Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E2

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_4496 Acetylornithine deacetylase (EC 3.5.1.16)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496
          Length = 385

 Score =  363 bits (933), Expect = e-105
 Identities = 190/379 (50%), Positives = 247/379 (65%), 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   LPSMKDQFAALIAAPSVSCTQPGLDQSNSAVIELLAGWLGDLGFSCDIQQVSPG---KFN 59

Query: 64  MLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDA 123
           +LAS G G GGL+LAGH+DTVPFD   W  DP  LTE DG+  GLG+ DMKGFFA +++A
Sbjct: 60  LLASFGSGPGGLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALVIEA 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   +  +    FTVP PTLN G 
Sbjct: 180 MERIDILGRSGHSSDPSLGHSALEAMHDAMGELRGLRLRWQREFRNPQFTVPQPTLNFGC 239

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

Query: 304 GYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLE 362
            +E   + +LV V E+L G + E V + TEAP++Q L C TLVLGPG I  AHQP EYLE
Sbjct: 300 PFEQAEDCELVRVAERLTGHRAEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLE 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: 479
Number of extensions: 15
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 Pf6N2E2_4496 (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.6547.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.2e-122  394.0   0.0   3.6e-122  393.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.9   0.0  3.6e-122  3.6e-122       3     365 .]      10     374 ..       8     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 393.9 bits;  conditional E-value: 3.6e-122
                                      TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegag 60 
                                                    +a+L+a +svs +      sn ++ie+++++l +lg++ + ++v  g  k+nlla+ G  +g g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496  10 FAALIAAPSVSCTqpgldqSNSAVIELLAGWLGDLGFSCDIQQVSPG--KFNLLASFG--SGPG 69 
                                                    789*********99********************************9..*********..999* PP

                                      TIGR01892  61 glvlsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlh 124
                                                    glvl+Gh+D+vP+d+a W +Dp++Lte dgr  g+G++DmkGF+alv++av+ l  ++ k+Pl 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496  70 GLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALVIEAVKPLLDQPFKQPLL 133
                                                    **************************************************************** PP

                                      TIGR01892 125 lvlsaDeevglaGakkliealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdr 188
                                                    ++++ Dee ++aGa+ l++a+ +  + a++GePt+l+++R hkG +  ++ + Gr+ghss+p  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496 134 ILATCDEESSMAGARALADAGRPLGRAAVIGEPTGLRPIRLHKGVMMERIDILGRSGHSSDPSL 197
                                                    **************************************************************** PP

                                      TIGR01892 189 GvsaielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRp 252
                                                    G sa e +++++++l +l+ + +re  +  Ft+p +tln G ++GG+  n+i+++C ++++lRp
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496 198 GHSALEAMHDAMGELRGLRLRWQREFRNPQFTVPQPTLNFGCIHGGDNPNRICGQCSMEFDLRP 261
                                                    **************************************************************** PP

                                      TIGR01892 253 ipGmdpeellallekiaeevkekapgfevkveelsatpaleleedaelvalleklaGaaaevvs 316
                                                    +pGmdp+ l a +++ ++++ e++  +     + +  p +e  ed elv+++e+l+G++ae+v+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496 262 LPGMDPQVLRAAIQQKLDPIAERHKVKIDYAPLFPEVPPFEQAEDCELVRVAERLTGHRAEAVA 325
                                                    ********************88888887888899999*************************** PP

                                      TIGR01892 317 ygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                                    +gtea++lq+lG+e++vlGPGdi  ahqp+eY+e++ l+++ +ll++l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4496 326 FGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLEMSRLQPTVQLLRQLI 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.04
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for Amino acid biosynthesis