GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Marinobacter algicola DG893

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_007155433.1 MDG893_RS18850 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000170835.1:WP_007155433.1
          Length = 389

 Score =  220 bits (560), Expect = 7e-62
 Identities = 131/384 (34%), Positives = 208/384 (54%), Gaps = 5/384 (1%)

Query: 47  DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105
           D   F+  L   E+ +R  +R   ++ + P +TE     +F   I   +G +G+ G ++ 
Sbjct: 8   DLLQFDKQLDETERQVRDSIRSFCDQRLMPGITEANRHEKFDRSIFTDMGELGMLGATLP 67

Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165
           + YG PGL+     +   E+ RVD++  + + V SSL +  I   G EA K++ LP LA 
Sbjct: 68  EEYGGPGLNHVCYGLIAREVERVDSAYRSALSVQSSLVIHPIHAFGQEALKKRILPQLAS 127

Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225
              V C+ LTEP++GSD   + T A KV+GG+ ++G K WI NS  AD+ +++A+     
Sbjct: 128 GEKVGCFGLTEPNHGSDPGNMETRAKKVDGGYLVSGSKTWITNSPIADVCVVWAK--LEG 185

Query: 226 QINGFIVKKD-APGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284
           +I GF+++++ A GL   KI  K  LR  + G I +  VFVPDE++L  V   +     L
Sbjct: 186 KITGFVIEREGAKGLDTPKIEGKFSLRASETGSIFMDEVFVPDENKL-DVEGLKGPFSCL 244

Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344
             +R  ++W  +G +   +     Y  ERKQFG PLAA QL Q+KL  M   +       
Sbjct: 245 NKARFGISWGSLGAAEFCWHAALNYTLERKQFGKPLAANQLIQKKLADMQTEITLGLQGA 304

Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404
            +L ++ + G  +    S+ K     KA + A + R++ GGNGI  ++ V +   +LE +
Sbjct: 305 LQLGRMIDAGNYSTDAISMLKRNNCGKALDIARVARDMHGGNGIADEYHVIRHVMNLEAV 364

Query: 405 YTYEGTYDINTLVTGREVTGIASF 428
            TYEGT+D++ L+ GR  TGI +F
Sbjct: 365 NTYEGTHDVHALILGRGQTGIQAF 388


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: 347
Number of extensions: 14
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: 389
Length adjustment: 31
Effective length of query: 405
Effective length of database: 358
Effective search space:   144990
Effective search space used:   144990
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