Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E3

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate AO353_08690 AO353_08690 acetylornithine deacetylase

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08690
          Length = 382

 Score =  362 bits (930), Expect = e-105
 Identities = 193/379 (50%), Positives = 243/379 (64%), Gaps = 5/379 (1%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPV-PGTRNKFN 63
           LP   + + ALIA PS+S T+ +LDQSN  +I LLA W  DLGF+ ++Q V PG   KFN
Sbjct: 3   LPSMKDQFAALIAAPSVSCTQPSLDQSNRAVIDLLATWLGDLGFSCDIQQVSPG---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 VLPLLDKPFKQPLMILATCDEESSMAGARALAAAGRPLGRVAVIGEPTGLKPIRMHKGVM 179

Query: 184 SNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGH 243
              I I GQSGHSSDP  G +A+E MHDA+G +  LR   +  +H   F+VP PTLN G 
Sbjct: 180 MERIDILGQSGHSSDPRLGHSALEAMHDAMGELRGLRLQWQREFHNPQFSVPQPTLNFGC 239

Query: 244 IHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIP 303
           IHGGD  NRIC  C L  D+RPLPGM  N L   +   L PV+E    ++    L P +P
Sbjct: 240 IHGGDNPNRICGQCSLEFDLRPLPGMDPNALRAAIRQKLEPVAELHQVKIDYAPLFPEVP 299

Query: 304 GYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLE 362
            +E   + +LV+V E+L G   E V + TEAP++Q L C TLVLGPG I  AHQP EYLE
Sbjct: 300 PFEQAADSELVQVAERLTGHLAEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLE 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: 461
Number of extensions: 18
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 AO353_08690 AO353_08690 (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.2462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.5e-121  391.8   0.0   1.7e-121  391.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690  AO353_08690 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690  AO353_08690 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.7   0.0  1.7e-121  1.7e-121       3     365 .]      10     374 ..       8     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 391.7 bits;  conditional E-value: 1.7e-121
                                     TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagg 61 
                                                   +a+L+a +svs +      sn ++i++++ +l +lg++ + ++v  g  k+nlla+ G  +g gg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690  10 FAALIAAPSVSCTqpsldqSNRAVIDLLATWLGDLGFSCDIQQVSPG--KFNLLASFG--SGPGG 70 
                                                   789*********9999******************************9..*********..999** PP

                                     TIGR01892  62 lvlsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlv 126
                                                   lvl+Gh+D+vP+d+a W +Dp++Lte dgr  g+G++DmkGF+al+++av  l  ++ k+Pl+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690  71 LVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALAIEAVLPLLDKPFKQPLMIL 135
                                                   ***************************************************************** PP

                                     TIGR01892 127 lsaDeevglaGakkliealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvs 191
                                                   ++ Dee ++aGa+ l++a+ +  ++a++GePt+l+++R hkG +  ++ + G++ghss+p  G s
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690 136 ATCDEESSMAGARALAAAGRPLGRVAVIGEPTGLKPIRMHKGVMMERIDILGQSGHSSDPRLGHS 200
                                                   ***************************************************************** PP

                                     TIGR01892 192 aielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGm 256
                                                   a e +++++++l +l+ + +re ++  F +p +tln G ++GG+  n+i+++C l+++lRp+pGm
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690 201 ALEAMHDAMGELRGLRLQWQREFHNPQFSVPQPTLNFGCIHGGDNPNRICGQCSLEFDLRPLPGM 265
                                                   ***************************************************************** PP

                                     TIGR01892 257 dpeellallekiaeevkekapgfevkveelsatpaleleedaelvalleklaGaaaevvsygtea 321
                                                   dp++l a +++ +e+v e +  +     + +  p +e  +d+elv+++e+l+G+ ae+v++gtea
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690 266 DPNALRAAIRQKLEPVAELHQVKIDYAPLFPEVPPFEQAADSELVQVAERLTGHLAEAVAFGTEA 330
                                                   ***************9665555555566788999******************************* PP

                                     TIGR01892 322 gllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                                   ++lq+lG+e++vlGPGdi  ahqp+eY+e++ l+++  ll++l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08690 331 PYLQRLGCETLVLGPGDIACAHQPGEYLEMSRLQPTVHLLRQLI 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.33
//
[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