Alignments for a candidate for argE in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Sphingomonas wittichii RW1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012050495.1 SWIT_RS21830 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000016765.1:WP_012050495.1
          Length = 388

 Score =  275 bits (703), Expect = 2e-78
 Identities = 155/372 (41%), Positives = 212/372 (56%), Gaps = 10/372 (2%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           IL  LVGF +V    N +++ W+R YL  HG+   +     G ++N+FAT+ P +  G I
Sbjct: 7   ILRTLVGFPTVSADSNMELIEWVRDYLAGHGVEAHLTFDAAGRKANLFATVVPGDG-GLI 65

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     W+SDPF   +   R+YGRGT DMKGF+A  LA VP++ A+   RPL
Sbjct: 66  LSGHTDVVPVTGQQWSSDPFAAELRDGRVYGRGTCDMKGFIAVALALVPEMRALDGARPL 125

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HLALSYDEE GCRG P MI  L     +  G I+GEPTGM+AI  HKG    R TV GR+
Sbjct: 126 HLALSYDEELGCRGAPRMIDDLVRRGVRAGGCIVGEPTGMKAIIGHKGAGMYRCTVTGRA 185

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHV-FEPPYSSLQIGTVKGGQAVNI 244
            HSS    G+NAI   A ++ +      RL      H  F+ PYS++Q+  + GG A NI
Sbjct: 186 AHSSLAPTGVNAIEYAACIVMKLREIGRRLEAIEPRHAGFDVPYSTIQVNRIDGGTAGNI 245

Query: 245 IPDSCEVEFEARAISGVDPAELLAPV--RKTAEALTTLGFE-----VEWQELSAYPALSL 297
           + D CE+  + R +   D A L+A V      E L  +        +  +E++  P   +
Sbjct: 246 VADRCELRIDIRHLPATDRAALIAEVAAHVADELLPEMRLRAPEAAISIEEVADIPPFEI 305

Query: 298 EPDAPLAALLEELTGRE-ALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
             DA L   +      E A   V++G+EAGLFQRAGI  +ICGPG I +AH+PDE++ I+
Sbjct: 306 AADASLVREVVRSNSVEGACGHVAFGSEAGLFQRAGIPTVICGPGSIEQAHRPDEFVAIE 365

Query: 357 ELMACRAMVEAL 368
           +L  C  M+  +
Sbjct: 366 QLERCDGMLRTM 377


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: 428
Number of extensions: 18
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: 388
Length adjustment: 30
Effective length of query: 344
Effective length of database: 358
Effective search space:   123152
Effective search space used:   123152
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_012050495.1 SWIT_RS21830 (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.24900.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-119  383.0   0.3   8.6e-119  382.8   0.3    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012050495.1  SWIT_RS21830 acetylornithine dea


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012050495.1  SWIT_RS21830 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.8   0.3  8.6e-119  8.6e-119       2     363 ..       7     376 ..       6     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: 382.8 bits;  conditional E-value: 8.6e-119
                                 TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDv 70 
                                               il+ Lv+f++vsa sn++lie+v+dyl+ +gv+++    a g  k nl+a++ p  g+ggl+lsGhtDv
  lcl|NCBI__GCF_000016765.1:WP_012050495.1   7 ILRTLVGFPTVSADSNMELIEWVRDYLAGHGVEAHLTFDAAG-RKANLFATVVP--GDGGLILSGHTDV 72 
                                               89********************************99999988.9********96..669********** PP

                                 TIGR01892  71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139
                                               vPv +++W+sDpf    +dgr+YgrGt+DmkGF+a++La vp++ a +  +Plhl+ls+Dee g++Ga+
  lcl|NCBI__GCF_000016765.1:WP_012050495.1  73 VPVTGQQWSSDPFAAELRDGRVYGRGTCDMKGFIAVALALVPEMRALDGARPLHLALSYDEELGCRGAP 141
                                               ********************************************************************* PP

                                 TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205
                                               ++i+ l     r+   ivGePt+++a+  hkG    + tv+Gr +hss + +Gv+aie aa ++ +l +
  lcl|NCBI__GCF_000016765.1:WP_012050495.1 142 RMIDDLVrrgVRAGGCIVGEPTGMKAIIGHKGAGMYRCTVTGRAAHSSLAPTGVNAIEYAACIVMKLRE 210
                                               *****99777789999***************************************************** PP

                                 TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.. 271
                                                  +l+  e+ + +F++py+t+++ +++GG+a ni+a+ Cel +++R +p  d ++l a++ +  ++  
  lcl|NCBI__GCF_000016765.1:WP_012050495.1 211 IGRRLEAiEPRHAGFDVPYSTIQVNRIDGGTAGNIVADRCELRIDIRHLPATDRAALIAEVAAHVADel 279
                                               *******8888899********************************************99988766557 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelva.lleklaGa.aaevvsygteagllqelGieavvlG 335
                                                  ++ +ap+  + +ee+  +p +e+ +da+lv+ +++  + + a   v++g+eagl+q++Gi++v++G
  lcl|NCBI__GCF_000016765.1:WP_012050495.1 280 lpeMRLRAPEAAISIEEVADIPPFEIAADASLVReVVRSNSVEgACGHVAFGSEAGLFQRAGIPTVICG 348
                                               778999************************99853777777778999********************** PP

                                 TIGR01892 336 PGdidqahqpdeYveieelkrcraller 363
                                               PG+i+qah+pde+v ie+l+rc+ +l+ 
  lcl|NCBI__GCF_000016765.1:WP_012050495.1 349 PGSIEQAHRPDEFVAIEQLERCDGMLRT 376
                                               ************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (388 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.13
//
[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