GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Nitratiruptor tergarcus DSM 16512

Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_084275691.1 B8779_RS06290 3-isopropylmalate dehydratase small subunit

Query= BRENDA::Q58673
         (168 letters)



>NCBI__GCF_900176045.1:WP_084275691.1
          Length = 167

 Score =  192 bits (489), Expect = 2e-54
 Identities = 92/164 (56%), Positives = 122/164 (74%), Gaps = 1/164 (0%)

Query: 3   SIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKN 62
           ++I G+VWKFG+N+DTD I+ ARYL  + P ELA+ VM  ADP+F KK++PGDIIV G+N
Sbjct: 2   NVITGKVWKFGDNIDTDLIIAARYLNTSDPHELAKHVMEDADPEFVKKLQPGDIIVAGEN 61

Query: 63  FGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEV 122
           FGCGSSREHAP+ LK AG++ V+A+SFARIFYRNA N+GLP+ E K  ++K+NEGD + +
Sbjct: 62  FGCGSSREHAPIALKAAGVAAVVAKSFARIFYRNAFNMGLPIFELKE-TDKINEGDLISI 120

Query: 123 NLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAE 166
           ++E G IK+L          +P FM E+L  GGLM Y K K+ E
Sbjct: 121 DMEKGVIKDLDKHNEYTFTPIPPFMQELLSCGGLMNYAKAKILE 164


Lambda     K      H
   0.317    0.139    0.405 

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: 121
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: 168
Length of database: 167
Length adjustment: 18
Effective length of query: 150
Effective length of database: 149
Effective search space:    22350
Effective search space used:    22350
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: 43 (21.2 bits)

Align candidate WP_084275691.1 B8779_RS06290 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR02087 (3-isopropylmalate dehydratase, small subunit)

# 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.aa/TIGR02087.hmm
# target sequence database:        /tmp/gapView.1537205.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02087  [M=157]
Accession:   TIGR02087
Description: LEUD_arch: 3-isopropylmalate dehydratase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-70  221.3   0.0    2.9e-70  221.1   0.0    1.0  1  NCBI__GCF_900176045.1:WP_084275691.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084275691.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.1   0.0   2.9e-70   2.9e-70       1     155 [.       6     159 ..       6     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.1 bits;  conditional E-value: 2.9e-70
                             TIGR02087   1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaalalkaa 73 
                                           G+vwkfGd++dtd ii +ryl t d++elakh+me++dpef kk ++Gd+ivaG+nfG+Gssre+a++alkaa
  NCBI__GCF_900176045.1:WP_084275691.1   6 GKVWKFGDNIDTDLIIAARYLNTSDPHELAKHVMEDADPEFVKKLQPGDIIVAGENFGCGSSREHAPIALKAA 78 
                                           9************************************************************************ PP

                             TIGR02087  74 GvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleeledllleile 146
                                           Gvaav+a+sfarifyrna n+Glp+ +++  t++i++Gd +++d+ekg i+ + k++++++ +++ ++ e+l+
  NCBI__GCF_900176045.1:WP_084275691.1  79 GVAAVVAKSFARIFYRNAFNMGLPIFELK-ETDKINEGDLISIDMEKGVIKDLDKHNEYTFTPIPPFMQELLS 150
                                           **************************999.78***************************************** PP

                             TIGR02087 147 eGGlleylk 155
                                            GGl++y k
  NCBI__GCF_900176045.1:WP_084275691.1 151 CGGLMNYAK 159
                                           *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (157 nodes)
Target sequences:                          1  (167 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: 14.80
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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