GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pco in Pseudomonas simiae WCS417

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF2715 PS417_13850 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>lcl|FitnessBrowser__WCS417:GFF2715 PS417_13850 acyl-CoA
           dehydrogenase
          Length = 375

 Score =  158 bits (400), Expect = 2e-43
 Identities = 111/375 (29%), Positives = 182/375 (48%), Gaps = 6/375 (1%)

Query: 54  LLTPEEQA-IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCP 111
           +L  EEQ  I    R+  ++ + P   E+  +  FP     ++  +G  G  + + +G  
Sbjct: 1   MLPNEEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60

Query: 112 GLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVAC 171
                A A+A  EIA  D +CST + VH+S+G + +   G++ QKE++L  LA    +  
Sbjct: 61  DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGA 120

Query: 172 WALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQIN 228
           +ALTEP  GSDAS L T A      + +NG K++I +   A ++I+FA          I+
Sbjct: 121 FALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGIS 180

Query: 229 GFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVS 287
            FIV  D+PG    ++ +K+G        IL ++V VP  +RL      ++     L   
Sbjct: 181 AFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGG 240

Query: 288 RVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRL 347
           RV +A Q +G++   ++    Y +ER+ FG P+   Q    +L  M   +     M    
Sbjct: 241 RVGIASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300

Query: 348 CKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTY 407
             L ++G+    +AS+ K + S  A +  S   + LGG G L+DF + + + D+     Y
Sbjct: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIY 360

Query: 408 EGTYDINTLVTGREV 422
           EGT DI  +V  R +
Sbjct: 361 EGTSDIQRMVISRNL 375


Lambda     K      H
   0.319    0.133    0.399 

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: 314
Number of extensions: 15
Number of successful extensions: 3
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: 436
Length of database: 375
Length adjustment: 31
Effective length of query: 405
Effective length of database: 344
Effective search space:   139320
Effective search space used:   139320
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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