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_RS09285 BPHYT_RS09285 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__BFirm:BPHYT_RS09285
          Length = 404

 Score =  267 bits (682), Expect = 4e-76
 Identities = 145/370 (39%), Positives = 213/370 (57%), Gaps = 13/370 (3%)

Query: 9   KLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR---GYI 65
           +LV   +V   PN  ++  +R  L + G+   +     G  +N+FATI         G +
Sbjct: 23  RLVSMDTVSRNPNLGLIETVRDELRAVGVEATLTHDESGKWANLFATIPAHNGETNGGVV 82

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     W SDPF+  +  D+LYGRGT DMKGF+ A L  VP++    L +P+
Sbjct: 83  LSGHTDVVPVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALTLVPEMQRTKLAKPI 142

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           H ALS+DEE GC G P +IA L +   +P G I+GEPT MR I AHKG  A +  VRG++
Sbjct: 143 HFALSFDEEVGCAGAPLLIADLMKRGVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQA 202

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244
            HSS   +GLNAI   A ++      AD+    GPF+ +++ P+++ Q  T+ GG A+N 
Sbjct: 203 AHSSLTPKGLNAIEYAARLICYIRDMADQFREQGPFDELYDVPFTTAQTSTIVGGNAINT 262

Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTL--------GFEVEWQELSAYPALS 296
           +P  C+ +FE R +  +DP  + A + + A   T L           +E  +++A P L 
Sbjct: 263 VPAECKFQFEFRNLPTLDPEPIFARIDQYARE-TLLPKMLREHPSAAIEITKIAAAPGLD 321

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
               A +  L+  LT  +    V+YGTEAGLF  AGI +I+CGPGDI +AHKP+E++ +D
Sbjct: 322 SSEQAAITQLVRALTADQDKRKVAYGTEAGLFSLAGIPSIVCGPGDIQQAHKPNEFVALD 381

Query: 357 ELMACRAMVE 366
           +L+AC   ++
Sbjct: 382 QLVACERFLQ 391


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: 383
Number of extensions: 14
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: 404
Length adjustment: 30
Effective length of query: 344
Effective length of database: 374
Effective search space:   128656
Effective search space used:   128656
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_RS09285 BPHYT_RS09285 (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.13423.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-115  372.5   0.0   1.3e-115  372.2   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS09285  BPHYT_RS09285 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS09285  BPHYT_RS09285 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2   0.0  1.3e-115  1.3e-115       4     364 ..      22     393 ..      20     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.3e-115
                                TIGR01892   4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkeg..agglvlsGhtDvv 71 
                                              ++Lv++d+vs+ +n+ lie v+d l+++gv++       g +  nl+a+i +++g  +gg+vlsGhtDvv
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285  22 TRLVSMDTVSRNPNLGLIETVRDELRAVGVEATLTHDESG-KWANLFATIPAHNGetNGGVVLSGHTDVV 90 
                                              78******************************99988888.99*******988652269*********** PP

                                TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkl 141
                                              Pvd+++W sDpf+   + ++LYgrGt+DmkGF+ ++L  vp+++ +kL kP+h +ls+Deevg+aGa+ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285  91 PVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALTLVPEMQRTKLAKPIHFALSFDEEVGCAGAPLL 160
                                              ********************************************************************** PP

                                TIGR01892 142 ieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvalad 208
                                              i+ l+    +p+  ivGePts++++ ahkG+ + +  vrG+ +hss + +G++aie aa+l+  + ++ad
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285 161 IADLMkrgVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQAAHSSLTPKGLNAIEYAARLICYIRDMAD 230
                                              **99977789************************************************************ PP

                                TIGR01892 209 klkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....v 272
                                              + ++ ++++e +++p++t +  t+ GG+a n ++a+C++++e+R +p +dpe + a + + a e     +
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285 231 QFREqGPFDELYDVPFTTAQTSTIVGGNAINTVPAECKFQFEFRNLPTLDPEPIFARIDQYAREtllpkM 300
                                              **99799***************************************************999998888888 PP

                                TIGR01892 273 kekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidq 341
                                               +++p   +++ +  a p+l+  e+a + +l++ l+ +   + v+ygteagl+  +Gi+++v+GPGdi+q
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285 301 LREHPSAAIEITKIAAAPGLDSSEQAAITQLVRALTADqDKRKVAYGTEAGLFSLAGIPSIVCGPGDIQQ 370
                                              899**********************************98999**************************** PP

                                TIGR01892 342 ahqpdeYveieelkrcrallerl 364
                                              ah+p+e+v +++l++c+ +l++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS09285 371 AHKPNEFVALDQLVACERFLQKF 393
                                              *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (404 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: 7.79
//
[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