GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Erythrobacter marinus HWDM-33

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_047093910.1 AAV99_RS08330 3-hydroxybutyrate dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_001013305.1:WP_047093910.1
          Length = 251

 Score =  129 bits (324), Expect = 6e-35
 Identities = 86/250 (34%), Positives = 123/250 (49%), Gaps = 7/250 (2%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIA---GVETHLLDVT 64
           L GK  L+T +  GIG A  +  A EGA V+         +E+A I    G      ++ 
Sbjct: 3   LEGKRALVTGSTSGIGLAIAKALAAEGASVVINGFGDA--DEIAGICAEIGATHSGANLM 60

Query: 65  DDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGM 124
           D   I+ ++A+ G +D+L N AG      + E   + W     LN  A+FHT R  +P M
Sbjct: 61  DVGEIETMMAEAGPLDILVNNAGMQHVCPVEEFPVEKWHQVIALNLTAVFHTTRLAVPAM 120

Query: 125 LAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTI 184
             K  G I+N ASA S       + AY ASK  V G TK+VA +    G+  N I PG +
Sbjct: 121 REKGWGRIINTASAHSKTAS-PFKSAYNASKHGVDGFTKTVALELAETGVTANCISPGYV 179

Query: 185 ESPSLNQRISTQAKETGKSEDEV-RAAFVARQPMGRIGKAEEVAALALYLASDESNFTTG 243
            +P +  +I    K  G +E++V     +A+QP  +  + EEV ALA +L   E    TG
Sbjct: 180 WTPLIEGQIPDTMKARGLTEEQVINDVLLAKQPTKKFVQVEEVGALATFLCRTEMGNVTG 239

Query: 244 SIHMIDGGWS 253
           +   IDGGW+
Sbjct: 240 ANWSIDGGWT 249


Lambda     K      H
   0.316    0.129    0.359 

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: 137
Number of extensions: 9
Number of successful extensions: 4
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: 254
Length of database: 251
Length adjustment: 24
Effective length of query: 230
Effective length of database: 227
Effective search space:    52210
Effective search space used:    52210
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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