GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Bacillus altitudinis 41KF2b

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_035702812.1 BA79_RS11170 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>NCBI__GCF_000691145.1:WP_035702812.1
          Length = 140

 Score =  103 bits (257), Expect = 1e-27
 Identities = 51/128 (39%), Positives = 87/128 (67%), Gaps = 1/128 (0%)

Query: 7   RIDHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTEDS 65
           +IDH+ IAV ++++  + +  L  ++  +IE +P+Q VKV+   +G+  IEL+E   + S
Sbjct: 3   QIDHIAIAVFSIQKTARTFSRLFNWEFSDIEVLPNQGVKVSFASLGDLHIELIEPMEDHS 62

Query: 66  PIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSVT 125
            +  F+ KRGEG+HH+A++  +I++ L +L++ G +LI +  + GA G +IAFI PK  +
Sbjct: 63  TLHTFLIKRGEGLHHIALKSGDIQADLSQLEELGMQLIQKGAQNGANGNRIAFISPKETS 122

Query: 126 GVLLELCE 133
           GVL+ELCE
Sbjct: 123 GVLIELCE 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: 75
Number of extensions: 6
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: 140
Length adjustment: 15
Effective length of query: 121
Effective length of database: 125
Effective search space:    15125
Effective search space used:    15125
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_035702812.1 BA79_RS11170 (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.2183587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.1e-40  125.3   0.1    1.2e-40  125.2   0.1    1.0  1  NCBI__GCF_000691145.1:WP_035702812.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035702812.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   1.2e-40   1.2e-40       1     129 []       3     130 ..       3     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 1.2e-40
                             TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeG 73 
                                           ++dh+aiav ++++ a+++  ++ +++s+ e lp+qgvkv f +lg+ ++el+ep+e+ s++  fl k+ geG
  NCBI__GCF_000691145.1:WP_035702812.1   3 QIDHIAIAVFSIQKTARTFSRLFNWEFSDIEVLPNQGVKVSFASLGDLHIELIEPMEDHSTLHTFLIKR-GEG 74 
                                           59*******************************************************************.*** PP

                             TIGR03081  74 lhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                           lhhial+  di+a l++l+e g++l+++ +++Ga G+++aF+ Pk+t+GvLiel+e
  NCBI__GCF_000691145.1:WP_035702812.1  75 LHHIALKSGDIQADLSQLEELGMQLIQKGAQNGANGNRIAFISPKETSGVLIELCE 130
                                           ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (140 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: 8.59
//
[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:

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