GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Shewanella sp. ANA-3

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate 7025403 Shewana3_2558 3-oxoacyl-[acyl-carrier-protein] reductase (RefSeq)

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__ANA3:7025403
          Length = 248

 Score =  111 bits (277), Expect = 3e-29
 Identities = 67/190 (35%), Positives = 94/190 (49%), Gaps = 9/190 (4%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           L+   KV +VTGA  GIG+  A    + GA VV         G  +S K A  + E +  
Sbjct: 5   LSLAGKVALVTGASRGIGRAIAETLVEAGAIVV---------GTATSEKGAAAIQEYLGD 55

Query: 63  AGGTAVANYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYRVHA 122
            G   V N    +    +  +  +  G VDIL+NNAGI RD    +M D +W+ +   + 
Sbjct: 56  KGFGLVLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNL 115

Query: 123 KGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQEGKS 182
              ++LS+     M +K FGRII   S  G  GN GQ NY + K  L+G + +LA+E  S
Sbjct: 116 TSLFRLSKPVMRTMMKKRFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVAS 175

Query: 183 KNIHCNTIAP 192
           + I  N IAP
Sbjct: 176 RQITVNAIAP 185


Lambda     K      H
   0.313    0.131    0.371 

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: 222
Number of extensions: 6
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: 441
Length of database: 248
Length adjustment: 28
Effective length of query: 413
Effective length of database: 220
Effective search space:    90860
Effective search space used:    90860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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