GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catC in Pseudomonas fluorescens GW456-L13

Align Muconolactone isomerase (EC 5.3.3.4) (characterized)
to candidate PfGW456L13_3823 Muconolactone isomerase (EC 5.3.3.4)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3823
         (96 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3823
          Length = 96

 Score =  200 bits (509), Expect = 3e-57
 Identities = 96/96 (100%), Positives = 96/96 (100%)

Query: 1  MLFHVKMTVNLPVDMNPEVAAKLKADEKALAQRLQEQGKWRHLWRIAGHYANYSVFDVDS 60
          MLFHVKMTVNLPVDMNPEVAAKLKADEKALAQRLQEQGKWRHLWRIAGHYANYSVFDVDS
Sbjct: 1  MLFHVKMTVNLPVDMNPEVAAKLKADEKALAQRLQEQGKWRHLWRIAGHYANYSVFDVDS 60

Query: 61 VQELHDLLMQLPLFPYMAIEIDAMCRHPSSIRDDDR 96
          VQELHDLLMQLPLFPYMAIEIDAMCRHPSSIRDDDR
Sbjct: 61 VQELHDLLMQLPLFPYMAIEIDAMCRHPSSIRDDDR 96


Lambda     K      H
   0.324    0.136    0.422 

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: 94
Number of extensions: 1
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: 96
Length of database: 96
Length adjustment: 10
Effective length of query: 86
Effective length of database: 86
Effective search space:     7396
Effective search space used:     7396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.1 bits)
S2: 39 (19.6 bits)

Align candidate PfGW456L13_3823 (Muconolactone isomerase (EC 5.3.3.4))
to HMM TIGR03221 (catC: muconolactone delta-isomerase (EC 5.3.3.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03221.hmm
# target sequence database:        /tmp/gapView.2464760.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03221  [M=90]
Accession:   TIGR03221
Description: muco_delta: muconolactone delta-isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    3.3e-50  154.4   0.2    3.6e-50  154.3   0.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3823  Muconolactone isomerase (EC 5.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3823  Muconolactone isomerase (EC 5.3.3.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.2   3.6e-50   3.6e-50       1      90 []       2      91 ..       2      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 3.6e-50
                                               TIGR03221  1 lflvrmdvnlPedlpaekaaelkaeekalaqelqreGkwrhlwrvvGeyanvsifdv 57
                                                            lf+v+m+vnlP+d+++e aa+lka+ekalaq+lq++Gkwrhlwr++G+yan+s+fdv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3823  2 LFHVKMTVNLPVDMNPEVAAKLKADEKALAQRLQEQGKWRHLWRIAGHYANYSVFDV 58
                                                            8******************************************************** PP

                                               TIGR03221 58 esndelhellsglPlfpymdievtalarhPsai 90
                                                            +s +elh+ll++lPlfpym ie++a++rhPs+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3823 59 DSVQELHDLLMQLPLFPYMAIEIDAMCRHPSSI 91
                                                            *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (90 nodes)
Target sequences:                          1  (96 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 6.88
//
[ok]

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:

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