Alignments for a candidate for argE in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Burkholderia phytofirmans PsJN

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BPHYT_RS11720 BPHYT_RS11720 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__BFirm:BPHYT_RS11720
          Length = 387

 Score =  299 bits (766), Expect = 8e-86
 Identities = 156/372 (41%), Positives = 223/372 (59%), Gaps = 10/372 (2%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           +L +L+GF +V    N +++ +IRGYL   G+  ++    E  ++N+FATIGP+E  G +
Sbjct: 9   LLERLIGFATVSRDSNLEMIDFIRGYLGELGVESELFYNAERSKANLFATIGPREGGGIV 68

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     WT D FRL     RLYGRG  DMKG++A+VLAAVP L    L+ P+
Sbjct: 69  LSGHTDVVPVEGQAWTVDAFRLTERDGRLYGRGAADMKGYIASVLAAVPGLRERELKLPV 128

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HLA SYDEE GC GV  M+A L +   +P   +IGEPT ++ +  HKGK A R  V+G  
Sbjct: 129 HLAFSYDEEVGCLGVRPMLAELAQRAHKPALCLIGEPTELKPVLGHKGKLAMRCQVKGAP 188

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKGGQAVN 243
            HS+    G+NAI   A ++ + + E   L+  P  H   F+PP+S++Q G + GG+A+N
Sbjct: 189 CHSAYAPYGVNAIQYAARMIGR-LEEIGELLARPEHHDARFDPPFSTVQTGVINGGRALN 247

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEA-------LTTLGFEVEWQELSAYPALS 296
           I+P  CE +FE RA+ G D   +   ++  AEA             ++ +Q LSAYP L+
Sbjct: 248 IVPAECEFDFEVRALPGFDANRVADELQIYAEAELLPKMRAVKSDTDIRFQSLSAYPGLA 307

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
             PD+  A LL  L+G      V++GTE GLF  AGI  ++CGPG + + HKPDE++ + 
Sbjct: 308 TSPDSEAARLLALLSGSTEYGTVAFGTEGGLFDEAGIPTVVCGPGSMDQGHKPDEFVTVA 367

Query: 357 ELMACRAMVEAL 368
           +L  C AM+  L
Sbjct: 368 QLRECDAMLARL 379


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: 413
Number of extensions: 13
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 BPHYT_RS11720 BPHYT_RS11720 (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.6722.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.3e-129  417.0   0.0   3.8e-129  416.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS11720  BPHYT_RS11720 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS11720  BPHYT_RS11720 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.8   0.0  3.8e-129  3.8e-129       2     364 ..       9     379 ..       8     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.8 bits;  conditional E-value: 3.8e-129
                                TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 
                                              +l++L++f +vs+ sn+++i+++++yl elgv+ e   +a+   k nl+a+iGp+e  gg+vlsGhtDvv
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720   9 LLERLIGFATVSRDSNLEMIDFIRGYLGELGVESELFYNAER-SKANLFATIGPRE-GGGIVLSGHTDVV 76 
                                              6899************************************99.*************.79*********** PP

                                TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkl 141
                                              Pv+++aWt D+frLte+dgrLYgrG+aDmkG++a vLaavp l   +Lk P+hl++s+Deevg++G++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720  77 PVEGQAWTVDAFRLTERDGRLYGRGAADMKGYIASVLAAVPGLRERELKLPVHLAFSYDEEVGCLGVRPM 146
                                              ********************************************************************** PP

                                TIGR01892 142 ieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvalad 208
                                              ++ la   ++pal ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+ai+ aa++++rl++  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 147 LAELAqraHKPALCLIGEPTELKPVLGHKGKLAMRCQVKGAPCHSAYAPYGVNAIQYAARMIGRLEEIGE 216
                                              *99997778899********************************************************** PP

                                TIGR01892 209 klkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....v 272
                                               l r e+++  F+pp++t++ G+++GG+a ni++a+Ce+ +e+R++pG d +++  +l+  ae+     +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 217 LLARpEHHDARFDPPFSTVQTGVINGGRALNIVPAECEFDFEVRALPGFDANRVADELQIYAEAellpkM 286
                                              ****999999*************************************************99998888766 PP

                                TIGR01892 273 kekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidq 341
                                              ++ + +++++ + lsa+p+l++ +d+e+++ll+ l+G+ +  +v++gte gl+ e+Gi++vv+GPG++dq
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 287 RAVKSDTDIRFQSLSAYPGLATSPDSEAARLLALLSGStEYGTVAFGTEGGLFDEAGIPTVVCGPGSMDQ 356
                                              6777788889999*************************8999**************************** PP

                                TIGR01892 342 ahqpdeYveieelkrcrallerl 364
                                               h+pde+v + +l++c+a+l+rl
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 357 GHKPDEFVTVAQLRECDAMLARL 379
                                              ********************997 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.04
# Mc/sec: 2.93
//
[ok]

This GapMind analysis is from Apr 09 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