GapMind for catabolism of small carbon sources

 

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

Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate PfGW456L13_2425 Phenylacetate-CoA oxygenase, PaaI subunit

Query= metacyc::MONOMER-15949
         (253 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2425
           Phenylacetate-CoA oxygenase, PaaI subunit
          Length = 253

 Score =  412 bits (1060), Expect = e-120
 Identities = 197/253 (77%), Positives = 221/253 (87%)

Query: 1   MNPNHDLIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAA 60
           MN   DLIEYLLRLGDSALIQGQRLC+WCG+APALEEELALMNVGLDLVGQARNWL+YAA
Sbjct: 1   MNNKTDLIEYLLRLGDSALIQGQRLCQWCGKAPALEEELALMNVGLDLVGQARNWLEYAA 60

Query: 61  ELLADGRDADHLAFRRDERAYRNLLLVEQPNGDFAVTMAKQFLYDAWHFQVLDGLSRSGD 120
           ELL DGRDADHLAFRRDERAYRNLLLVEQPNGDFA+TM KQFLYDAWH  VL GLS+S D
Sbjct: 61  ELLDDGRDADHLAFRRDERAYRNLLLVEQPNGDFAITMLKQFLYDAWHLPVLQGLSQSSD 120

Query: 121 ARVAGIAAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLWRFTVEMSDGDEVE 180
            R+AGIAAKA+KEVTYHLRRSGEW++R+GDGTEES+RRM AAIP++WRFTVE+   D+ E
Sbjct: 121 ERIAGIAAKAVKEVTYHLRRSGEWIERMGDGTEESNRRMLAAIPEVWRFTVELIAADDSE 180

Query: 181 QRLCEAGIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRRGLHSEHLGLLLAE 240
           QRLC AGI PD A +A  WQ KV ++F +ATLP+P     FYL+ R+GLH+EHLG+LLAE
Sbjct: 181 QRLCAAGITPDIASVATQWQTKVEQIFTSATLPVPAAPSYFYLNARKGLHTEHLGILLAE 240

Query: 241 MQFLQRAYPDATW 253
           MQ L RAYPDATW
Sbjct: 241 MQCLPRAYPDATW 253


Lambda     K      H
   0.321    0.136    0.421 

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: 302
Number of extensions: 3
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: 253
Length of database: 253
Length adjustment: 24
Effective length of query: 229
Effective length of database: 229
Effective search space:    52441
Effective search space used:    52441
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 (21.9 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 (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