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.29253.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: 11.95
//
[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:

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:

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