GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gbuA in Pseudomonas putida KT2440

Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate PP_4523 PP_4523 putative Agmatinase

Query= metacyc::MONOMER-11557
         (320 letters)



>lcl|FitnessBrowser__Putida:PP_4523 PP_4523 putative Agmatinase
          Length = 320

 Score =  652 bits (1682), Expect = 0.0
 Identities = 320/320 (100%), Positives = 320/320 (100%)

Query: 1   MRPTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRF 60
           MRPTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRF
Sbjct: 1   MRPTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRF 60

Query: 61  GPRQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHN 120
           GPRQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHN
Sbjct: 61  GPRQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHN 120

Query: 121 VIPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEG 180
           VIPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEG
Sbjct: 121 VIPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEG 180

Query: 181 LLDCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVY 240
           LLDCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVY
Sbjct: 181 LLDCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVY 240

Query: 241 LSFDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTS 300
           LSFDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTS
Sbjct: 241 LSFDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTS 300

Query: 301 LLGANLLFEMLCVLPGVVRR 320
           LLGANLLFEMLCVLPGVVRR
Sbjct: 301 LLGANLLFEMLCVLPGVVRR 320


Lambda     K      H
   0.322    0.141    0.431 

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: 576
Number of extensions: 19
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: 320
Length of database: 320
Length adjustment: 28
Effective length of query: 292
Effective length of database: 292
Effective search space:    85264
Effective search space used:    85264
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: 48 (23.1 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