GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Methylibium petroleiphilum PM1

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000015725.1:WP_041929725.1
          Length = 391

 Score =  234 bits (597), Expect = 4e-66
 Identities = 132/375 (35%), Positives = 211/375 (56%), Gaps = 2/375 (0%)

Query: 55  LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113
           L+ +E+A+R   +      +AP + E +   +    I  ++G +G+ G ++ + YG  GL
Sbjct: 17  LSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76

Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173
           +     +   E+ RVD+   + + V SSL M+ I   G+EAQK+KYLP LA+   + C+ 
Sbjct: 77  NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136

Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVK 233
           LTEP++GSD   L T A  V+GG+ ++G K WI NS  AD+ +++A++    QI GFI+ 
Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKD-DGGQIRGFILD 195

Query: 234 KDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAW 293
           K   GL+A  +  K+GLR    G+I++  VF P+E+  P V   +     L  +R  +AW
Sbjct: 196 KGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEVRGLKGPFTCLNSARYGIAW 255

Query: 294 QPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYET 353
             +G +   +    +Y+ +R QFG PLAA QL Q+KL  M   +        RL ++ + 
Sbjct: 256 GALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGRMKDE 315

Query: 354 GQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDI 413
           G       S+ K     K+ E A + R+++GGNGI  +F VA+   +LE + TYEGT+D+
Sbjct: 316 GTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEGTHDV 375

Query: 414 NTLVTGREVTGIASF 428
           + L+ GR +TGI +F
Sbjct: 376 HALILGRAITGIQAF 390


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: 366
Number of extensions: 20
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 405
Effective length of database: 360
Effective search space:   145800
Effective search space used:   145800
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