GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Chryseobacterium arthrosphaerae CC-VM-7

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065397571.1 BBI00_RS04080 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001684965.1:WP_065397571.1
          Length = 392

 Score =  220 bits (560), Expect = 7e-62
 Identities = 134/392 (34%), Positives = 211/392 (53%), Gaps = 4/392 (1%)

Query: 40  TFPPCTS--DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGA 97
           ++ P TS  DYY  + LLT E + IR+ VR+ +E  V P + +  +       +  +LG 
Sbjct: 2   SYYPLTSIPDYYGIDALLTEEHKLIRQSVRDWVESFVMPQIDQAAQNHTDLPGLMRELGK 61

Query: 98  MGVAGGSIK-GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQK 156
           +G  G  I   YG  GL   +  +   E+ R D++  +   V SSL M  I   GSE QK
Sbjct: 62  IGALGPYIPVEYGGSGLDQISYGLIMQELERGDSAVRSAASVQSSLVMFPINEFGSEEQK 121

Query: 157 EKYLPSLAQLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLI 216
           +KYLP LA    +  + LTEP++GSD   + T    +   + +NG K WI NS   D+ +
Sbjct: 122 KKYLPKLAAGEMIGSFGLTEPNHGSDPGSMETYFKDMGDHYLLNGAKMWITNSPLCDIAV 181

Query: 217 IFARNTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNS 276
           ++A+N    ++ G IV++   G    +  NK  LR  + G+++  +V VP E+ LPGV  
Sbjct: 182 VWAKNEE-GKVQGLIVERGMEGFTTPETHNKWSLRASKTGELVFNDVKVPKENLLPGVTG 240

Query: 277 FQDTSKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGN 336
            +     L  +R  ++W  IG ++  Y    +Y KERKQFG P+ ++QL Q+KL + L  
Sbjct: 241 LKGPLSCLNSARYGISWGVIGAAIDCYCTAVQYSKERKQFGKPIGSYQLQQKKLAEFLTE 300

Query: 337 VQAMFLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAK 396
           +    L+  +L  L    + TP Q S+ K      A + A   R++LGG GI+ +F + +
Sbjct: 301 ITKAQLLCLQLGNLKNDHKATPAQISMAKRNNVKMAIDIARESRQILGGMGIMGEFPMMR 360

Query: 397 AFCDLEPIYTYEGTYDINTLVTGREVTGIASF 428
              +LE + TYEGT+D++ L+TG ++TGI +F
Sbjct: 361 HAANLESVITYEGTHDVHLLITGLDITGINAF 392


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: 381
Number of extensions: 10
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: 392
Length adjustment: 31
Effective length of query: 405
Effective length of database: 361
Effective search space:   146205
Effective search space used:   146205
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