOMER-18073
         (163 letters)



>NCBI__GCF_000746085.1:WP_036260175.1
          Length = 152

 Score =  127 bits (320), Expect = 6e-35
 Identities = 62/143 (43%), Positives = 89/143 (62%)

Query: 12  IKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLF 71
           + ++VN   ++    P + LV  LR+ +GL GTK GC    CGAC V L+G++V++C   
Sbjct: 2   LDLRVNDAAHQVDAPPEMPLVWVLRDLIGLRGTKFGCGIGACGACIVHLDGQAVRACITT 61

Query: 72  AVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEE 131
           A +A G  ITTIEGL+     H +Q A+K+  A QCG+C PG +MQA  LL + P P++E
Sbjct: 62  AAEAHGKAITTIEGLAGAHGDHSLQRAWKQVNAPQCGYCQPGQLMQAAALLAQTPKPTDE 121

Query: 132 EVRDGLHGNICRCTGYQNIVKAV 154
           ++   + GNICRC  YQ I  A+
Sbjct: 122 QITSAMAGNICRCGAYQRIKAAI 144


Lambda     K      H
   0.322    0.138    0.409 

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: 87
Number of extensions: 2
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: 163
Length of database: 152
Length adjustment: 17
Effective length of query: 146
Effective length of database: 135
Effective search space:    19710
Effective search space used:    19710
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: 43 (21.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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