Alignments for a candidate for argE in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Methylocystis bryophila S285

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_085771629.1 B1812_RS10970 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_002117405.1:WP_085771629.1
          Length = 384

 Score =  237 bits (604), Expect = 5e-67
 Identities = 142/376 (37%), Positives = 197/376 (52%), Gaps = 18/376 (4%)

Query: 9   KLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYIISG 68
           +LV F +     N D+++ +  YL   G++   +P   GD++ +FATIGP    G ++SG
Sbjct: 13  RLVSFDTESAKSNLDLIADVEAYLREQGVSFVRIPNAAGDKAALFATIGPHVEGGVLLSG 72

Query: 69  HMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPLHLA 128
           H DVVP     W++DPF+LR E +RL GRG  DMKGF A  LA +P+  A  L+RP+H+ 
Sbjct: 73  HTDVVPVTGQAWSADPFKLRREGERLIGRGAVDMKGFDAVCLAMIPEFKAAALKRPIHIL 132

Query: 129 LSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRSGHS 188
           LSYDEE  C G    I R      QP   I+GEPT M+   AHK        VRG   HS
Sbjct: 133 LSYDEETTCVGPIDAIRRFGHDLPQPGAVIVGEPTSMQVADAHKSVTTYTTHVRGFEVHS 192

Query: 189 SRPDQGLNAIHGVAGVL--TQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQAVNIIP 246
           +    G++A+H    ++   + +  A R  G P    F+PPYSS+ +G + GG A NI+ 
Sbjct: 193 ANLHTGVSAVHVACRLVCELERIGAALREEGDPSGR-FDPPYSSIHVGVISGGTARNIVA 251

Query: 247 DSCEVEFEARAISGVDPAELLAPVRKTAEALTTL--------GFEVEWQELSAYPALSLE 298
             C   +E R   G+  A +    ++ A  + TL        G  VE    +  P L+ +
Sbjct: 252 RDCAFNWEFR---GLPQAPMHLAQQRLAAFVETLAPQFAAFPGTGVETITEAEVPGLAPQ 308

Query: 299 PDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDEL 358
           P +    L   L       +V Y +EAG FQR G  A+ICGPG I  AH+PDE+I I +L
Sbjct: 309 PGSGAEVLALRLARANRTISVPYASEAGRFQRGGTPAVICGPGRIDEAHQPDEFIEIAQL 368

Query: 359 MAC----RAMVEALGA 370
            AC    R +V  L A
Sbjct: 369 AACVDFMRGLVRELSA 384


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: 382
Number of extensions: 15
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: 384
Length adjustment: 30
Effective length of query: 344
Effective length of database: 354
Effective search space:   121776
Effective search space used:   121776
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_085771629.1 B1812_RS10970 (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.21487.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-107  345.2   0.1   2.6e-107  345.0   0.1    1.0  1  lcl|NCBI__GCF_002117405.1:WP_085771629.1  B1812_RS10970 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085771629.1  B1812_RS10970 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.0   0.1  2.6e-107  2.6e-107       4     364 ..      12     378 ..       9     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 345.0 bits;  conditional E-value: 2.6e-107
                                 TIGR01892   4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvP 72 
                                               ++Lv+fd+ sa+sn+dli  ve+yl+e+gv+  ++p+a g +k  l+a+iGp++ +gg++lsGhtDvvP
  lcl|NCBI__GCF_002117405.1:WP_085771629.1  12 ERLVSFDTESAKSNLDLIADVEAYLREQGVSFVRIPNAAG-DKAALFATIGPHV-EGGVLLSGHTDVVP 78 
                                               68**************************************.************9.9************* PP

                                 TIGR01892  73 vdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkl 141
                                               v ++aW++Dpf+L+ + +rL grG+ DmkGF a+ La +p+ +aa Lk+P+h++ls+Dee+++ G  + 
  lcl|NCBI__GCF_002117405.1:WP_085771629.1  79 VTGQAWSADPFKLRREGERLIGRGAVDMKGFDAVCLAMIPEFKAAALKRPIHILLSYDEETTCVGPIDA 147
                                               ********************************************************************* PP

                                 TIGR01892 142 ieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvala 207
                                               i +     ++p  +ivGePts++   ahk   +   +vrG e hs++ ++Gvsa+++a +l+ +l++  
  lcl|NCBI__GCF_002117405.1:WP_085771629.1 148 IRRFGhdlPQPGAVIVGEPTSMQVADAHKSVTTYTTHVRGFEVHSANLHTGVSAVHVACRLVCELERIG 216
                                               999877889************************************************************ PP

                                 TIGR01892 208 dklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee...v 272
                                                 l++ +d+   F+ppy+++++G++ GG+a ni+a+ C ++ e+R +p  +++  ++ l +  e+    
  lcl|NCBI__GCF_002117405.1:WP_085771629.1 217 AALREeGDPSGRFDPPYSSIHVGVISGGTARNIVARDCAFNWEFRGLPQAPMHLAQQRLAAFVETlapQ 285
                                               ***98789*************************************999876654444444444431115 PP

                                 TIGR01892 273 kekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdid 340
                                                +  pg++v++ +    p+l++++ + ++ l+ +la a ++  v+y++eag +q+ G++av++GPG id
  lcl|NCBI__GCF_002117405.1:WP_085771629.1 286 FAAFPGTGVETITEAEVPGLAPQPGSGAEVLALRLARAnRTISVPYASEAGRFQRGGTPAVICGPGRID 354
                                               5889**********************99999999887769999************************** PP

                                 TIGR01892 341 qahqpdeYveieelkrcrallerl 364
                                               +ahqpde++ei +l +c ++++ l
  lcl|NCBI__GCF_002117405.1:WP_085771629.1 355 EAHQPDEFIEIAQLAACVDFMRGL 378
                                               ********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (384 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: 8.85
//
[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