GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pseudomonas simiae WCS417

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate GFF5313 PS417_27200 acetylornithine deacetylase

Query= SwissProt::P23908
         (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.31652.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: 10.05
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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