Alignments for a candidate for argE in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Halomonas desiderata SP1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_086511020.1 BZY95_RS16665 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_002151265.1:WP_086511020.1
          Length = 383

 Score =  275 bits (704), Expect = 1e-78
 Identities = 160/385 (41%), Positives = 221/385 (57%), Gaps = 19/385 (4%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           M AAE+L +LVGF +V    N D+++++ GYL+ HG+    +   +G ++N+ A IGP  
Sbjct: 1   MTAAEMLERLVGFATVSRDSNLDLIAFVEGYLDEHGVKHWRVESDDGRKANLLARIGPDV 60

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEAD-RLYGRGTTDMKGFLAAVLAAVPKLAAM 119
             G ++SGH DVVP     W++DPF L  + D +LYGRGT DMKGF+A  LA +P+    
Sbjct: 61  EGGVVLSGHTDVVPVDGQPWSTDPFTLIDKGDGKLYGRGTCDMKGFIACALAELPEWLKR 120

Query: 120 PLRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARL 179
            L +P++LALSYDEE GC G P MI RL     +P   I+GEPT M+ + AHKG    R 
Sbjct: 121 GLDKPIYLALSYDEEVGCIGAPRMIERLMADHPRPTAVIVGEPTLMQPVVAHKGATNLRT 180

Query: 180 TVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKG 238
           TV GR+ HSS+ DQG++AIH  A ++T+       L   G  +  F   +SSL +G + G
Sbjct: 181 TVTGRASHSSQVDQGVSAIHVAARLVTKIEDVMSELRAEGRVDEAFNVAHSSLHVGKIAG 240

Query: 239 GQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELS-------- 290
           G A+NI+   C  E+E R +      EL   V   A  L     E E Q  +        
Sbjct: 241 GTAINIMARECTFEWEIRHLPSDRFEELFERVNAFAAEL-----EAEMQRRAPETSIVTE 295

Query: 291 ----AYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRA 346
                 PAL+ + +A +  L  EL G +   AV+Y TEAG FQR G+  +ICGPG I +A
Sbjct: 296 ALNLTVPALADDNNAEVLDLCRELLGEQPSGAVAYATEAGQFQRVGLPTVICGPGSIRQA 355

Query: 347 HKPDEYILIDELMACRAMVEALGAR 371
           H+PDEYI I++L A    ++ALG R
Sbjct: 356 HQPDEYIEIEQLAAGTRFMQALGRR 380


Lambda     K      H
   0.319    0.137    0.410 

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: 395
Number of extensions: 15
Number of successful extensions: 4
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: 374
Length of database: 383
Length adjustment: 30
Effective length of query: 344
Effective length of database: 353
Effective search space:   121432
Effective search space used:   121432
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_086511020.1 BZY95_RS16665 (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.6492.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-132  428.1   0.1   1.6e-132  427.9   0.1    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511020.1  BZY95_RS16665 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511020.1  BZY95_RS16665 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.9   0.1  1.6e-132  1.6e-132       1     364 [.       5     377 ..       5     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.9 bits;  conditional E-value: 1.6e-132
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               e+l++Lv+f +vs+ sn+dli +ve+yl+e+gv+  +++  dg  k nlla iGp + +gg+vlsGhtD
  lcl|NCBI__GCF_002151265.1:WP_086511020.1   5 EMLERLVGFATVSRDSNLDLIAFVEGYLDEHGVKHWRVESDDG-RKANLLARIGPDV-EGGVVLSGHTD 71 
                                               6799************************************999.9***********9.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtek.dgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaG 137
                                               vvPvd+++W++Dpf+L +k dg+LYgrGt+DmkGF+a++La +p+  +  L kP++l+ls+Deevg+ G
  lcl|NCBI__GCF_002151265.1:WP_086511020.1  72 VVPVDGQPWSTDPFTLIDKgDGKLYGRGTCDMKGFIACALAELPEWLKRGLDKPIYLALSYDEEVGCIG 140
                                               ****************88769************************************************ PP

                                 TIGR01892 138 akklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarl 203
                                               a+++ie+l+   +rp+ +ivGePt +++v ahkG    + tv+Gr +hss+ d+Gvsai++aa+l++++
  lcl|NCBI__GCF_002151265.1:WP_086511020.1 141 APRMIERLMadhPRPTAVIVGEPTLMQPVVAHKGATNLRTTVTGRASHSSQVDQGVSAIHVAARLVTKI 209
                                               *******998999******************************************************** PP

                                 TIGR01892 204 valadklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee 271
                                               ++   +l+  + ++eaF++ +++l++G++ GG+a ni+a++C ++ e+R +p    eel + +++ a+e
  lcl|NCBI__GCF_002151265.1:WP_086511020.1 210 EDVMSELRAeGRVDEAFNVAHSSLHVGKIAGGTAINIMARECTFEWEIRHLPSDRFEELFERVNAFAAE 278
                                               ******987689****************************************************99988 PP

                                 TIGR01892 272 ....vkekapgfevkveels.atpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvl 334
                                                   ++++ap++ +++e l+ + pal+ +++ae+ +l ++l+G+ +  +v+y+teag++q++G+++v++
  lcl|NCBI__GCF_002151265.1:WP_086511020.1 279 leaeMQRRAPETSIVTEALNlTVPALADDNNAEVLDLCRELLGEqPSGAVAYATEAGQFQRVGLPTVIC 347
                                               676788999**999998876267*********************8889********************* PP

                                 TIGR01892 335 GPGdidqahqpdeYveieelkrcrallerl 364
                                               GPG+i+qahqpdeY+eie+l ++  ++++l
  lcl|NCBI__GCF_002151265.1:WP_086511020.1 348 GPGSIRQAHQPDEYIEIEQLAAGTRFMQAL 377
                                               **************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (383 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.19
//
[ok]

This GapMind analysis is from Apr 10 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