GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Desulfovibrio vulgaris Hildenborough

Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate 208496 DVU2983 3-isopropylmalate dehydratase, small subunit

Query= BRENDA::Q58673
         (168 letters)



>MicrobesOnline__882:208496
          Length = 167

 Score =  162 bits (409), Expect = 3e-45
 Identities = 76/158 (48%), Positives = 112/158 (70%)

Query: 7   GRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCG 66
           G   K G+++DTDAI+PAR+LV T  ++L +  M G +  +  +VK GDI+VGG+NFGCG
Sbjct: 5   GTAHKVGDHIDTDAIIPARFLVTTDAQKLGENCMEGLEHGWVARVKSGDIMVGGRNFGCG 64

Query: 67  SSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLET 126
           SSREHAP+ + GAG+  V+A SFARIFYRN  N+GL L+E     +K+ +GD++EV+  +
Sbjct: 65  SSREHAPIAILGAGMPVVVAHSFARIFYRNGFNMGLLLLEVGDDVDKIADGDDIEVDAAS 124

Query: 127 GEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKM 164
           G I N TTG  +    +P+ M E+L+ GGL+PY++ ++
Sbjct: 125 GVITNRTTGATITCAPVPQSMRELLDTGGLVPYVRARL 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: 109
Number of extensions: 3
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: 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 208496 DVU2983 (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.30607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    6.4e-55  171.3   0.0    7.2e-55  171.1   0.0    1.0  1  lcl|MicrobesOnline__882:208496  DVU2983 3-isopropylmalate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208496  DVU2983 3-isopropylmalate dehydratase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.0   7.2e-55   7.2e-55       1     155 [.       5     159 ..       5     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 7.2e-55
                       TIGR02087   1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaalalkaaGvaavi 79 
                                     G ++k Gd++dtdaiiP+r+l ttd ++l++ +meg++  +  +v++Gd++v G+nfG+Gssre+a++a+  aG+  v+
  lcl|MicrobesOnline__882:208496   5 GTAHKVGDHIDTDAIIPARFLVTTDAQKLGENCMEGLEHGWVARVKSGDIMVGGRNFGCGSSREHAPIAILGAGMPVVV 83 
                                     789**************************************************************************** PP

                       TIGR02087  80 aesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleeledllleileeGGlleylk 155
                                     a+sfarifyrn  n+Gl l+++ d +++i dGd +evd  +g i + +   ++++ ++++ ++e+l+ GGl+ y++
  lcl|MicrobesOnline__882:208496  84 AHSFARIFYRNGFNMGLLLLEVGDDVDKIADGDDIEVDAASGVITNRTTGATITCAPVPQSMRELLDTGGLVPYVR 159
                                     ***********************999************************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.80
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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