Alignments for a candidate for argE in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Marinobacter adhaerens HP15

Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate GFF3373 HP15_3315 acetylornithine deacetylase (ArgE)

Query= SwissProt::P23908
         (383 letters)



>FitnessBrowser__Marino:GFF3373
          Length = 389

 Score =  372 bits (955), Expect = e-108
 Identities = 189/378 (50%), Positives = 249/378 (65%), Gaps = 1/378 (0%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNM 64
           +P   ++   LI+ PSIS+     D SN  ++  LA+W + LGF+VE+  VPG   KFN+
Sbjct: 11  VPGIRDMLARLISLPSISSASAKWDHSNEPVVRTLAEWLEALGFSVEILEVPGMPGKFNL 70

Query: 65  LASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDAL 124
           + ++G G GGL+L+GHTDTVPFDD RW  DPFTLTE D + YGLGT DMKGFF   ++A 
Sbjct: 71  IGTLGSGPGGLVLSGHTDTVPFDDKRWQSDPFTLTERDNRWYGLGTCDMKGFFPLAIEAA 130

Query: 125 RDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHIS 184
           R      LK+PL ILATADEE+SM GAR  AE    +   A+IGEPTSL+PVR HKG + 
Sbjct: 131 RAFVDEDLKQPLIILATADEESSMDGARALAEAGKPKARYAVIGEPTSLKPVRMHKGIMM 190

Query: 185 NAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHI 244
             ++ +GQSGHSS+PA G NA+E MH+A+  +L LR   +E+Y    F V +PTLNLG I
Sbjct: 191 ERLKFEGQSGHSSNPALGRNAMEGMHEALTELLALRSGWQEKYRNPNFEVQFPTLNLGCI 250

Query: 245 HGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPG 304
           HGGD  NRICA CELH D+RPLPGM +  L   +   + P+++R    L  + L   +P 
Sbjct: 251 HGGDNPNRICAQCELHFDLRPLPGMNMETLRQAILSKVQPIADRRELSLEFEPLFDGVPP 310

Query: 305 YECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLET 363
           +E P +  LV+  EKL G     V + TEAP++Q L   TLV+GPGSI+QAHQPDE++E 
Sbjct: 311 FETPADAALVKACEKLTGHTAHAVAFATEAPWLQKLGLETLVMGPGSIDQAHQPDEFIEL 370

Query: 364 RFIKPTRELITQVIHHFC 381
             I PT +++  +I  FC
Sbjct: 371 SQIDPTVKVLRGLIRQFC 388


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: 440
Number of extensions: 12
Number of successful extensions: 2
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: 389
Length adjustment: 30
Effective length of query: 353
Effective length of database: 359
Effective search space:   126727
Effective search space used:   126727
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 GFF3373 HP15_3315 (acetylornithine deacetylase (ArgE))
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.18259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-126  407.9   0.0   2.3e-126  407.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3373  HP15_3315 acetylornithine deacet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3373  HP15_3315 acetylornithine deacetylase (ArgE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.7   0.0  2.3e-126  2.3e-126       1     364 [.      16     383 ..      16     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 407.7 bits;  conditional E-value: 2.3e-126
                           TIGR01892   1 eilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                         ++la+L++++s+s        sn +++  ++++le+lg++ve l+v++   k+nl+ + G  +g gglvlsGhtD
  lcl|FitnessBrowser__Marino:GFF3373  16 DMLARLISLPSISSAsakwdhSNEPVVRTLAEWLEALGFSVEILEVPGMPGKFNLIGTLG--SGPGGLVLSGHTD 88 
                                         57999*******998899999***************************************..999********** PP

                           TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkliea 144
                                         +vP+d+++W sDpf+Lte+d+r Yg+Gt+DmkGF+ l+++a++    ++Lk+Pl ++++aDee ++ Ga+ l+ea
  lcl|FitnessBrowser__Marino:GFF3373  89 TVPFDDKRWQSDPFTLTERDNRWYGLGTCDMKGFFPLAIEAARAFVDEDLKQPLIILATADEESSMDGARALAEA 163
                                         *************************************************************************** PP

                           TIGR01892 145 larrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkredleeaF 219
                                         + ++++ a++GePtsl++vR hkG++  +++ +G++ghss+p+ G +a+e ++++l++l+al+   ++++ +  F
  lcl|FitnessBrowser__Marino:GFF3373 164 GKPKARYAVIGEPTSLKPVRMHKGIMMERLKFEGQSGHSSNPALGRNAMEGMHEALTELLALRSGWQEKYRNPNF 238
                                         *************************************************************************** PP

                           TIGR01892 220 tppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapgfevkve.elsatpale 293
                                         +++++tln+G ++GG+  n+i+a+Cel+++lRp+pGm++e l + + +  +++  +  +   + e +    p +e
  lcl|FitnessBrowser__Marino:GFF3373 239 EVQFPTLNLGCIHGGDNPNRICAQCELHFDLRPLPGMNMETLRQAILSKVQPIA-DRRELSLEFEpLFDGVPPFE 312
                                         *********************************************999999984.4444445544167889**** PP

                           TIGR01892 294 leedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                         +++da lv+  ekl+G++a++v+++tea+ lq+lG+e++v+GPG+idqahqpde++e++++ ++ ++l+ l
  lcl|FitnessBrowser__Marino:GFF3373 313 TPADAALVKACEKLTGHTAHAVAFATEAPWLQKLGLETLVMGPGSIDQAHQPDEFIELSQIDPTVKVLRGL 383
                                         ****************************************************************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (389 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.24
//
[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