Alignments for a candidate for epi in Desulfallas geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for epi in Desulfallas geothermicus DSM 3669

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_092483262.1 BM299_RS09150 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>NCBI__GCF_900115975.1:WP_092483262.1
          Length = 133

 Score =  161 bits (407), Expect = 4e-45
 Identities = 80/132 (60%), Positives = 101/132 (76%), Gaps = 1/132 (0%)

Query: 4   MFKRIDHVGIAVKNLEEAIKIWEG-LGFKVEEIEEVPDQKVKVAVIKVGENRIELLEATT 62
           M K+IDH+GIAVK++  A   +E  LG KV E E V +QKVKVA I  G++ +ELLE+TT
Sbjct: 1   MIKKIDHIGIAVKDMAAAKAFYENVLGLKVTEEEVVEEQKVKVAFIPTGDSEVELLESTT 60

Query: 63  EDSPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPK 122
            D PIA++IEK GEGI H+A RV+N+E +L +LK  G +LIDEKPR GAGGAKIAF+HPK
Sbjct: 61  PDGPIARYIEKNGEGIQHIAFRVDNLEERLAQLKAAGVRLIDEKPRRGAGGAKIAFLHPK 120

Query: 123 SVTGVLLELCER 134
           +  G L+ELCER
Sbjct: 121 ATFGTLVELCER 132


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: 102
Number of extensions: 9
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: 133
Length adjustment: 15
Effective length of query: 121
Effective length of database: 118
Effective search space:    14278
Effective search space used:    14278
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 WP_092483262.1 BM299_RS09150 (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.7394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.5e-52  163.7   0.2    1.6e-52  163.6   0.2    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092483262.1  BM299_RS09150 methylmalonyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092483262.1  BM299_RS09150 methylmalonyl-CoA epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   0.2   1.6e-52   1.6e-52       1     129 []       4     131 ..       4     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 1.6e-52
                                 TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekk 69 
                                               k+dh++iavkd+ +a+++y++vlG+kv+eee ++eq+vkv+f+  g++++elle+++ d+pia+++ek+
  lcl|NCBI__GCF_900115975.1:WP_092483262.1   4 KIDHIGIAVKDMAAAKAFYENVLGLKVTEEEVVEEQKVKVAFIPTGDSEVELLESTTPDGPIARYIEKN 72 
                                               79******************************************************************* PP

                                 TIGR03081  70 kgeGlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                                geG+ hia++vd++e+ l++lk +gvrl+de+pr Ga+G+k+aFlhPk t G L+el+e
  lcl|NCBI__GCF_900115975.1:WP_092483262.1  73 -GEGIQHIAFRVDNLEERLAQLKAAGVRLIDEKPRRGAGGAKIAFLHPKATFGTLVELCE 131
                                               .*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (133 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: 5.36
//
[ok]

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources