GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Clostridium tyrobutyricum FAM22553

Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_023625258.1 PN53_RS01915 acetolactate synthase small subunit

Query= metacyc::MONOMER-11901
         (169 letters)



>NCBI__GCF_000816635.1:WP_023625258.1
          Length = 163

 Score =  167 bits (423), Expect = 8e-47
 Identities = 85/159 (53%), Positives = 122/159 (76%), Gaps = 1/159 (0%)

Query: 5   HIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVVK 64
           +++SVLV N PGVL +I+GLF+RR YNI S+T G T+  +ISRMTIV  GDD + EQ+ K
Sbjct: 4   YVLSVLVENHPGVLSKIAGLFSRRGYNIHSLTVGITEDPEISRMTIVSVGDDYMFEQINK 63

Query: 65  QLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESLT 124
           QLNKLIEVIKVIDL + + V REL L+K+ A + ++K  +++ A+ FR  ++D+ ++S+ 
Sbjct: 64  QLNKLIEVIKVIDLSDHKAVARELSLVKVSADS-NNKVLIMEIAHTFRAKVLDMDEKSMI 122

Query: 125 VQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRGPKI 163
           ++ITG + KIS+FI+L++P GIKE  RTGLT+L RG K+
Sbjct: 123 IEITGSERKISSFIELMRPYGIKESIRTGLTSLQRGNKL 161


Lambda     K      H
   0.317    0.134    0.362 

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: 105
Number of extensions: 3
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: 169
Length of database: 163
Length adjustment: 18
Effective length of query: 151
Effective length of database: 145
Effective search space:    21895
Effective search space used:    21895
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: 43 (21.2 bits)

Align candidate WP_023625258.1 PN53_RS01915 (acetolactate synthase small subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))

# 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/TIGR00119.hmm
# target sequence database:        /tmp/gapView.3272818.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00119  [M=158]
Accession:   TIGR00119
Description: acolac_sm: acetolactate synthase, 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-65  205.6   1.5    2.5e-65  205.4   1.5    1.0  1  NCBI__GCF_000816635.1:WP_023625258.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_023625258.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   1.5   2.5e-65   2.5e-65       2     158 .]       3     159 ..       2     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 2.5e-65
                             TIGR00119   2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvl 74 
                                           k vlsvlven+pGvLs+++Glf+rrg+ni+sltvg te++++srmtiv  gdd + eqi+kql+kl++v+kv 
  NCBI__GCF_000816635.1:WP_023625258.1   3 KYVLSVLVENHPGVLSKIAGLFSRRGYNIHSLTVGITEDPEISRMTIVSVGDDYMFEQINKQLNKLIEVIKVI 75 
                                           78*********************************************************************** PP

                             TIGR00119  75 dlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikeva 147
                                           dl++++ v rel lvkvsa ++++  i+e++++fr++v+D+ e+s+i+e++g+e kis+f++l++++gike  
  NCBI__GCF_000816635.1:WP_023625258.1  76 DLSDHKAVARELSLVKVSADSNNKVLIMEIAHTFRAKVLDMDEKSMIIEITGSERKISSFIELMRPYGIKESI 148
                                           ************************************************************************* PP

                             TIGR00119 148 rsGlvalsrge 158
                                           r+Gl++l rg+
  NCBI__GCF_000816635.1:WP_023625258.1 149 RTGLTSLQRGN 159
                                           *********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (163 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: 10.13
//
[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