GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Streptacidiphilus oryzae TH49

Align methylmalonyl CoA epimerase subunit (EC 5.1.99.1) (characterized)
to candidate WP_037579705.1 BS73_RS15090 methylmalonyl-CoA epimerase

Query= metacyc::MONOMER-13075
         (148 letters)



>NCBI__GCF_000744815.1:WP_037579705.1
          Length = 147

 Score =  110 bits (276), Expect = 7e-30
 Identities = 56/133 (42%), Positives = 84/133 (63%), Gaps = 2/133 (1%)

Query: 10  IDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAP 69
           IDH+  AC D D+  ++Y+ T+G+   H E N EQGV E M+          + +Q++ P
Sbjct: 5   IDHIGIACFDLDKTVEFYRATYGFEVFHTEVNEEQGVREAMLRINRTDDGGASYLQLLEP 64

Query: 70  LNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINF 129
           + ++S V KWLAK NG  G+HH+A+   D+D  S  +R +GV++LY+EP+ G+  +RI F
Sbjct: 65  VREDSAVGKWLAK-NGE-GVHHIAFGTADVDGDSEAIRGKGVRVLYEEPRRGSMDSRITF 122

Query: 130 MHPKSGKGVLIEL 142
           +HPK   GVL EL
Sbjct: 123 LHPKDCHGVLTEL 135


Lambda     K      H
   0.317    0.133    0.408 

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: 88
Number of extensions: 5
Number of successful extensions: 3
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: 148
Length of database: 147
Length adjustment: 16
Effective length of query: 132
Effective length of database: 131
Effective search space:    17292
Effective search space used:    17292
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_037579705.1 BS73_RS15090 (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.2178477.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.4e-45  139.9   0.0    3.9e-45  139.7   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037579705.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037579705.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.0   3.9e-45   3.9e-45       1     128 [.       4     136 ..       4     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 3.9e-45
                             TIGR03081   1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelge......tklellepleedspiakfle 67 
                                           ++dh++ia+ dl++ +++yr+++G++v ++e ++eqgv++++l+++       ++l+llep+ eds++ k+l+
  NCBI__GCF_000744815.1:WP_037579705.1   4 RIDHIGIACFDLDKTVEFYRATYGFEVFHTEVNEEQGVREAMLRINRtddggaSYLQLLEPVREDSAVGKWLA 76 
                                           79*****************************************99865678889******************* PP

                             TIGR03081  68 kkkgeGlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLiele 128
                                           k+ geG+hhia+ + d++  +e ++ kgvr+l+eepr G+   +++FlhPkd++GvL+el+
  NCBI__GCF_000744815.1:WP_037579705.1  77 KN-GEGVHHIAFGTADVDGDSEAIRGKGVRVLYEEPRRGSMDSRITFLHPKDCHGVLTELV 136
                                           **.********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (147 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: 8.32
//
[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