GapMind for catabolism of small carbon sources

 

Aligments for a candidate for epi in Echinicola vietnamensis KMM 6221, DSM 17526

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate Echvi_0089 Echvi_0089 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>lcl|FitnessBrowser__Cola:Echvi_0089 Echvi_0089 methylmalonyl-CoA
           epimerase
          Length = 134

 Score =  120 bits (302), Expect = 6e-33
 Identities = 56/129 (43%), Positives = 96/129 (74%), Gaps = 1/129 (0%)

Query: 6   KRIDHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTED 64
           ++I+H+GIAVK+L+++ +++  L G +  + E V D+ V  +  +VG+ +IELLEAT  D
Sbjct: 2   RKIEHLGIAVKDLKKSNELFSRLFGKEAYKEERVEDEGVLTSFFQVGDVKIELLEATAPD 61

Query: 65  SPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSV 124
           SPIAKFI+KR EG+HH+A  V++I ++++ LK+ G++++++ P+ GA    + F+HP+S 
Sbjct: 62  SPIAKFIDKRAEGVHHVAFAVDDIYAEMDRLKKAGFEILNDVPKKGADHKLVVFLHPRST 121

Query: 125 TGVLLELCE 133
            GVL+ELC+
Sbjct: 122 NGVLVELCQ 130


Lambda     K      H
   0.317    0.138    0.389 

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: 93
Number of extensions: 4
Number of successful extensions: 2
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 (21.6 bits)
S2: 42 (20.8 bits)

Align candidate Echvi_0089 Echvi_0089 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))

# 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/TIGR03081.hmm
# target sequence database:        /tmp/gapView.971.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03081  [M=129]
Accession:   TIGR03081
Description: metmalonyl_epim: methylmalonyl-CoA epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
      5e-45  139.4   0.3    5.6e-45  139.2   0.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0089  Echvi_0089 methylmalonyl-CoA epi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0089  Echvi_0089 methylmalonyl-CoA epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.3   5.6e-45   5.6e-45       1     129 []       3     130 ..       3     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 5.6e-45
                            TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeGl 74 
                                          k++h++iavkdl++  +l+  ++G +  +ee+++++gv + f+++g+ k+elle+++ dspiakf++k+ +eG+
  lcl|FitnessBrowser__Cola:Echvi_0089   3 KIEHLGIAVKDLKKSNELFSRLFGKEAYKEERVEDEGVLTSFFQVGDVKIELLEATAPDSPIAKFIDKR-AEGV 75 
                                          79*******************************************************************.**** PP

                            TIGR03081  75 hhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                          hh+a++vddi a ++ lk++g ++l++ p+ Ga  k v+FlhP++t+GvL+el++
  lcl|FitnessBrowser__Cola:Echvi_0089  76 HHVAFAVDDIYAEMDRLKKAGFEILNDVPKKGADHKLVVFLHPRSTNGVLVELCQ 130
                                          *****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 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: 5.97
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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