GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Algoriphagus aquaeductus T4

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_003253485.1:WP_111393848.1
          Length = 401

 Score =  251 bits (641), Expect = 3e-71
 Identities = 138/384 (35%), Positives = 209/384 (54%), Gaps = 2/384 (0%)

Query: 47  DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIK 106
           D+   +DLLT E++ IR  +R+ ++KE++P + ++ +KA FP+ I  K G +G  G  + 
Sbjct: 19  DFLDLDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLP 78

Query: 107 -GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165
             YGC GL   +  +   EI R D+   +   V  SL M  I   G+E Q+ KYLP LA 
Sbjct: 79  VEYGCGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLAS 138

Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225
              + C+ LTEPD+GS+ SG+ T    +   + +NG K WI NS  AD+ +++A+N    
Sbjct: 139 GELLGCFGLTEPDHGSNPSGMVTNFKDMGDHYLLNGAKMWISNSPKADIAVVWAKNEE-G 197

Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285
           +I G IV++   G    +  NK  LR    G+++  NV VP E+ LPG          L 
Sbjct: 198 RIQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLGAPMMCLD 257

Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345
            +R  +AW  IG +M  Y+   RY  ER QFG P+  FQL Q+KL +ML  +    L+ W
Sbjct: 258 SARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITKAQLLAW 317

Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405
           ++ K+   G+      S+ K      A   A   R++ GG GI  ++ + +   +LE + 
Sbjct: 318 KVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMMNLESVI 377

Query: 406 TYEGTYDINTLVTGREVTGIASFK 429
           TYEGT+DI+ L+ G E+TGI +FK
Sbjct: 378 TYEGTHDIHLLILGNEITGIQAFK 401


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: 375
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: 401
Length adjustment: 32
Effective length of query: 404
Effective length of database: 369
Effective search space:   149076
Effective search space used:   149076
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