GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Erythrobacter marinus HWDM-33

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_047093223.1 AAV99_RS06380 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001013305.1:WP_047093223.1
          Length = 394

 Score =  226 bits (577), Expect = 7e-64
 Identities = 134/385 (34%), Positives = 207/385 (53%), Gaps = 2/385 (0%)

Query: 46  SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105
           +D ++ +D L+ EE+ +R       + E+ P + E + K      + P +GA G+ G +I
Sbjct: 10  ADPFNLDDQLSEEERMVRDAAHGFAQGELQPRVIEAYSKEIDAPELFPLMGAAGLLGVTI 69

Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164
            + YG  G +  A  +   EI RVD+   +   V SSL M  I   GS+ Q+ +YLP LA
Sbjct: 70  PEEYGGAGANYVAYGLVAREIERVDSGYRSMASVQSSLVMHPIHAYGSDEQRARYLPGLA 129

Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT 224
               + C+ LTEPD GSD SG+ T A K   G+ ++G K WI NS FAD+ +++A++   
Sbjct: 130 SGQLIGCFGLTEPDAGSDPSGMRTYAKKDGDGYSLSGAKTWISNSPFADVFVVWAKSEAH 189

Query: 225 -NQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283
            +++ GFI++K   GL A KI  K+ LR    G I +  V +P +  LP V   +     
Sbjct: 190 GDKVRGFILEKGMEGLAAPKIGGKLSLRASTTGMIQMDEVKLPADALLPNVEGMKGPFGC 249

Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343
           L  +R  ++W  IG +   Y    +Y  +R QFG PLA+ QL Q KL  M   +      
Sbjct: 250 LNRARYGISWGSIGAAEFCYSAARQYGLDRHQFGVPLASKQLYQLKLADMATEIALGLQA 309

Query: 344 GWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEP 403
             R+ +L + G+  P   S+ K     KA + A   R++ GGNGI  ++ V +   +LE 
Sbjct: 310 SLRVGRLLDEGRYAPEMISVVKRNNVGKALDVARTARDMHGGNGISEEYQVMRHMANLET 369

Query: 404 IYTYEGTYDINTLVTGREVTGIASF 428
           + TYEGT+D++ L+ GR +TGI++F
Sbjct: 370 VNTYEGTHDVHALILGRAITGISAF 394


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: 348
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: 394
Length adjustment: 31
Effective length of query: 405
Effective length of database: 363
Effective search space:   147015
Effective search space used:   147015
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 24 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