Alignments for a candidate for argE in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Burkholderia vietnamiensis G4

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_011879826.1 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_000016205.1:WP_011879826.1
          Length = 387

 Score =  294 bits (752), Expect = 3e-84
 Identities = 153/379 (40%), Positives = 230/379 (60%), Gaps = 12/379 (3%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           +L +LVGF +V    N  ++ +IR YL+ +G+  ++    EG +++++ATIGP++  G  
Sbjct: 9   LLARLVGFATVSRDSNLAMIDFIRDYLDGYGVTSELFYNAEGTKASLYATIGPRDRSGIA 68

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     WT +PFRL     RLYGRGT DMKGF+A++LAAVP L A PL  P+
Sbjct: 69  LSGHTDVVPVDGQAWTVEPFRLTERDGRLYGRGTADMKGFIASMLAAVPALVARPLHTPV 128

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HL LSYDEE GC GV  M+  L     +P   +IGEPTG++ +  HKGK A R  V+G +
Sbjct: 129 HLLLSYDEEIGCVGVRPMLEALAGREHRPRVCVIGEPTGLQPVLGHKGKLAMRCHVKGAA 188

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH---VFEPPYSSLQIGTVKGGQAV 242
            HS+    G+NAI   A ++ + + E    +  P EH    F+PP+S++Q G + GG+A+
Sbjct: 189 CHSAYAPLGVNAIDYAAKLIAR-LGEIGAALARP-EHRDERFDPPFSTVQTGLISGGRAL 246

Query: 243 NIIPDSCEVEFEARAISGVDPAELLAPVRKTAEA-------LTTLGFEVEWQELSAYPAL 295
           NI+P  CE +FE RA+   D  ++ + +++ A+              ++  Q L AYP L
Sbjct: 247 NIVPAECEFDFEVRALPSFDAHDVPSQLQQYAQGELLPRMRAVQPDTDIRLQALGAYPGL 306

Query: 296 SLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILI 355
           +  PD+  A L+  L+G +A   V++GTE GLF  AG+  ++CGPG + + HKPDE++ +
Sbjct: 307 ATAPDSDAARLIAMLSGSDAFGTVAFGTEGGLFGAAGMPTVVCGPGSMDQGHKPDEFVTL 366

Query: 356 DELMACRAMVEALGARCTA 374
           ++L  C AM+  L +   A
Sbjct: 367 EQLHGCDAMLGRLVSHVAA 385


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: 417
Number of extensions: 14
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: 387
Length adjustment: 30
Effective length of query: 344
Effective length of database: 357
Effective search space:   122808
Effective search space used:   122808
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_011879826.1 (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.8034.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-125  404.4   0.0   2.6e-125  404.2   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011879826.1  acetylornithine deacetylase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011879826.1  acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.2   0.0  2.6e-125  2.6e-125       3     365 .]      10     380 ..       8     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.2 bits;  conditional E-value: 2.6e-125
                                 TIGR01892   3 lakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 
                                               la+Lv+f +vs+ sn+++i++++dyl+  gv+ e   +a+g +k  l a+iGp++ ++g++lsGhtDvv
  lcl|NCBI__GCF_000016205.1:WP_011879826.1  10 LARLVGFATVSRDSNLAMIDFIRDYLDGYGVTSELFYNAEG-TKASLYATIGPRD-RSGIALSGHTDVV 76 
                                               899**************************************.************9.************* PP

                                 TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakk 140
                                               Pvd++aWt +pfrLte+dgrLYgrGtaDmkGF+a +Laavp l a +L+ P+hl+ls+Dee+g+ G++ 
  lcl|NCBI__GCF_000016205.1:WP_011879826.1  77 PVDGQAWTVEPFRLTERDGRLYGRGTADMKGFIASMLAAVPALVARPLHTPVHLLLSYDEEIGCVGVRP 145
                                               ********************************************************************* PP

                                 TIGR01892 141 lieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlval 206
                                               ++eala   +rp++ ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+ai  aakl+arl + 
  lcl|NCBI__GCF_000016205.1:WP_011879826.1 146 MLEALAgreHRPRVCVIGEPTGLQPVLGHKGKLAMRCHVKGAACHSAYAPLGVNAIDYAAKLIARLGEI 214
                                               ******9999*********************************************************** PP

                                 TIGR01892 207 adklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee... 271
                                                  l r e+ +e F+pp++t++ G + GG+a ni++a+Ce+ +e+R++p  d +++ ++l++ a+    
  lcl|NCBI__GCF_000016205.1:WP_011879826.1 215 GAALARpEHRDERFDPPFSTVQTGLISGGRALNIVPAECEFDFEVRALPSFDAHDVPSQLQQYAQGell 283
                                               ******88999***************************************************9998888 PP

                                 TIGR01892 272 ..vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPG 337
                                                 +++ +p+++++ + l a+p+l++ +d+++++l++ l+G+ a  +v++gte gl+  +G+++vv+GPG
  lcl|NCBI__GCF_000016205.1:WP_011879826.1 284 prMRAVQPDTDIRLQALGAYPGLATAPDSDAARLIAMLSGSdAFGTVAFGTEGGLFGAAGMPTVVCGPG 352
                                               8889999*********************************9999************************* PP

                                 TIGR01892 338 didqahqpdeYveieelkrcrallerlv 365
                                               ++dq h+pde+v +e+l+ c+a+l rlv
  lcl|NCBI__GCF_000016205.1:WP_011879826.1 353 SMDQGHKPDEFVTLEQLHGCDAMLGRLV 380
                                               ************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (387 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.86
//
[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