GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroD in Shewanella sp. ANA-3

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate 7023277 Shewana3_0511 3-dehydroquinate dehydratase (RefSeq)

Query= SwissProt::P43877
         (154 letters)



>lcl|FitnessBrowser__ANA3:7023277 Shewana3_0511 3-dehydroquinate
           dehydratase (RefSeq)
          Length = 144

 Score =  189 bits (480), Expect = 2e-53
 Identities = 94/142 (66%), Positives = 110/142 (77%), Gaps = 2/142 (1%)

Query: 3   KILLLNGPNLNMLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINRIH 62
           K+LL+NGPNLN+LG+REP +YG QTL+DI   L + AQA G EL++ Q+N E  LIN IH
Sbjct: 4   KVLLINGPNLNLLGRREPSVYGHQTLADIVALLSEQAQAAGVELEHIQSNAEFELINAIH 63

Query: 63  QAFQNTDFIIINPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDVAKG 122
               +   IIINP AFTHTSVA+RDALL V IPF EVHLSNVHAREPFRHHSYLSD A G
Sbjct: 64  AT--DAQMIIINPAAFTHTSVALRDALLGVDIPFFEVHLSNVHAREPFRHHSYLSDKAIG 121

Query: 123 VICGLGAKGYDYALDFAISELQ 144
           VICG GA+GY++AL  AI  L+
Sbjct: 122 VICGFGAQGYEFALAAAIKRLK 143


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: 113
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: 154
Length of database: 144
Length adjustment: 16
Effective length of query: 138
Effective length of database: 128
Effective search space:    17664
Effective search space used:    17664
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 7023277 Shewana3_0511 (3-dehydroquinate dehydratase (RefSeq))
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.22823.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.6e-63  198.7   0.2    1.8e-63  198.5   0.2    1.0  1  lcl|FitnessBrowser__ANA3:7023277  Shewana3_0511 3-dehydroquinate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023277  Shewana3_0511 3-dehydroquinate dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.2   1.8e-63   1.8e-63       1     140 [.       4     141 ..       4     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 1.8e-63
                         TIGR01088   1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgivinpaalt 77 
                                       k+l++nGPnlnlLG+rep+vyG++tl +i++ll+e+a++++ve+e++qsn e eli++ih +   ++ i+inpaa+t
  lcl|FitnessBrowser__ANA3:7023277   4 KVLLINGPNLNLLGRREPSVYGHQTLADIVALLSEQAQAAGVELEHIQSNAEFELINAIHATD--AQMIIINPAAFT 78 
                                       699*********************************************************988..789********* PP

                         TIGR01088  78 htsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealvea 140
                                       htsvalrDal+ v +P+ evhlsnvhare+fr++s+l++ a Gvi+G+Ga+gy++al a+++ 
  lcl|FitnessBrowser__ANA3:7023277  79 HTSVALRDALLGVDIPFFEVHLSNVHAREPFRHHSYLSDKAIGVICGFGAQGYEFALAAAIKR 141
                                       *********************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (141 nodes)
Target sequences:                          1  (144 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 3.73
//
[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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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