Alignments for a candidate for argE in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Methylocella silvestris BL2

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012590053.1 MSIL_RS05240 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000021745.1:WP_012590053.1
          Length = 393

 Score =  222 bits (565), Expect = 2e-62
 Identities = 133/367 (36%), Positives = 190/367 (51%), Gaps = 10/367 (2%)

Query: 3   AAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR 62
           A  +L +LVGF +     N  +V+ +  YL   G     +P   GD++ +F TIGPK   
Sbjct: 15  AIAMLERLVGFDTESSKSNLALVAAVETYLRECGADYVKIPNAIGDKAALFITIGPKIDG 74

Query: 63  GYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLR 122
           G ++SGH DVVP     W+SDPF+LR E  RLYGRG  DMKGF +  LA +P+     L 
Sbjct: 75  GVVLSGHTDVVPVEGQSWSSDPFQLRREEGRLYGRGACDMKGFDSICLAMIPEFQKAALS 134

Query: 123 RPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVR 182
           RP+H+ LSYDEE  CRG    I R      +P   ++GEPT M+   AHK     R  V 
Sbjct: 135 RPIHILLSYDEETTCRGSLDTIRRFGADLPRPGAILVGEPTLMQVADAHKAIVTYRTIVH 194

Query: 183 GRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL--VGGPFEHVFEPPYSSLQIGTVKGGQ 240
           G   HSS+P  G NA+     ++T+     + L   G P    F+PP S++++G + GG 
Sbjct: 195 GHEAHSSKPYLGANAVETACDLVTELYRFNEELGRRGDPSGR-FDPPASTIEVGVIHGGT 253

Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRK--TAEALTTLGFEVEWQELSAY-----P 293
           A NI+   C  ++E R++        LA +       AL  L    +   +  +     P
Sbjct: 254 ARNILAKQCAFDWEFRSLPDTPQNLALAHLESYIARVALPNLTRNAKDASIETFAEVEVP 313

Query: 294 ALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYI 353
            L   P +   +L  +L    +  +V Y TEAG FQ AG   ++CGPG I +AH+PDE++
Sbjct: 314 GLGPAPGSVAESLALKLARSNSTISVPYATEAGQFQAAGAPTVVCGPGSIDQAHQPDEFL 373

Query: 354 LIDELMA 360
            I ++ A
Sbjct: 374 EIAQVEA 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: 384
Number of extensions: 18
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: 374
Length of database: 393
Length adjustment: 30
Effective length of query: 344
Effective length of database: 363
Effective search space:   124872
Effective search space used:   124872
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_012590053.1 MSIL_RS05240 (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.27969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-110  353.5   0.0   7.7e-110  353.3   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012590053.1  MSIL_RS05240 acetylornithine dea


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012590053.1  MSIL_RS05240 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.3   0.0  7.7e-110  7.7e-110       2     364 ..      18     388 ..      17     389 .. 0.94

  Alignments for each domain:
  == domain 1  score: 353.3 bits;  conditional E-value: 7.7e-110
                                 TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDv 70 
                                               +l++Lv+fd+ s +sn++l+  ve yl+e g    ++p+a g +k  l+ +iGpk  +gg+vlsGhtDv
  lcl|NCBI__GCF_000021745.1:WP_012590053.1  18 MLERLVGFDTESSKSNLALVAAVETYLRECGADYVKIPNAIG-DKAALFITIGPKI-DGGVVLSGHTDV 84 
                                               6899*****************************9999*9999.************9.9*********** PP

                                 TIGR01892  71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139
                                               vPv++++W+sDpf+L+ ++grLYgrG++DmkGF  + La +p+ ++a L +P+h++ls+Dee++++G  
  lcl|NCBI__GCF_000021745.1:WP_012590053.1  85 VPVEGQSWSSDPFQLRREEGRLYGRGACDMKGFDSICLAMIPEFQKAALSRPIHILLSYDEETTCRGSL 153
                                               ********************************************************************* PP

                                 TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205
                                               + i +     +rp  ++vGePt ++   ahk +++ +  v+G+e+hss+p  G++a+e+a +l+++l +
  lcl|NCBI__GCF_000021745.1:WP_012590053.1 154 DTIRRFGadlPRPGAILVGEPTLMQVADAHKAIVTYRTIVHGHEAHSSKPYLGANAVETACDLVTELYR 222
                                               ***9986688*********************************************************** PP

                                 TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevk 273
                                                +++l r +d+   F+pp +t+++G+++GG+a ni+a++C +  e+R++p  + +  la+le+  + v 
  lcl|NCBI__GCF_000021745.1:WP_012590053.1 223 FNEELGRrGDPSGRFDPPASTIEVGVIHGGTARNILAKQCAFDWEFRSLPDTPQNLALAHLESYIARVA 291
                                               *****98799*****************************************999999999999888865 PP

                                 TIGR01892 274 ekapgfevk.....veelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGP 336
                                                 ++ +++k     +      p+l + + ++++ l+ kla + ++  v+y+teag++q +G+++vv+GP
  lcl|NCBI__GCF_000021745.1:WP_012590053.1 292 LPNLTRNAKdasieTFAEVEVPGLGPAPGSVAESLALKLARSnSTISVPYATEAGQFQAAGAPTVVCGP 360
                                               55555554400000445566899999************998768999********************** PP

                                 TIGR01892 337 GdidqahqpdeYveieelkrcrallerl 364
                                               G+idqahqpde++ei +++++ ++++rl
  lcl|NCBI__GCF_000021745.1:WP_012590053.1 361 GSIDQAHQPDEFLEIAQVEAGIEFMRRL 388
                                               *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (393 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: 12.00
//
[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