GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaC in Klebsiella michiganensis M5al

Align phenylacetyl-CoA 1,2-epoxidase (EC 1.14.13.149) (characterized)
to candidate BWI76_RS13100 BWI76_RS13100 phenylacetate-CoA oxygenase subunit PaaI

Query= BRENDA::P76079
         (248 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS13100 BWI76_RS13100
           phenylacetate-CoA oxygenase subunit PaaI
          Length = 251

 Score =  384 bits (987), Expect = e-112
 Identities = 184/247 (74%), Positives = 212/247 (85%)

Query: 2   NQLTAYTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAG 61
           N + AY LRLGDN LVL+QRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAG
Sbjct: 5   NPVAAYALRLGDNGLVLAQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAG 64

Query: 62  EGDEDTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAA 121
            GDEDTLAF R+ERQF NLLL EQPNGNFADT+ARQ+FID WHVAL+ RL+ SRD QLAA
Sbjct: 65  SGDEDTLAFGRNERQFCNLLLAEQPNGNFADTLARQFFIDVWHVALYGRLVSSRDTQLAA 124

Query: 122 ISAKAIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSE 181
           I+AKA+KE RYH RFSRGWLERLGNGT +S Q+MQ A++ LWRFT ELF AD ++I LS 
Sbjct: 125 IAAKALKEVRYHQRFSRGWLERLGNGTALSAQRMQDAVDNLWRFTGELFQADALEIELSA 184

Query: 182 EGIAVDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQR 241
           +GIAVDPR L+A W+A V A +++A L +P+E  +R GGK+GLH+EHLGP+LAEMQYLQR
Sbjct: 185 QGIAVDPRELQAEWQATVRAALSDAGLQIPEEAPFRHGGKQGLHSEHLGPLLAEMQYLQR 244

Query: 242 VLPGQQW 248
             PGQ+W
Sbjct: 245 AYPGQRW 251


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: 271
Number of extensions: 7
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: 248
Length of database: 251
Length adjustment: 24
Effective length of query: 224
Effective length of database: 227
Effective search space:    50848
Effective search space used:    50848
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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