GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Desulfovibrio vulgaris Hildenborough

Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate 209572 DVU0626 acetolactate synthase, small subunit

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



>MicrobesOnline__882:209572
          Length = 159

 Score =  118 bits (296), Expect = 4e-32
 Identities = 62/160 (38%), Positives = 104/160 (65%), Gaps = 3/160 (1%)

Query: 1   MKNTHIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVE 60
           MKNT  +SVLV N+ GV+ + + +F +   N++SI+   T++ D+SR+ + V+G + + +
Sbjct: 1   MKNT--LSVLVRNQVGVVAQATEVFRQHNVNLNSISCAETEAFDVSRLMLTVEGQEHLFD 58

Query: 61  QVVKQLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQ 120
            V   L     V++V DL   + V+REL L+K+ A T  + +QV+Q   +FR  +V + Q
Sbjct: 59  AVKADLASKDFVLEVEDLSARDLVDRELALVKV-AVTRETTTQVMQVCEVFRATVVGMGQ 117

Query: 121 ESLTVQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRG 160
           E++T++ITGD  K+  FI+L++P GI+ ++RTG  AL RG
Sbjct: 118 ETMTLEITGDMRKVDGFIRLLRPFGIRSLARTGSVALARG 157


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: 52
Number of extensions: 6
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: 159
Length adjustment: 18
Effective length of query: 151
Effective length of database: 141
Effective search space:    21291
Effective search space used:    21291
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 209572 DVU0626 (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.5045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
      7e-41  125.9   4.2    7.8e-41  125.8   4.2    1.0  1  lcl|MicrobesOnline__882:209572  DVU0626 acetolactate synthase, s


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209572  DVU0626 acetolactate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   4.2   7.8e-41   7.8e-41       1     158 []       1     158 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 7.8e-41
                       TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldltes 79 
                                     +k +lsvlv+n+ Gv+++ + +f++ + n++s+  +ete  d+sr+ ++veg+++  + ++  l     vl+v+dl+ +
  lcl|MicrobesOnline__882:209572   1 MKNTLSVLVRNQVGVVAQATEVFRQHNVNLNSISCAETEAFDVSRLMLTVEGQEHLFDAVKADLASKDFVLEVEDLSAR 79 
                                     6899*************************************************************************** PP

                       TIGR00119  80 eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlvalsrge 158
                                     + v+rel+lvkv ++ e+ ++++++ e+fr+ vv + ++++++e++g+  k++ f++ll++fgi+ +ar+G val+rg+
  lcl|MicrobesOnline__882:209572  80 DLVDRELALVKVAVTRETTTQVMQVCEVFRATVVGMGQETMTLEITGDMRKVDGFIRLLRPFGIRSLARTGSVALARGD 158
                                     *****************************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (159 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: 6.19
//
[ok]

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