GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaA in Pseudomonas simiae WCS417

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate GFF3028 PS417_15495 FAD-dependent oxidoreductase

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>FitnessBrowser__WCS417:GFF3028
          Length = 422

 Score =  243 bits (619), Expect = 1e-68
 Identities = 142/420 (33%), Positives = 217/420 (51%), Gaps = 2/420 (0%)

Query: 13  LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72
           LW   +   V   AL    K DV ++G G TGLS A+HL E+G SV VLEA + G G SG
Sbjct: 4   LWSATAPSVVPTPALRESVKVDVAIVGAGYTGLSTALHLAERGVSVCVLEANEPGWGASG 63

Query: 73  RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132
           RN G VN      P+ +    G ++   L   +  +   VF +IE+ GIDC    KG + 
Sbjct: 64  RNGGQVNPTLKYDPEQLVQMFGPERAEPLISTVSSSADLVFKLIEKHGIDCAPVRKGWMQ 123

Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192
           +++   G+A L AR +QW RRG  V+ L  +      G+D  +   LD RAG I P+ Y 
Sbjct: 124 VSYTEKGVAGLHARADQWARRGVPVQRLDASTVASRMGSDAFAGGWLDGRAGAIQPLAYA 183

Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGA-VRAEKVVISTGAYTEGDWSNL 251
           +GL  A    G +I  QS+V  L R+G GW+++TA GA V A++VV++T  Y+   W  +
Sbjct: 184 RGLVGAALAAGVRIHGQSAVTDLRRQGAGWQLQTASGARVMADQVVLATNGYSGNLWPGM 243

Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311
            +       + VA+ PL G  A+++LP  +     + +L   R+D  GRLL+G  G  ++
Sbjct: 244 AQSVLAANSFIVATTPLSGSVAERILPGQETVSTAQRLLLYFRKDSHGRLLMGGRGLFND 303

Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371
             +    +  +R  +  +P+LG +++E  W G I  T D +  + +PAPGL    G NGR
Sbjct: 304 PTSPTDFAHLERSLALLFPQLGPLQFEYRWAGRIAITRDFMPHVHQPAPGLTLALGCNGR 363

Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYHAGQCLRVV 431
           G    T +G+  A  L   +A+    P +P+  +    L+  +  +G + Y     L +V
Sbjct: 364 GIALCTSLGQQLAGKLCDSQAE-FAYPVTPLQRLPMHGLQRFYIGAGVAWYSLLDRLNIV 422


Lambda     K      H
   0.319    0.135    0.419 

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: 457
Number of extensions: 15
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: 432
Length of database: 422
Length adjustment: 32
Effective length of query: 400
Effective length of database: 390
Effective search space:   156000
Effective search space used:   156000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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