GapMind for catabolism of small carbon sources

 

Alignments for a candidate for epi in Haloterrigena daqingensis JX313

Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_076581962.1 BB347_RS05905 methylmalonyl-CoA epimerase

Query= SwissProt::O58010
         (136 letters)



>NCBI__GCF_001971705.1:WP_076581962.1
          Length = 127

 Score = 96.7 bits (239), Expect = 1e-25
 Identities = 53/126 (42%), Positives = 77/126 (61%), Gaps = 4/126 (3%)

Query: 9   DHVGIAVKNLEEAIKIWEGL-GFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTEDSPI 67
           +H GIA ++ +E  +++  L G  V   EE     ++V  ++ G+   ELLE   ED  I
Sbjct: 4   EHAGIATEDAQELAELYSDLFGLAVAHEEEFDG--MRVVFLECGDGYFELLEPF-EDGTI 60

Query: 68  AKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSVTGV 127
           A+++E  G GIHHLA+  E+IE+ LE  ++    LIDE+PR GA G  +AF+HPK   G+
Sbjct: 61  AQYLEANGSGIHHLALATEDIEAALETAREHDVSLIDEEPRPGAWGHSVAFLHPKDTGGI 120

Query: 128 LLELCE 133
           LLEL E
Sbjct: 121 LLELVE 126


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: 50
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: 127
Length adjustment: 14
Effective length of query: 122
Effective length of database: 113
Effective search space:    13786
Effective search space used:    13786
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: 41 (20.4 bits)

Align candidate WP_076581962.1 BB347_RS05905 (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.3084980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    7.1e-49  151.8   0.1    7.9e-49  151.7   0.1    1.0  1  NCBI__GCF_001971705.1:WP_076581962.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001971705.1:WP_076581962.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.7   0.1   7.9e-49   7.9e-49       2     129 .]       3     126 ..       2     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.7 bits;  conditional E-value: 7.9e-49
                             TIGR03081   2 ldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeGl 74 
                                           ++h +ia++d++e+a+ly d++G++v++eee+  +g++vvfle g++++ellep  ed++ia++le + g+G+
  NCBI__GCF_001971705.1:WP_076581962.1   3 FEHAGIATEDAQELAELYSDLFGLAVAHEEEF--DGMRVVFLECGDGYFELLEP-FEDGTIAQYLEAN-GSGI 71 
                                           79******************************..89******************.689*********9.**** PP

                             TIGR03081  75 hhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129
                                           hh+al+++dieaalet++e++v l+deepr Ga+G++vaFlhPkdtgG+L+el+e
  NCBI__GCF_001971705.1:WP_076581962.1  72 HHLALATEDIEAALETAREHDVSLIDEEPRPGAWGHSVAFLHPKDTGGILLELVE 126
                                           *****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (129 nodes)
Target sequences:                          1  (127 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: 7.54
//
[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