GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvI in Desulfovibrio vulgaris Miyazaki F

Align Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate 8501909 DvMF_2624 acetolactate synthase, small subunit (RefSeq)

Query= curated2:O28555
         (159 letters)



>lcl|FitnessBrowser__Miya:8501909 DvMF_2624 acetolactate synthase,
           small subunit (RefSeq)
          Length = 160

 Score =  118 bits (296), Expect = 4e-32
 Identities = 58/158 (36%), Positives = 99/158 (62%), Gaps = 1/158 (0%)

Query: 1   MKHTIAVLVENKPGVLARVAGLFRRRGFNIESLTVGTTERDDLSRMTIVVEGDDKVVEQV 60
           MKHT++VLV+N+ G +A    +FRRRG +  S++   TE  D+SR+ + VE  +  +E +
Sbjct: 1   MKHTLSVLVKNRAGAVAEATDVFRRRGISFRSISCAETEDFDVSRLVLTVEDHEAELESI 60

Query: 61  IKQLNKLIETIKVSEITESS-VERELCLIRVHAPPEKRGEIVELTNIFRARIVDVSRDSF 119
            ++L        V +++    V+REL L++V    E   +I+++  +FRA ++ + +++ 
Sbjct: 61  AEELRAQDVVAMVEDLSRRDFVDRELVLVKVDVTRETTTQIMQVCEVFRASVIGMGQETM 120

Query: 120 IIEVTGDEDKVSAFIDLMRQYGIKELARTGKVAMVRGN 157
            +E+TGD  KV  FI ++R +GI+ LARTG VAM RG+
Sbjct: 121 TVEMTGDTQKVDGFIRMLRPFGIRSLARTGVVAMKRGD 158


Lambda     K      H
   0.319    0.137    0.365 

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: 81
Number of extensions: 5
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: 159
Length of database: 160
Length adjustment: 17
Effective length of query: 142
Effective length of database: 143
Effective search space:    20306
Effective search space used:    20306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 43 (21.2 bits)

Align candidate 8501909 DvMF_2624 (acetolactate synthase, small subunit (RefSeq))
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.21609.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.8e-42  130.0   5.5    4.2e-42  129.9   5.5    1.0  1  lcl|FitnessBrowser__Miya:8501909  DvMF_2624 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501909  DvMF_2624 acetolactate synthase, small subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   5.5   4.2e-42   4.2e-42       1     158 []       1     158 [.       1     158 [. 0.99

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 4.2e-42
                         TIGR00119   1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldlt 77 
                                       +kh+lsvlv+n++G+++  + +f+rrg    s+  +ete+ d+sr+ ++ve ++  +e i   l+ +  v  v+dl+
  lcl|FitnessBrowser__Miya:8501909   1 MKHTLSVLVKNRAGAVAEATDVFRRRGISFRSISCAETEDFDVSRLVLTVEDHEAELESIAEELRAQDVVAMVEDLS 77 
                                       79*****************************************************************9999****** PP

                         TIGR00119  78 eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlval 154
                                        ++ v+relvlvkv ++ e+ ++i+++ e+fr++v+ + +++++ve++g+ +k++ f+++l++fgi+ +ar+G+va+
  lcl|FitnessBrowser__Miya:8501909  78 RRDFVDRELVLVKVDVTRETTTQIMQVCEVFRASVIGMGQETMTVEMTGDTQKVDGFIRMLRPFGIRSLARTGVVAM 154
                                       ***************************************************************************** PP

                         TIGR00119 155 srge 158
                                        rg+
  lcl|FitnessBrowser__Miya:8501909 155 KRGD 158
                                       **85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (158 nodes)
Target sequences:                          1  (160 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 5.59
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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