GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaE in Pseudomonas fluorescens GW456-L13

Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate PfGW456L13_2423 Phenylacetate-CoA oxygenase/reductase, PaaK subunit

Query= metacyc::MONOMER-15950
         (357 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2423
           Phenylacetate-CoA oxygenase/reductase, PaaK subunit
          Length = 358

 Score =  629 bits (1623), Expect = 0.0
 Identities = 315/358 (87%), Positives = 335/358 (93%), Gaps = 1/358 (0%)

Query: 1   MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60
           MSKFHSLTIK+VR ETRDAVSIAF++P +L DSF FTQGQHLVMRTQLDGEEVRRSYSIC
Sbjct: 1   MSKFHSLTIKDVRAETRDAVSIAFEIPQDLQDSFHFTQGQHLVMRTQLDGEEVRRSYSIC 60

Query: 61  TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120
           TGVNDGELR+A+KRV GGRFSA+ANE LKAG  LEVMPP+GHF VELD ARHGNYLAVAA
Sbjct: 61  TGVNDGELRIAVKRVTGGRFSAFANEQLKAGHTLEVMPPAGHFCVELDPARHGNYLAVAA 120

Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180
           GSGITPILSIIKTTLETEPHSRVTLLYGNRSS+  LFREQLEDLKNRYLQRLNLIF+FSR
Sbjct: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSSGALFREQLEDLKNRYLQRLNLIFVFSR 180

Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240
           EQQDVDLYNGRI+A+KC QLFSRW+D+KALDAAFICGPQ MTETVRD LKA GMA ERIH
Sbjct: 181 EQQDVDLYNGRINAEKCEQLFSRWLDIKALDAAFICGPQEMTETVRDSLKAKGMAPERIH 240

Query: 241 FELFAAAGSAQKREARESAAQ-DSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAEL 299
           FELFAAAGS QKREARE+A Q DS+VSQITVISDGR L+F+LPRNSQSILDAGNAQGAEL
Sbjct: 241 FELFAAAGSQQKREAREAARQVDSAVSQITVISDGRALAFDLPRNSQSILDAGNAQGAEL 300

Query: 300 PYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQI 357
           PYSCKAGVCSTCKCKV+EGEVEMDSN ALEDYEVAAGYVLSCQ FPISDKVVLDFDQ+
Sbjct: 301 PYSCKAGVCSTCKCKVIEGEVEMDSNHALEDYEVAAGYVLSCQAFPISDKVVLDFDQL 358


Lambda     K      H
   0.319    0.133    0.377 

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: 547
Number of extensions: 10
Number of successful extensions: 2
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: 357
Length of database: 358
Length adjustment: 29
Effective length of query: 328
Effective length of database: 329
Effective search space:   107912
Effective search space used:   107912
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: 49 (23.5 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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