GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Brucella inopinata BO1

Align BadH (characterized)
to candidate WP_008505361.1 BIBO1_RS08590 glucose 1-dehydrogenase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_000182725.1:WP_008505361.1
          Length = 246

 Score =  162 bits (409), Expect = 8e-45
 Identities = 92/250 (36%), Positives = 134/250 (53%), Gaps = 7/250 (2%)

Query: 3   RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           R ++K  ++TGG  GIG AT R F +EGAK+ + D + D  +++A  +  A   A  ++ 
Sbjct: 2   RFKDKVVIVTGGASGIGEATARAFIREGAKVVIADFS-DHGQQLADELAGAHEQALFIKT 60

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122
           D+AD  +V A I  T    G +DI+  NAG     P  + +   W++ I INLTG     
Sbjct: 61  DVADTKAVQALIVRTVENYGRLDIMFANAGIAADAPIDELDEAAWQKTIDINLTGVYLCD 120

Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182
              +  M  +  G IVN  S  + VG SG   YAA KGG+   ++TLA ++    I VN 
Sbjct: 121 KYAIDQMRSQGGGVIVNCGSIHSHVGKSGVTAYAAAKGGVKLLTQTLAIDYGPQNIRVNA 180

Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242
           VCPG  DT LL ++      P+   +A     P+GRLG+ +++A A+ F  SD+A F+ G
Sbjct: 181 VCPGYIDTPLLKNI------PDDKKQALVALHPMGRLGRAEEVANAVLFLASDEASFVNG 234

Query: 243 QVLSVSGGLT 252
             L V GG T
Sbjct: 235 ASLLVDGGYT 244


Lambda     K      H
   0.318    0.135    0.398 

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: 159
Number of extensions: 11
Number of successful extensions: 3
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: 255
Length of database: 246
Length adjustment: 24
Effective length of query: 231
Effective length of database: 222
Effective search space:    51282
Effective search space used:    51282
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.

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