GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argE in Pseudomonas fluorescens FW300-N2C3

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_13080 AO356_13080 acetylornithine deacetylase

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080 AO356_13080
           acetylornithine deacetylase
          Length = 385

 Score =  362 bits (930), Expect = e-105
 Identities = 190/379 (50%), Positives = 247/379 (65%), Gaps = 5/379 (1%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPV-PGTRNKFN 63
           LP   + + ALIATPS+S T+  LDQSN+ +I LLA W  +LGF+ +VQ V PG   KFN
Sbjct: 3   LPSMKDQFAALIATPSVSCTQPGLDQSNSAVIELLAGWLTELGFSCDVQQVSPG---KFN 59

Query: 64  MLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDA 123
           +LAS G G GGL+LAGH+DTVPFD   W  DP  LTE DG+  GLG+ DMKGFFA  ++A
Sbjct: 60  LLASFGSGPGGLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALAIEA 119

Query: 124 LRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHI 183
           ++ +     K+PL ILAT DEE+SMAGAR  A+        A+IGEPT L+P+R HKG +
Sbjct: 120 VKPLLDQPFKQPLLILATCDEESSMAGARALADAGRPLGRAAVIGEPTGLRPIRLHKGVM 179

Query: 184 SNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGH 243
              I I G+SGHSSDP+ G +A+E MHDA+G +  LR   +  +    F+VP PTLN G 
Sbjct: 180 MERIDILGRSGHSSDPSLGRSALEAMHDAMGELRGLRLQWQREFRNPQFSVPQPTLNFGC 239

Query: 244 IHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIP 303
           IHGGD  NRIC  C +  D+RPLPGM    L   +   L P++ER   ++    L P +P
Sbjct: 240 IHGGDNPNRICGQCSMEFDLRPLPGMDPQVLRAAIRQKLEPIAERHQVKIDYAPLFPEVP 299

Query: 304 GYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLE 362
            +E   + +LV V E+L G + E V + TEAP++Q L C TLVLGPG I  AHQP EYLE
Sbjct: 300 PFEQAEDAELVRVAERLTGHRAEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLE 359

Query: 363 TRFIKPTRELITQVIHHFC 381
              ++PT +L+ Q+I H+C
Sbjct: 360 MSRLQPTVQLLRQLIGHYC 378


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: 471
Number of extensions: 16
Number of successful extensions: 3
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: 385
Length adjustment: 30
Effective length of query: 353
Effective length of database: 355
Effective search space:   125315
Effective search space used:   125315
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 AO356_13080 AO356_13080 (acetylornithine deacetylase)
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.18840.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.7e-123  397.5   0.0   3.1e-123  397.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080  AO356_13080 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080  AO356_13080 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.4   0.0  3.1e-123  3.1e-123       3     365 .]      10     374 ..       8     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 397.4 bits;  conditional E-value: 3.1e-123
                                       TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkega 59 
                                                     +a+L+a++svs +      sn ++ie+++++l elg++ +v++v  g  k+nlla+ G  +g 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080  10 FAALIATPSVSCTqpgldqSNSAVIELLAGWLTELGFSCDVQQVSPG--KFNLLASFG--SGP 68 
                                                     789*********99********************************9..*********..999 PP

                                       TIGR01892  60 gglvlsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkP 122
                                                     gglvl+Gh+D+vP+d+a W +Dp++Lte dgr  g+G++DmkGF+al+++av+ l  ++ k+P
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080  69 GGLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALAIEAVKPLLDQPFKQP 131
                                                     *************************************************************** PP

                                       TIGR01892 123 lhlvlsaDeevglaGakkliealarrpalaivGePtslvavRahkGkasakvtvrGreghssr 185
                                                     l ++++ Dee ++aGa+ l++a+ +  + a++GePt+l+++R hkG +  ++ + Gr+ghss+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080 132 LLILATCDEESSMAGARALADAGRPLGRAAVIGEPTGLRPIRLHKGVMMERIDILGRSGHSSD 194
                                                     *************************************************************** PP

                                       TIGR01892 186 pdrGvsaielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvl 248
                                                     p  G sa e +++++++l +l+ + +re  +  F +p +tln G ++GG+  n+i+++C +++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080 195 PSLGRSALEAMHDAMGELRGLRLQWQREFRNPQFSVPQPTLNFGCIHGGDNPNRICGQCSMEF 257
                                                     *************************************************************** PP

                                       TIGR01892 249 elRpipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelvalleklaGaa 311
                                                     +lRp+pGmdp+ l a +++ +e++ e++  +     + +  p +e  edaelv+++e+l+G++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080 258 DLRPLPGMDPQVLRAAIRQKLEPIAERHQVKIDYAPLFPEVPPFEQAEDAELVRVAERLTGHR 320
                                                     ************************88888777788889999********************** PP

                                       TIGR01892 312 aevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                                     ae+v++gtea++lq+lG+e++vlGPGdi  ahqp+eY+e++ l+++ +ll++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13080 321 AEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLEMSRLQPTVQLLRQLI 374
                                                     **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (385 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.08
//
[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