GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Dinoroseobacter shibae DFL-12

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= BRENDA::Q18AQ1
         (378 letters)



>FitnessBrowser__Dino:3607424
          Length = 382

 Score =  253 bits (645), Expect = 8e-72
 Identities = 150/373 (40%), Positives = 216/373 (57%), Gaps = 3/373 (0%)

Query: 7   KYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTV 66
           +++ML E+  +F   E  P      ++     E  ++  + G++    P+ YGG GGD  
Sbjct: 10  EHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGGDFG 69

Query: 67  GYIMAVEELSRV-CGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLT 125
                + E++R      G     H+ + +  I  YG+EEQKQK+L  + SGE +GA  +T
Sbjct: 70  HEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVSGEMVGALAMT 129

Query: 126 EPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIV 185
           EP AG+D  G +T AV DG+ Y L+GSKIFITN    ++ VV A TD S G KG+S  ++
Sbjct: 130 EPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVSLVVL 189

Query: 186 E-KGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKE-GQGFKIAMSTLDGGRI 243
           E +G  GFS G    K+G+  S TSEL F++  IP ENLLG E G+GF   M+ L   R+
Sbjct: 190 ETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLPQERL 249

Query: 244 GIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAI 303
            IAA A+G  +GA++ TV Y KER  FG P+ +FQNT+F+LA+ + K   AR  + +   
Sbjct: 250 IIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLNECMA 309

Query: 304 NKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEG 363
               GK    +AAMAK +  +T  EV  + VQLHGGYGY  +Y + +M  DA++  IY G
Sbjct: 310 EHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDARVQRIYGG 369

Query: 364 TSEVQRMVISGKL 376
           T+E+ + +I   L
Sbjct: 370 TNEIMKELIGRAL 382


Lambda     K      H
   0.315    0.133    0.373 

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: 364
Number of extensions: 18
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: 378
Length of database: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
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: 42 (22.0 bits)
S2: 50 (23.9 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