GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Desulforamulus ruminis DSM 2154

Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_013840435.1 DESRU_RS01890 3-isopropylmalate dehydratase small subunit

Query= BRENDA::Q58673
         (168 letters)



>NCBI__GCF_000215085.1:WP_013840435.1
          Length = 165

 Score =  202 bits (513), Expect = 3e-57
 Identities = 94/160 (58%), Positives = 123/160 (76%)

Query: 5   IKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFG 64
           ++G+VW+FGN+VDTD I+ ARYL  + P ELAQ  M  ADP F  KVK GDI+V GKNFG
Sbjct: 3   LQGKVWRFGNDVDTDIIIAARYLNSSDPAELAQHCMEDADPQFSSKVKTGDIMVAGKNFG 62

Query: 65  CGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNL 124
           CGSSREHAP+ +K AG+SCV+A+SFARIFYRNA N+GLP+ EC    E+V EG+EL V+ 
Sbjct: 63  CGSSREHAPIAIKAAGLSCVVAKSFARIFYRNAFNIGLPIFECPEAVEEVKEGEELTVDA 122

Query: 125 ETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKM 164
            TG+I N TTG+  +   +PEFM +I++AGGL+ Y+K ++
Sbjct: 123 ATGKIINHTTGKEYQAAPIPEFMSQIIDAGGLISYVKGRV 162


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: 130
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: 168
Length of database: 165
Length adjustment: 18
Effective length of query: 150
Effective length of database: 147
Effective search space:    22050
Effective search space used:    22050
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_013840435.1 DESRU_RS01890 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR02084 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

# 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/TIGR02084.hmm
# target sequence database:        /tmp/gapView.1613065.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02084  [M=156]
Accession:   TIGR02084
Description: leud: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.2e-79  248.8   0.1    9.3e-79  248.6   0.1    1.0  1  NCBI__GCF_000215085.1:WP_013840435.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840435.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.6   0.1   9.3e-79   9.3e-79       1     155 [.       5     159 ..       5     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.6 bits;  conditional E-value: 9.3e-79
                             TIGR02084   1 gkvlkygdnvdtdviiparylntsdpkelakhcmedldkefkkkvkegdilvagknfgcgssrehapiaikas 73 
                                           gkv+++g++vdtd ii aryln+sdp ela+hcmed+d +f  kvk+gdi+vagknfgcgssrehapiaika+
  NCBI__GCF_000215085.1:WP_013840435.1   5 GKVWRFGNDVDTDIIIAARYLNSSDPAELAQHCMEDADPQFSSKVKTGDIMVAGKNFGCGSSREHAPIAIKAA 77 
                                           89*********************************************************************** PP

                             TIGR02084  74 giscviaksfarifyrnainiglpiveseeavdeleegdevevdlekgiiknvkkgkeykakpfpeflkeilk 146
                                           g+scv+aksfarifyrna niglpi e+ eav+e++eg+e+ vd   g i n ++gkey+a p pef+ +i++
  NCBI__GCF_000215085.1:WP_013840435.1  78 GLSCVVAKSFARIFYRNAFNIGLPIFECPEAVEEVKEGEELTVDAATGKIINHTTGKEYQAAPIPEFMSQIID 150
                                           ************************************************************************* PP

                             TIGR02084 147 aegllnyvk 155
                                           a+gl++yvk
  NCBI__GCF_000215085.1:WP_013840435.1 151 AGGLISYVK 159
                                           *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (156 nodes)
Target sequences:                          1  (165 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: 16.96
//
[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