GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Rhizobium etli CFN 42

Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate WP_011427916.1 RHE_RS24315 4-carboxymuconolactone decarboxylase

Query= BRENDA::Q6SJC5
         (136 letters)



>NCBI__GCF_000092045.1:WP_011427916.1
          Length = 134

 Score =  165 bits (418), Expect = 2e-46
 Identities = 78/126 (61%), Positives = 100/126 (79%)

Query: 10  TPTDRYTTGMDTRRRVLGDAHVDRAEACKSDFDAPFQTLITEGAWGTVWASDAISPRERS 69
           +P++RY  GM TRR VLGDAHVDRA A ++ FD PFQ LITE AWG VW+   ++ RERS
Sbjct: 6   SPSERYRQGMATRRAVLGDAHVDRAAAGETGFDRPFQELITEAAWGHVWSRPTLTKRERS 65

Query: 70  MLTLALLAATGNFEEIPMHIRATARTGASQSDVIEAFQHVAIYAGVPRANHAIRLAKETY 129
           ++T+ALLAA G  EE+ MH+RATA TGA++ D+ EA  HVAIYAGVP ANHAI++AK+ +
Sbjct: 66  IVTIALLAALGQDEEVAMHVRATANTGATRDDICEALLHVAIYAGVPAANHAIKIAKQAF 125

Query: 130 AEMEAE 135
           A+M+AE
Sbjct: 126 AQMDAE 131


Lambda     K      H
   0.317    0.128    0.374 

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: 91
Number of extensions: 2
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: 136
Length of database: 134
Length adjustment: 15
Effective length of query: 121
Effective length of database: 119
Effective search space:    14399
Effective search space used:    14399
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: 42 (20.8 bits)

Align candidate WP_011427916.1 RHE_RS24315 (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.1821811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.7e-65  203.0   1.2    7.7e-65  202.8   1.2    1.0  1  NCBI__GCF_000092045.1:WP_011427916.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_011427916.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.8   1.2   7.7e-65   7.7e-65       2     122 ..       8     128 ..       7     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.8 bits;  conditional E-value: 7.7e-65
                             TIGR02425   2 keryeqGlkvrravlGdahvdralaaktdfdaefqeliteaaWGtvWardglskrerslvtiallaalgreee 74 
                                           +ery+qG+++rravlGdahvdra a++t fd++fqeliteaaWG+vW+r+ l+krers+vtiallaalg++ee
  NCBI__GCF_000092045.1:WP_011427916.1   8 SERYRQGMATRRAVLGDAHVDRAAAGETGFDRPFQELITEAAWGHVWSRPTLTKRERSIVTIALLAALGQDEE 80 
                                           68*********************************************************************** PP

                             TIGR02425  75 lalhvraaantGvteddikevllqvaiyaGvPaankalklakevlael 122
                                           +a+hvra+antG+t+ddi+e+ll+vaiyaGvPaan+a+k+ak+++a++
  NCBI__GCF_000092045.1:WP_011427916.1  81 VAMHVRATANTGATRDDICEALLHVAIYAGVPAANHAIKIAKQAFAQM 128
                                           *********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (123 nodes)
Target sequences:                          1  (134 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: 11.79
//
[ok]

This GapMind analysis is from Apr 09 2024. 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