GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate Echvi_1810 Echvi_1810 3-dehydroquinate dehydratase, type II

Query= SwissProt::P43877
         (154 letters)



>lcl|FitnessBrowser__Cola:Echvi_1810 Echvi_1810 3-dehydroquinate
           dehydratase, type II
          Length = 139

 Score =  135 bits (340), Expect = 3e-37
 Identities = 65/136 (47%), Positives = 91/136 (66%), Gaps = 2/136 (1%)

Query: 3   KILLLNGPNLNMLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINRIH 62
           KIL++NGPNLN+LGKREP IYGS++  D    L+ +       L Y+Q+N E  L+N+IH
Sbjct: 2   KILIINGPNLNLLGKREPEIYGSKSFEDFFGELETTFS--NISLSYYQSNVEGELVNKIH 59

Query: 63  QAFQNTDFIIINPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDVAKG 122
           +     D I++N GA+THTSVAI DA+  V+ P +E+H+SN++ RE FRH S +S    G
Sbjct: 60  EVGFTYDAILLNAGAYTHTSVAISDAIAGVTTPVMEIHISNIYKRETFRHKSIISKECIG 119

Query: 123 VICGLGAKGYDYALDF 138
           +I GLG KGY   + +
Sbjct: 120 MIAGLGLKGYALGIQY 135


Lambda     K      H
   0.320    0.137    0.395 

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: 86
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: 154
Length of database: 139
Length adjustment: 16
Effective length of query: 138
Effective length of database: 123
Effective search space:    16974
Effective search space used:    16974
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: 42 (20.8 bits)

Align candidate Echvi_1810 Echvi_1810 (3-dehydroquinate dehydratase, type II)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

# 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/TIGR01088.hmm
# target sequence database:        /tmp/gapView.6649.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01088  [M=141]
Accession:   TIGR01088
Description: aroQ: 3-dehydroquinate dehydratase, type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    1.4e-57  179.4   0.1    1.5e-57  179.3   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1810  Echvi_1810 3-dehydroquinate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1810  Echvi_1810 3-dehydroquinate dehydratase, type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.1   1.5e-57   1.5e-57       1     139 [.       2     138 ..       2     139 .] 0.97

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 1.5e-57
                            TIGR01088   1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgivinpa 74 
                                          kil++nGPnlnlLGkrep++yGs ++e+    le++    +++++++qsn egel++kihe+  ++d+i++n++
  lcl|FitnessBrowser__Cola:Echvi_1810   2 KILIINGPNLNLLGKREPEIYGSKSFEDFFGELETTF--SNISLSYYQSNVEGELVNKIHEVGFTYDAILLNAG 73 
                                          79***************************99998765..689******************************** PP

                            TIGR01088  75 althtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealve 139
                                          a+thtsva+ Da+a v+ Pv+e+h+sn+++re fr+ks++++ + G+i GlG+kgy l++++ +e
  lcl|FitnessBrowser__Cola:Echvi_1810  74 AYTHTSVAISDAIAGVTTPVMEIHISNIYKRETFRHKSIISKECIGMIAGLGLKGYALGIQYFLE 138
                                          ************************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (139 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: 3.50
//
[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