Aligments for a candidate for argE in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Aligments for a candidate for argE in Pseudomonas simiae WCS417

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF5313 PS417_27200 acetylornithine deacetylase

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



>FitnessBrowser__WCS417:GFF5313
          Length = 382

 Score =  363 bits (933), Expect = e-105
 Identities = 191/379 (50%), Positives = 244/379 (64%), Gaps = 5/379 (1%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPV-PGTRNKFN 63
           LP   E + ALIA PS+S T+ +LDQ+N  +I LLA W  DLGF +++Q V PG   KFN
Sbjct: 3   LPSMKEQFAALIAAPSVSCTQASLDQTNRPVIDLLASWLGDLGFAIDIQQVSPG---KFN 59

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

Query: 124 LRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHI 183
           +  +     K+PL ILAT DEE+SM+GAR  AE        A+IGEPT L+P+R HKG +
Sbjct: 120 VLPLLDQTFKQPLLILATCDEESSMSGARALAEAGRPLGRAAVIGEPTGLKPIRLHKGVM 179

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

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

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

Query: 363 TRFIKPTRELITQVIHHFC 381
              + PT  L+ ++I H+C
Sbjct: 360 MSRLTPTVRLLRELIEHYC 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: 444
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: 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 GFF5313 PS417_27200 (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.3401.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-119  385.0   0.0     2e-119  384.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5313  PS417_27200 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5313  PS417_27200 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.8   0.0    2e-119    2e-119       3     365 .]      10     374 ..       8     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 384.8 bits;  conditional E-value: 2e-119
                           TIGR01892   3 lakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 
                                         +a+L+a +svs +      +n ++i++++++l +lg+a++ ++v  g  k+nlla+ G  +g gglvl+Gh+D+v
  lcl|FitnessBrowser__WCS417:GFF5313  10 FAALIAAPSVSCTqasldqTNRPVIDLLASWLGDLGFAIDIQQVSPG--KFNLLASFG--SGPGGLVLAGHSDTV 80 
                                         789********99999999***************************9..*********..999************ PP

                           TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146
                                         P+d a W +Dp++Lte dgr  g+G++DmkGF+al+++av  l  +  k+Pl ++++ Dee ++ Ga+ l+ea+ 
  lcl|FitnessBrowser__WCS417:GFF5313  81 PYDAALWKTDPLKLTEVDGRWVGLGSCDMKGFFALAIEAVLPLLDQTFKQPLLILATCDEESSMSGARALAEAGR 155
                                         ****************************************99999****************************** PP

                           TIGR01892 147 rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaFtp 221
                                         +  + a++GePt+l+++R hkG +  ++ + G++ghss+p  G sa e +++++++l +l+   +re+ +  F +
  lcl|FitnessBrowser__WCS417:GFF5313 156 PLGRAAVIGEPTGLKPIRLHKGVMMERIDILGQSGHSSDPSLGHSALEAMHDAIGELRGLRLGWQREYRNPQFSV 230
                                         *************************************************************************** PP

                           TIGR01892 222 pyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkveelsatpalelee 296
                                         p +t+n G ++GG+  n+i+++C l+++lRp+pGmdpe l a +++ +e++ e++  +     + +a p +e +e
  lcl|FitnessBrowser__WCS417:GFF5313 231 PQPTMNFGCIHGGDNPNRICGQCSLEFDLRPLPGMDPEVLRAAIRQKLEPLAERHQVKIDYAPLFPAVPPFEQPE 305
                                         ***************************************************8888777777788899999***** PP

                           TIGR01892 297 daelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                         d+elv+++e+l+G++ae+v++gtea++lq+lG+e++vlGPGdi  ahqp+eY+e++ l+++  ll++l+
  lcl|FitnessBrowser__WCS417:GFF5313 306 DTELVRVAERLTGHRAEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLEMSRLTPTVRLLRELI 374
                                         *************************************************************99999875 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: 11.42
//
[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:

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