GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Crocosphaera subtropica ATCC 51142

Align BadH (characterized)
to candidate WP_009546719.1 CCE_RS01045 glucose 1-dehydrogenase

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



>NCBI__GCF_000017845.1:WP_009546719.1
          Length = 265

 Score =  140 bits (354), Expect = 2e-38
 Identities = 91/262 (34%), Positives = 142/262 (54%), Gaps = 13/262 (4%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVF---DLN-LDAA----EKVAGAIRD 52
           M  L  K  ++TG   GIG A   R   EG+ +A+    D+N LD      EK+   + +
Sbjct: 1   MEELTGKNILVTGATSGIGQAIAARLVAEGSNVALNYRNDINKLDDTKKMIEKMTSKMDN 60

Query: 53  AGGTAEAVRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIA 112
            GG    V  D+++   +           G +DILVNNAG  I+ P  + E  +++++I 
Sbjct: 61  KGGQYLPVEGDVSEEKDILRMYDEVIKKWGSLDILVNNAGIQIYDPSEQVETDDFDKVIN 120

Query: 113 INLTGA-LHMHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAR 171
           +NL GA L    A+   +   + G I+N++S    +       YA  KGG+ + ++TLA 
Sbjct: 121 VNLRGAYLCAREAIQHFLNTEKKGIILNVSSVHEIIPRPQYVSYAISKGGIKSMTQTLAL 180

Query: 172 EHARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAF 231
           E+A +GI VN + PG TDT++  D      +P+K  +A  + IPLGR+G P+++A A AF
Sbjct: 181 EYAPYGIRVNAIAPGATDTSINDDWLD---DPQKK-QAMKRRIPLGRVGTPEEMAAAAAF 236

Query: 232 FGSDDAGFITGQVLSVSGGLTM 253
             SD+A +ITGQ L + GG+T+
Sbjct: 237 LMSDEAQYITGQTLFIDGGMTL 258


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: 145
Number of extensions: 7
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: 265
Length adjustment: 24
Effective length of query: 231
Effective length of database: 241
Effective search space:    55671
Effective search space used:    55671
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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