GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)

Query= reanno::Phaeo:GFF329
         (391 letters)



>FitnessBrowser__Dino:3609683
          Length = 391

 Score =  714 bits (1842), Expect = 0.0
 Identities = 355/391 (90%), Positives = 372/391 (95%)

Query: 1   MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60
           MTNVVIASAARTAVGSFGG+FA TPAHDLG+AVL+A+V RAGI+K EVSETILGQVLT  
Sbjct: 1   MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVARAGIEKGEVSETILGQVLTGG 60

Query: 61  QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120
           QGQNPARQAHINAGLPQESAAW LNQVCGSGLRAVAL AQHIQLGDA IVCAGGQENMTL
Sbjct: 61  QGQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENMTL 120

Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180
           SPH ANLRAG KMGDM +ID+MIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA
Sbjct: 121 SPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180

Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240
           SQNKAEAAQKAGKF DE+ AFT+KTRKGDI+VD+DEYIRHGAT+EAMQKLRPAF KDGSV
Sbjct: 181 SQNKAEAAQKAGKFDDEVVAFTIKTRKGDIVVDKDEYIRHGATMEAMQKLRPAFTKDGSV 240

Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300
           TAANASGLNDGAA  LLMSA++AEKRGI P+ARIASYATAGLDPSIMGVGPIYASRKALE
Sbjct: 241 TAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVGPIYASRKALE 300

Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360
           KAGW VDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASG RVLNTL
Sbjct: 301 KAGWKVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGARVLNTL 360

Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391
           LFEM+RRDAKKGLATLCIGGGMGVA+CVERP
Sbjct: 361 LFEMQRRDAKKGLATLCIGGGMGVALCVERP 391


Lambda     K      H
   0.316    0.130    0.376 

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: 620
Number of extensions: 12
Number of successful extensions: 1
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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: 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