GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Brevibacterium jeotgali SJ5-8

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_101588067.1 BJEO58_RS04410 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_900169175.1:WP_101588067.1
          Length = 405

 Score =  209 bits (533), Expect = 1e-58
 Identities = 120/372 (32%), Positives = 198/372 (53%), Gaps = 9/372 (2%)

Query: 66  VRECMEKEVAPIMTEYWEKAEFPFH-ITPKLGAMGVAGGSIKGYGCPGLSITANAIATAE 124
           VR  + + V   + +++     P   +   LG +GV G  ++GY C G + T   +A  E
Sbjct: 32  VRSWLNEHVRDNIGDWYLDGTIPARELAEGLGELGVLGMHLEGYECAGSTATQYGLACRE 91

Query: 125 IARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNGSDAS 184
           +  VD+   + + V  SL M +I   GSE QK+++LP +A    + C+ LTEPD GSD +
Sbjct: 92  LEAVDSGLRSLVSVQGSLAMFSIHHWGSEEQKQEWLPQMAAGRAIGCFGLTEPDVGSDPA 151

Query: 185 GLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQ-------INGFIVKKDAP 237
           G+ T ATK    W +NG K WI NS  +D+++++A+    ++       + GF+V  D P
Sbjct: 152 GMKTRATKDGSDWILNGAKMWITNSPVSDVMVVWAKTDEVDEKTGEKGVVRGFVVPTDTP 211

Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIG 297
           G++  ++  K+ LR    G+I+L NV +P+   LP  +  +     L+ +R  + +   G
Sbjct: 212 GVETPEVQRKLSLRASITGEIVLDNVRLPESAMLPKASGLKGPLSALSEARYGIVFGVTG 271

Query: 298 ISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQ-M 356
            +    +   RY   R QF  PL++FQ++QQKL +  G   A+ L    + +L ++   +
Sbjct: 272 AARDSLEEALRYTDTRIQFDRPLSSFQISQQKLAKAFGEYSAITLTAAHIGRLKDSAAGV 331

Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416
            P Q SLGK      A   A   R L GG+GI +++   +   +LE + TYEGT++++ L
Sbjct: 332 RPEQISLGKMVNVDTAMNIARDLRALFGGSGITSEYSPLRHAINLETVLTYEGTHEVHQL 391

Query: 417 VTGREVTGIASF 428
             GR +TGI +F
Sbjct: 392 TLGRAMTGINAF 403


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: 338
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: 405
Length adjustment: 32
Effective length of query: 404
Effective length of database: 373
Effective search space:   150692
Effective search space used:   150692
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