Alignments for a candidate for aroD in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroD in Escherichia coli BW25113

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 15812 b1693 3-dehydroquinate dehydratase (NCBI)

Query= BRENDA::P05194
         (252 letters)



>FitnessBrowser__Keio:15812
          Length = 252

 Score =  481 bits (1239), Expect = e-141
 Identities = 252/252 (100%), Positives = 252/252 (100%)

Query: 1   MKTVTVKDLVIGTGAPKIIVSLMAKDIASVKSEALAYREADFDILEWRVDHYADLSNVES 60
           MKTVTVKDLVIGTGAPKIIVSLMAKDIASVKSEALAYREADFDILEWRVDHYADLSNVES
Sbjct: 1   MKTVTVKDLVIGTGAPKIIVSLMAKDIASVKSEALAYREADFDILEWRVDHYADLSNVES 60

Query: 61  VMAAAKILRETMPEKPLLFTFRSAKEGGEQAISTEAYIALNRAAIDSGLVDMIDLELFTG 120
           VMAAAKILRETMPEKPLLFTFRSAKEGGEQAISTEAYIALNRAAIDSGLVDMIDLELFTG
Sbjct: 61  VMAAAKILRETMPEKPLLFTFRSAKEGGEQAISTEAYIALNRAAIDSGLVDMIDLELFTG 120

Query: 121 DDQVKETVAYAHAHDVKVVMSNHDFHKTPEAEEIIARLRKMQSFDADIPKIALMPQSTSD 180
           DDQVKETVAYAHAHDVKVVMSNHDFHKTPEAEEIIARLRKMQSFDADIPKIALMPQSTSD
Sbjct: 121 DDQVKETVAYAHAHDVKVVMSNHDFHKTPEAEEIIARLRKMQSFDADIPKIALMPQSTSD 180

Query: 181 VLTLLAATLEMQEQYADRPIITMSMAKTGVISRLAGEVFGSAATFGAVKKASAPGQISVN 240
           VLTLLAATLEMQEQYADRPIITMSMAKTGVISRLAGEVFGSAATFGAVKKASAPGQISVN
Sbjct: 181 VLTLLAATLEMQEQYADRPIITMSMAKTGVISRLAGEVFGSAATFGAVKKASAPGQISVN 240

Query: 241 DLRTVLTILHQA 252
           DLRTVLTILHQA
Sbjct: 241 DLRTVLTILHQA 252


Lambda     K      H
   0.317    0.130    0.351 

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: 360
Number of extensions: 3
Number of successful extensions: 1
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: 252
Length of database: 252
Length adjustment: 24
Effective length of query: 228
Effective length of database: 228
Effective search space:    51984
Effective search space used:    51984
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: 46 (22.3 bits)

Align candidate 15812 b1693 (3-dehydroquinate dehydratase (NCBI))
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (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/TIGR01093.hmm
# target sequence database:        /tmp/gapView.11220.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01093  [M=229]
Accession:   TIGR01093
Description: aroD: 3-dehydroquinate dehydratase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
      2e-91  292.2   0.8    2.3e-91  292.0   0.8    1.0  1  lcl|FitnessBrowser__Keio:15812  b1693 3-dehydroquinate dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15812  b1693 3-dehydroquinate dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.0   0.8   2.3e-91   2.3e-91       1     228 [.      17     245 ..      17     246 .. 0.99

  Alignments for each domain:
  == domain 1  score: 292.0 bits;  conditional E-value: 2.3e-91
                       TIGR01093   1 kilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkfkgdee 79 
                                     ki+v+l+akd++ +++e+ +++e ++Di+E+RvD+++d+s+ +sv+a+a+ l+e+++++pl++T+R++keGG+++ ++e
  lcl|FitnessBrowser__Keio:15812  17 KIIVSLMAKDIASVKSEALAYREADFDILEWRVDHYADLSNVESVMAAAKILRETMPEKPLLFTFRSAKEGGEQAISTE 95 
                                     69***************************************************************************** PP

                       TIGR01093  80 erleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverlekaqsldaDivKiavm 158
                                     ++++++++ai+++lvd++D+El++ +++vke++++a+++++k+++SnHdf+ktp++ee+++rl+k+qs+daDi+Kia m
  lcl|FitnessBrowser__Keio:15812  96 AYIALNRAAIDSGLVDMIDLELFTGDDQVKETVAYAHAHDVKVVMSNHDFHKTPEAEEIIARLRKMQSFDADIPKIALM 174
                                     ******************************************************************************* PP

                       TIGR01093 159 aksieDvltLleitlkveeek.dkplialsMgekGkisRvlgavlgsvltfgslgkasAPGQisvkelrel 228
                                     ++s++DvltLl++tl+++e++ d+p+i++sM+++G isR++g+v+gs++tfg+++kasAPGQisv++lr +
  lcl|FitnessBrowser__Keio:15812 175 PQSTSDVLTLLAATLEMQEQYaDRPIITMSMAKTGVISRLAGEVFGSAATFGAVKKASAPGQISVNDLRTV 245
                                     ********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (252 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: 6.94
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis