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_047092433.1 AAV99_RS03120 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001013305.1:WP_047092433.1
          Length = 386

 Score =  163 bits (412), Expect = 1e-44
 Identities = 113/375 (30%), Positives = 180/375 (48%), Gaps = 5/375 (1%)

Query: 55  LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113
           L  E Q IR  V    ++ +AP+  +   +  FP  + P++GA+G+ G ++ +  G  GL
Sbjct: 11  LGEEAQMIRDSVGRFADERIAPLAAKVDAEDWFPIELWPEMGALGLHGMTVSEDDGGTGL 70

Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173
               + IA  E++R  AS       HS+L +  IA  GS  QK KYLP L     V   A
Sbjct: 71  GYLEHTIAIEEVSRASASVGLSYGAHSNLCVNQIARWGSAEQKAKYLPGLISGEHVGSLA 130

Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQINGF 230
           ++E   GSD   +   A  V+GG+ +NG K WI N  +A+ L+++A+   T     I  F
Sbjct: 131 MSETGAGSDVVSMKLKADSVQGGYVLNGTKFWITNGHYAETLVVYAKTDATGGSKGITAF 190

Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRV 289
           +++KD PG    +   K+G++     +++ ++  VPD + L  V    Q     L   RV
Sbjct: 191 LIEKDMPGFSCGQKIEKMGMKGSPTSELVFEDCEVPDANVLGEVGKGVQVLMSGLDYERV 250

Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK 349
           +++   +GI     D    Y++ER QFG  +  FQL Q K+  M   +Q+     + + K
Sbjct: 251 VLSGVQLGIMQACLDTVIPYVRERNQFGKRIGDFQLIQAKVADMYVALQSARAYTYAVAK 310

Query: 350 LYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEG 409
             + GQ T   A+      S  A   A    + LGG G   D+ V +   D + +    G
Sbjct: 311 ACDKGQTTRFDAAGTILLSSENAFRVAGEAIQALGGAGYTTDWPVERYLRDAKLLDIGAG 370

Query: 410 TYDINTLVTGREVTG 424
           T +I  ++ GRE+ G
Sbjct: 371 TNEIRRMLIGRELIG 385


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: 362
Number of extensions: 16
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: 386
Length adjustment: 31
Effective length of query: 405
Effective length of database: 355
Effective search space:   143775
Effective search space used:   143775
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