GapMind for catabolism of small carbon sources

 

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

Align phenylacetyl-CoA 1,2-epoxidase (EC 1.14.13.149) (characterized)
to candidate WP_058857309.1 AS188_RS01200 phenylacetate-CoA oxygenase subunit PaaC

Query= BRENDA::P76079
         (248 letters)



>NCBI__GCF_001482365.1:WP_058857309.1
          Length = 275

 Score =  200 bits (509), Expect = 2e-56
 Identities = 115/242 (47%), Positives = 150/242 (61%), Gaps = 3/242 (1%)

Query: 7   YTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDED 66
           Y L LGD+ L+L+QRLG W   APELE D+ALANI LDLLG AR FL+YA    G+  ED
Sbjct: 37  YALWLGDDALMLAQRLGWWIARAPELEEDIALANIALDLLGHARFFLTYAGTAWGK-TED 95

Query: 67  TLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKA 126
            LA+ RDE +F +  LVEQ NG+F  TIARQ     +   L+ RL++S D  LAAI+ KA
Sbjct: 96  DLAYFRDEEEFRSCRLVEQENGDFGQTIARQLIFSYYQYELYRRLVDSSDATLAAIADKA 155

Query: 127 IKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAV 186
           +KE +YH   +  W+ RLG GT+ S +++Q  ++ +W +  ELF  DE+  AL  EGIAV
Sbjct: 156 LKEVQYHQDHASQWILRLGLGTEESKRRVQDGLDYMWPYVDELFHDDELIDAL--EGIAV 213

Query: 187 DPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQRVLPGQ 246
            P TLRA ++  +   + EA L VP       G + G  +E  G +LAEMQ L R  PG 
Sbjct: 214 RPSTLRADFDRRIAEILGEAGLEVPGIPGAWGGDRSGEFSEQRGHILAEMQVLARQHPGA 273

Query: 247 QW 248
            W
Sbjct: 274 TW 275


Lambda     K      H
   0.320    0.135    0.405 

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: 218
Number of extensions: 8
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: 248
Length of database: 275
Length adjustment: 25
Effective length of query: 223
Effective length of database: 250
Effective search space:    55750
Effective search space used:    55750
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 (21.8 bits)
S2: 47 (22.7 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