GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Pontibacillus litoralis JSM 072002

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000775615.1:WP_036834462.1
          Length = 379

 Score =  182 bits (462), Expect = 2e-50
 Identities = 123/372 (33%), Positives = 187/372 (50%), Gaps = 5/372 (1%)

Query: 56  TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLS 114
           T E+  +RK VR+   KEVAPI+ +  ++  FP  +  ++G +G+ G  I + YG  G+ 
Sbjct: 6   TEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFPIELIKQMGDIGLMGIPIPEQYGGSGMD 65

Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174
             +  IA  E+++V AS    + VH+S+G   I   G+E QK+KY+P LA    +  +AL
Sbjct: 66  FPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEFLGAFAL 125

Query: 175 TEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGFI 231
           TEP  GSDA  L   A +    + +NG K +I N   AD  I+FAR   N     +  FI
Sbjct: 126 TEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNKGVTAFI 185

Query: 232 VKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRVM 290
           V+++  G +  K  +K+G+       +   N  +P E RL      F+     L V R+ 
Sbjct: 186 VERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANLNVGRIG 245

Query: 291 VAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKL 350
           +A Q +GI+    +    Y KER+QFG P+A  Q    KL  M  +V+A  L+ +    L
Sbjct: 246 IAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLTYHAANL 305

Query: 351 YETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGT 410
              G     +AS+ K   S  A   A+   ++ GG G   D+ V + F D +    YEGT
Sbjct: 306 RHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVCEIYEGT 365

Query: 411 YDINTLVTGREV 422
            +I  +V G+ V
Sbjct: 366 NEIQRVVIGKHV 377


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: 337
Number of extensions: 15
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: 379
Length adjustment: 31
Effective length of query: 405
Effective length of database: 348
Effective search space:   140940
Effective search space used:   140940
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