GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Kocuria flava HO-9041

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_058857968.1 AS188_RS05245 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_001482365.1:WP_058857968.1
          Length = 412

 Score =  286 bits (731), Expect = 1e-81
 Identities = 140/364 (38%), Positives = 226/364 (62%)

Query: 65  KVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLSITANAIATAE 124
           + R  +E+++ P++ E+W++AE+   +  +LG + +    +   G   +S TA  +   E
Sbjct: 48  RARAFVEEDLLPVIGEHWDRAEYSLDLVRRLGELDLLRDGVAVEGFAPMSKTAAGLVCME 107

Query: 125 IARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNGSDAS 184
           ++R D S +T   V   L M +IA+CG+E Q++++LP +A    +  +ALTEP +GSD+ 
Sbjct: 108 LSRGDGSIATVTGVQGGLAMRSIAMCGTEEQRQRWLPRMATGELLGAFALTEPTHGSDSV 167

Query: 185 GLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKKDAPGLKATKI 244
           GL T A+ VEGGW +NG+K+WIGN +   + +++AR+    +++GF+V +++ G   T I
Sbjct: 168 GLETRASPVEGGWLLNGEKKWIGNGSMGGITVVWARSDADGRVHGFVVPQESEGYTGTTI 227

Query: 245 PNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIGISMGIYD 304
           P K+ LR +    I  +NVFVP+E+ LP   SF+DT+ VL  +R+ VAW  +G +   Y+
Sbjct: 228 PGKLALRAIHQAHIRFENVFVPEENVLPAARSFKDTAAVLFATRIGVAWGAVGHAQACYE 287

Query: 305 MCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQMTPGQASLG 364
              +Y  +R QFG PLAA Q+ Q++L +ML  +  + L+  R+ +  E G +T  QASL 
Sbjct: 288 SAVQYAAQRVQFGRPLAASQIVQERLARMLSELTQIQLLVARMTEREEAGTLTAEQASLA 347

Query: 365 KAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTLVTGREVTG 424
           K   +  AR  A+  R+LLGGNGIL    VA+ F D+E ++TYEGT  +  L+ GR +TG
Sbjct: 348 KYTATRAARSIAANARDLLGGNGILVRHRVARHFADVEALHTYEGTETVQALIVGRGITG 407

Query: 425 IASF 428
           I++F
Sbjct: 408 ISAF 411


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: 391
Number of extensions: 11
Number of successful extensions: 1
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: 412
Length adjustment: 32
Effective length of query: 404
Effective length of database: 380
Effective search space:   153520
Effective search space used:   153520
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: 51 (24.3 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