Alignments for a candidate for argE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Escherichia coli BW25113

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate 17996 b3957 acetylornithine deacetylase (NCBI)

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__Keio:17996
          Length = 383

 Score =  793 bits (2048), Expect = 0.0
 Identities = 383/383 (100%), Positives = 383/383 (100%)

Query: 1   MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN 60
           MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN
Sbjct: 1   MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN 60

Query: 61  KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI 120
           KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI
Sbjct: 61  KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI 120

Query: 121 LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK 180
           LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK
Sbjct: 121 LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK 180

Query: 181 GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN 240
           GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN
Sbjct: 181 GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN 240

Query: 241 LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP 300
           LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP
Sbjct: 241 LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP 300

Query: 301 PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360
           PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY
Sbjct: 301 PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360

Query: 361 LETRFIKPTRELITQVIHHFCWH 383
           LETRFIKPTRELITQVIHHFCWH
Sbjct: 361 LETRFIKPTRELITQVIHHFCWH 383


Lambda     K      H
   0.320    0.139    0.430 

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: 685
Number of extensions: 11
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: 383
Length of database: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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: 50 (23.9 bits)

Align candidate 17996 b3957 (acetylornithine deacetylase (NCBI))
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

# 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/TIGR01892.hmm
# target sequence database:        /tmp/gapView.29384.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01892  [M=365]
Accession:   TIGR01892
Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-178  579.7   0.0   1.3e-178  579.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:17996  b3957 acetylornithine deacetylas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17996  b3957 acetylornithine deacetylase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.6   0.0  1.3e-178  1.3e-178       1     365 []      10     377 ..      10     377 .. 1.00

  Alignments for each domain:
  == domain 1  score: 579.6 bits;  conditional E-value: 1.3e-178
                       TIGR01892   1 eilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 
                                     ei+++L+a++s+sa+      sn+dli++++d++++lg++vev+pv+++++k+n+la+iG  +gaggl+l+GhtD+vP+
  lcl|FitnessBrowser__Keio:17996  10 EIYRALIATPSISATeealdqSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIG--QGAGGLLLAGHTDTVPF 86 
                                     79**********************************************************..9**************** PP

                       TIGR01892  74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkliealarrpala 152
                                     d+++Wt+Dpf+Lte+dg+LYg+GtaDmkGF+a++L+a++d++++kLkkPl+++++aDee+++aGa++++e++a rp++a
  lcl|FitnessBrowser__Keio:17996  87 DDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCA 165
                                     ******************************************************************************* PP

                       TIGR01892 153 ivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFtppyatlniGtv 231
                                     i+GePtsl++vRahkG++s++++++G++ghss+p+rGv+aiel++++++++++l+d+lk+++++eaFt+py+tln+G++
  lcl|FitnessBrowser__Keio:17996 166 IIGEPTSLQPVRAHKGHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHI 244
                                     ******************************************************************************* PP

                       TIGR01892 232 kGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelvalleklaGa 310
                                     +GG+a+n+i+a+Cel++++Rp+pGm+++el++ll++++++v+e++pg+ +++e+++++p++e++++++lv+++ekl+Ga
  lcl|FitnessBrowser__Keio:17996 245 HGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPGYECPPNHQLVEVVEKLLGA 323
                                     ******************************************************************************* PP

                       TIGR01892 311 aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                     ++evv+y+tea+++q+l ++++vlGPG+i+qahqpdeY+e++++k++r+l+++++
  lcl|FitnessBrowser__Keio:17996 324 KTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLETRFIKPTRELITQVI 377
                                     *****************.**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (383 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: 00:00:00.01
# Mc/sec: 10.64
//
[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