GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argE in Pseudomonas fluorescens GW456-L13

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate PfGW456L13_912 Acetylornithine deacetylase (EC 3.5.1.16)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912
           Acetylornithine deacetylase (EC 3.5.1.16)
          Length = 382

 Score =  355 bits (911), Expect = e-102
 Identities = 191/379 (50%), Positives = 240/379 (63%), Gaps = 5/379 (1%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPV-PGTRNKFN 63
           LP   E + ALIA PS+S T+ +LDQ+N  +I LLA W  +LGF  ++Q V PG   KFN
Sbjct: 3   LPSMKEQFAALIAAPSVSCTQPSLDQTNRPVIDLLATWLGELGFTCDIQQVSPG---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+SM+GAR  AE        A+IGEPT L+P+R HKG +
Sbjct: 120 VIPLLDQPFKQPLLILATCDEESSMSGARALAEAGRPLGRAAVIGEPTGLKPIRMHKGIM 179

Query: 184 SNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGH 243
              I I GQSGHSSDP  G +A+E MHDAIG +  LR   +  +    F VP PT+N G 
Sbjct: 180 MERIDILGQSGHSSDPRLGHSALEAMHDAIGELRGLRLLWQREFRNPQFGVPTPTMNFGC 239

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

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

Query: 363 TRFIKPTRELITQVIHHFC 381
              ++PT  L+ Q+I H+C
Sbjct: 360 MSRLQPTVHLLRQLIEHYC 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: 457
Number of extensions: 17
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: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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 PfGW456L13_912 (Acetylornithine deacetylase (EC 3.5.1.16))
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.27587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   3.6e-119  384.0   0.0   4.1e-119  383.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.8   0.0  4.1e-119  4.1e-119       3     365 .]      10     374 ..       8     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.8 bits;  conditional E-value: 4.1e-119
                                              TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllav 52 
                                                            +a+L+a +svs +      +n ++i++++ +l elg++ + ++v  g  k+nlla+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912  10 FAALIAAPSVSCTqpsldqTNRPVIDLLATWLGELGFTCDIQQVSPG--KFNLLAS 63 
                                                            789*********99999999**************************9..******* PP

                                              TIGR01892  53 iGpkegagglvlsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvL 108
                                                             G  +g gglvl+Gh+D+vP+d+a W +Dp++Lte dgr  g+G++DmkGF+al++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912  64 FG--SGPGGLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALAI 117
                                                            **..999************************************************* PP

                                              TIGR01892 109 aavpdlaaakLkkPlhlvlsaDeevglaGakkliealarrpalaivGePtslvavR 164
                                                            +av  l  ++ k+Pl ++++ Dee ++ Ga+ l+ea+ +  + a++GePt+l+++R
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912 118 EAVIPLLDQPFKQPLLILATCDEESSMSGARALAEAGRPLGRAAVIGEPTGLKPIR 173
                                                            ******************************************************** PP

                                              TIGR01892 165 ahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFt 220
                                                             hkG++  ++ + G++ghss+p  G sa e +++++++l +l+   +re  +  F 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912 174 MHKGIMMERIDILGQSGHSSDPRLGHSALEAMHDAIGELRGLRLLWQREFRNPQFG 229
                                                            ******************************************************** PP

                                              TIGR01892 221 ppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkeka 276
                                                            +p +t+n G ++GG+  n+i+++C l+++lRp+pGmdp+ l a++ + +++v e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912 230 VPTPTMNFGCIHGGDNPNRICGQCSLEFDLRPLPGMDPKVLRAEILQKLKPVAERH 285
                                                            ***************************************************98888 PP

                                              TIGR01892 277 pgfevkveelsatpaleleedaelvalleklaGaaaevvsygteagllqelGieav 332
                                                              +     + +  p +e  edaelv+++ekl+G++ae+v++gtea++lq+lG+e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912 286 QVKIDYAPLFPEVPPFEQAEDAELVRIAEKLTGHSAEAVAFGTEAPYLQRLGCETL 341
                                                            7777778889999******************************************* PP

                                              TIGR01892 333 vlGPGdidqahqpdeYveieelkrcrallerlv 365
                                                            vlGPGdi  ahqp+eY+e++ l+++  ll++l+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_912 342 VLGPGDIACAHQPGEYLEMSRLQPTVHLLRQLI 374
                                                            *****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (382 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: 8.74
//
[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