Alignments for a candidate for pco in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for pco in Williamsia sterculiae CPCC 203464

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_076476002.1 BW971_RS02040 acyl-CoA oxidase

Query= BRENDA::Q33DR0
         (703 letters)



>NCBI__GCF_900156495.1:WP_076476002.1
          Length = 710

 Score =  495 bits (1275), Expect = e-144
 Identities = 280/664 (42%), Positives = 384/664 (57%), Gaps = 18/664 (2%)

Query: 5   VDRASSPASPGSTTAAADGAKVAVEPRVDVAALGEQLLGRWADIRLHARDLAGREVVQKV 64
           VD +  P +     A +   + + + R  V  L   L GRW D+R +AR+      +   
Sbjct: 28  VDNSDVPHAGNPEGAPSVPTQESADVRQLVDNLRRTLDGRWHDLREYAREKMDDPELLPD 87

Query: 65  EGLTHTEHRSRVFGQLKYLVDNNAVHRAFPSRLGGSDDHGGNIAGFEELVTADPSLQIKA 124
             LT  + R R F  LK L D +     F    GG+ D G  I G E L  AD SL +KA
Sbjct: 88  PSLTLEQTRERTFDHLKRLADLDFAAAGFRPEHGGTGDVGAAITGIEMLGYADLSLMVKA 147

Query: 125 GVQWGLFGSAVMHLGTREHHDKWLPGIMSLEIPGCFAMTETGHGSDVASIATTATYDEET 184
           GVQWGLFG A+ +LGT+ HHD+++  +++L++ G FAMTE GHGS+V ++ T ATYD +T
Sbjct: 148 GVQWGLFGGAIENLGTQRHHDRYVKDLINLDLLGSFAMTEIGHGSNVQALETVATYDPQT 207

Query: 185 QEFVIDTPFRAAWKDYIGNAANDGLAAVVFAQLIT-----RKVNHGVHAFYVDLRDPATG 239
           +EFV+ +    A K+YIG A      A VFAQL+T          GVH F V +RD +  
Sbjct: 208 EEFVVHSTTPDASKEYIGGAGQTATIAAVFAQLVTGGPDEEPTGRGVHCFVVPIRDESGA 267

Query: 240 DFLPGIGGEDDGIKGGLNGIDNGRLHFTNVRIPRTNLLNRYGDVAVDGTYSSTIESPGRR 299
           D LPGI   DDG KGGL G+DNG + F  VRIPR NLLN+Y DV  DGTY+S IE+  RR
Sbjct: 268 D-LPGITTHDDGYKGGLKGVDNGGITFDEVRIPRENLLNKYADVDADGTYTSPIENENRR 326

Query: 300 FFTMLGTLVQGRVSLDGAAVAASKVALQSAIHYAAERRQFNATSPTEEEVLLDYQRHQRR 359
           FFTMLGTL++GR S+   A AA + AL  A  Y   R+QF A     E  ++DY  HQRR
Sbjct: 327 FFTMLGTLIRGRTSVAATAGAAGRKALAIATRYGLSRKQFEAPDADHEIAIMDYLAHQRR 386

Query: 360 LFTRLATTYAASFAHEQLLQKFDDVFSGAH---DTDAD--------RQDLETLAAALKPL 408
           L   +AT+YA +FA  ++  +  +V  G     DT +D        +++LE L A LK +
Sbjct: 387 LLPLIATSYALAFAQNEVTNELHEVQGGPEQNPDTASDGDDSRAGRQRELEALVAGLKAM 446

Query: 409 STWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKRLLADYA 468
           +TWHA  T+  CREACGGAG+L  N+ + +R D+DV+ TFEGDNTVL QL+AK LL+ YA
Sbjct: 447 TTWHASHTINTCREACGGAGYLAANQLSIMRGDIDVFTTFEGDNTVLTQLLAKELLSAYA 506

Query: 469 KEFRGANFGVLARYVVDQAAGVALHRTGLRQVAQFVADSGSVQKSALALRDEEGQRTLLT 528
           ++ RG +    AR++ D A  V L ++  RQV Q + DS         L +   Q  LL 
Sbjct: 507 QDVRGLSTVGWARFIADMARDVFLEKSAARQVVQTLMDSSDEDTEKSELSNRGTQIRLLR 566

Query: 529 DRVQSMVAEVGAALKGAGKLPQHQAAALFNQHQNELIEAAQAHAELLQWEAFTEALAKVD 588
           +R   +V      L+ A + P   A  +FN  Q+ L++  QAH E +  E+F EA+   D
Sbjct: 567 NREDHLVRTCAQRLRRATE-PDADAFEVFNSAQDHLLKVGQAHVERVVLESFVEAIDNCD 625

Query: 589 DAGTKEVLTRLRDLFGLSLIEKHLSWYLMNGRLSMQRGRTVGTYINRLLVKIRPHALDLV 648
                E+L ++ DLF  SL+E+ L W+LM+  +S++R + +   +N L   +RPHA  LV
Sbjct: 626 SRAASELLGKVCDLFVYSLLEQDLDWFLMHRHVSVERAKAIRRGVNDLCADLRPHARTLV 685

Query: 649 DAFG 652
           DAFG
Sbjct: 686 DAFG 689


Lambda     K      H
   0.319    0.134    0.387 

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: 1132
Number of extensions: 42
Number of successful extensions: 6
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: 703
Length of database: 710
Length adjustment: 39
Effective length of query: 664
Effective length of database: 671
Effective search space:   445544
Effective search space used:   445544
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources