GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Caulobacter crescentus NA1000

Align SDR family oxidoreductase (characterized, see rationale)
to candidate CCNA_03495 CCNA_03495 D-beta-hydroxybutyrate dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__Caulo:CCNA_03495
          Length = 265

 Score =  141 bits (355), Expect = 2e-38
 Identities = 84/257 (32%), Positives = 131/257 (50%), Gaps = 13/257 (5%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTDD- 66
           L G+  ++T +  GIG A  +  A +G  ++   + + +  E A     ETH ++V    
Sbjct: 7   LQGQVAIVTGSTSGIGHAMADALAAQGCNIVMNGLGEMNAIERARAEMAETHGVEVLYHG 66

Query: 67  ----------DAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHT 116
                     D ++A  A+ G +D+L N AG      + +  +  WD    +N  + FH 
Sbjct: 67  ADMTRPIEIADMVRAAKAEFGELDILVNNAGVQHVAPVEDFPEDKWDLIIAVNLSSAFHA 126

Query: 117 IRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRC 176
            +A +P M  +  G IVNIASA   V     + AY A+K  ++GLTK+VA +    GI C
Sbjct: 127 TKAAVPIMKEQGRGRIVNIASAHGLVASPF-KSAYVAAKHGIMGLTKTVALEVAQHGITC 185

Query: 177 NAICPGTIESPSLNQRISTQAKETGKSEDEV-RAAFVARQPMGRIGKAEEVAALALYLAS 235
           NAICPG +++P +  +I+ QAK  G SE+ V R   +A QP  +    +++  + LYL S
Sbjct: 186 NAICPGFVKTPLVEAQIADQAKARGISEEAVMRDVILASQPTKQFVTFDQLNGMLLYLVS 245

Query: 236 DESNFTTGSIHMIDGGW 252
           D      G+ + IDGGW
Sbjct: 246 DLGASANGAAYQIDGGW 262


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: 119
Number of extensions: 7
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: 265
Length adjustment: 24
Effective length of query: 230
Effective length of database: 241
Effective search space:    55430
Effective search space used:    55430
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 Sep 17 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