GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Pseudomonas simiae WCS417

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF2918 PS417_14930 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__WCS417:GFF2918
          Length = 387

 Score =  152 bits (384), Expect = 2e-41
 Identities = 115/362 (31%), Positives = 177/362 (48%), Gaps = 23/362 (6%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           M+ N ++E  A R+ VR    +   A  R+  I+      E  V   + L   GW     
Sbjct: 1   MNPNDNEELNAIREGVRALCAEFDAAYWRR--IDEEKGFPEAFV---KALTDAGWLSAMI 55

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P+ YGG+G    +  +  EE+           G       +   GSE QK+ +LP++A+ 
Sbjct: 56  PEAYGGSGLGLAEASVILEEVNRCGGNSGTVHGQMYNMFTLLRHGSEAQKRLYLPKLASG 115

Query: 121 D-DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAA 179
           +      G +EP +G+D   +KT A K+GDK++INGQK W +  QH+D +  L RT P A
Sbjct: 116 ELRLQSMGVTEPSTGTDTTKIKTTAIKRGDKYVINGQKVWISRVQHSDLMILLARTTPLA 175

Query: 180 ---KKQEGISFILVDMKT---KGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKG 233
              KK EG+S  LVD++     G+TV+PI  +   HE NE+FFD++E+PL++L+G+E KG
Sbjct: 176 EVKKKSEGMSIFLVDLREAIGNGLTVQPIANM-VNHETNELFFDNLELPLDSLIGEEGKG 234

Query: 234 WDYAKFLLGNERTGIAR--VGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIE 291
           + Y    L  ERT IA   +G  +  I +    A      G+P+ ++   +  +A   IE
Sbjct: 235 FKYILDGLNAERTLIAAECIGDGRWFIEKASAYARDRVVFGRPIGQNQGVQFPIAEAHIE 294

Query: 292 LKALELTQLRVVA--DEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIG--PFAAPY 347
           ++A +L + R     D GK      N A    K   ++         ++  G   FA  Y
Sbjct: 295 IEAADLMRWRACEEYDSGKQAGASANMA----KYLAAKASWEAANACLQTHGGFGFACEY 350

Query: 348 DV 349
           DV
Sbjct: 351 DV 352


Lambda     K      H
   0.317    0.135    0.411 

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: 360
Number of extensions: 20
Number of successful extensions: 5
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: 396
Length of database: 387
Length adjustment: 31
Effective length of query: 365
Effective length of database: 356
Effective search space:   129940
Effective search space used:   129940
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 (21.6 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