GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Pseudomonas simiae WCS417

Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF1326 PS417_06740 4-carboxymuconolactone decarboxylase

Query= BRENDA::Q9L5B1
         (130 letters)



>FitnessBrowser__WCS417:GFF1326
          Length = 132

 Score =  106 bits (265), Expect = 1e-28
 Identities = 48/119 (40%), Positives = 73/119 (61%)

Query: 4   RYETGMKVRRRILGDAHVDRAEAAKTPFDTPFQEMIAETAWGNVWASDRITDRERSMLTL 63
           RY  G++VRR +LGDAHVDR+  A T F++ FQEMI   AWG++W    +    RS++T+
Sbjct: 6   RYAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITI 65

Query: 64  AVLAATGSFDEIPMHIRATARTGASKEDVAEAFQHVAIYAGVPKANHALKLAKQTYAEM 122
           A+L      +E+ +H+RA A  G ++ ++ E     AIY G+P AN    LA+  + E+
Sbjct: 66  AMLIGMNRSEELKLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124


Lambda     K      H
   0.317    0.128    0.371 

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: 60
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: 130
Length of database: 132
Length adjustment: 14
Effective length of query: 116
Effective length of database: 118
Effective search space:    13688
Effective search space used:    13688
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 41 (20.4 bits)

Align candidate GFF1326 PS417_06740 (4-carboxymuconolactone decarboxylase)
to HMM TIGR02425 (pcaC: 4-carboxymuconolactone decarboxylase (EC 4.1.1.44))

# 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/TIGR02425.hmm
# target sequence database:        /tmp/gapView.3351.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02425  [M=123]
Accession:   TIGR02425
Description: decarb_PcaC: 4-carboxymuconolactone decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    6.2e-62  193.4   0.1      7e-62  193.2   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF1326  PS417_06740 4-carboxymuconolacto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1326  PS417_06740 4-carboxymuconolactone decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.1     7e-62     7e-62       1     122 [.       3     124 ..       3     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 7e-62
                           TIGR02425   1 ekeryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreeel 75 
                                         ek+ry++Gl+vrr vlGdahvdr+l+a t+f++efqe+it++aWG++W+r+gl++++rsl+tia+l++++r+eel
  lcl|FitnessBrowser__WCS417:GFF1326   3 EKQRYAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITIAMLIGMNRSEEL 77 
                                         589************************************************************************ PP

                           TIGR02425  76 alhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122
                                         +lh+raaa +Gvt+++ikevl+q+aiy+G+Paan++++la++v++el
  lcl|FitnessBrowser__WCS417:GFF1326  78 KLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124
                                         ********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (123 nodes)
Target sequences:                          1  (132 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: 5.69
//
[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