GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Paraburkholderia bryophila 376MFSha3.1

Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate H281DRAFT_01593 H281DRAFT_01593 4-carboxymuconolactone decarboxylase

Query= BRENDA::Q6SJA7
         (118 letters)



>FitnessBrowser__Burk376:H281DRAFT_01593
          Length = 130

 Score =  112 bits (280), Expect = 2e-30
 Identities = 54/116 (46%), Positives = 73/116 (62%)

Query: 1   MTTRRAVLGDAHVDRAEAAKTELDAPFQSLITEAAWGTVWASDKISRRERSMLTLALLAA 60
           M  RRAVLGDAHVDR+ A +TEL   FQ+ IT  AWG +W  D + R  RS+LT+A++ A
Sbjct: 11  MGVRRAVLGDAHVDRSLANRTELTEEFQNFITRYAWGEIWTRDGLPRHTRSLLTIAMMVA 70

Query: 61  TGNFEEIPMHIRATANTGASKSDVIEAFQHVAIYAGVPKANHALKLAKQTYQEMEA 116
               EE+ +H+RA  N G ++  + E     AIY GVP AN A  LA + ++E +A
Sbjct: 71  LNRSEELALHLRAAKNNGVTREQIKEVLLQTAIYCGVPAANSAFHLADKLFREDDA 126


Lambda     K      H
   0.315    0.125    0.348 

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: 56
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: 118
Length of database: 130
Length adjustment: 14
Effective length of query: 104
Effective length of database: 116
Effective search space:    12064
Effective search space used:    12064
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 H281DRAFT_01593 H281DRAFT_01593 (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.28966.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.3e-61  192.3   0.2    1.5e-61  192.1   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01593  H281DRAFT_01593 4-carboxymuconol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01593  H281DRAFT_01593 4-carboxymuconolactone decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   0.2   1.5e-61   1.5e-61       2     121 ..       4     123 ..       3     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 1.5e-61
                                    TIGR02425   2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtialla 67 
                                                  ++rye+G+ vrravlGdahvdr+la++t++++efq++it++aWG++W+rdgl++++rsl+tia+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01593   4 EDRYEAGMGVRRAVLGDAHVDRSLANRTELTEEFQNFITRYAWGEIWTRDGLPRHTRSLLTIAMMV 69 
                                                  68**************************************************************** PP

                                    TIGR02425  68 algreeelalhvraaantGvteddikevllqvaiyaGvPaankalklakevlae 121
                                                  al+r+eelalh+raa+n+Gvt+++ikevllq+aiy+GvPaan+a++la +++ e
  lcl|FitnessBrowser__Burk376:H281DRAFT_01593  70 ALNRSEELALHLRAAKNNGVTREQIKEVLLQTAIYCGVPAANSAFHLADKLFRE 123
                                                  *************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (123 nodes)
Target sequences:                          1  (130 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: 3.71
//
[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