Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2C3

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_25400 AO356_25400 acetylornithine deacetylase

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25400
          Length = 389

 Score =  200 bits (508), Expect = 6e-56
 Identities = 135/381 (35%), Positives = 193/381 (50%), Gaps = 15/381 (3%)

Query: 13  RALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGA 72
           RAL+A     AT      SN  LI  + D+ + LG N E+      R K N+LASIG   
Sbjct: 7   RALLAELVSFATVSR--DSNLALIEFVRDYLQGLGVNSELI-YNAERTKANLLASIGPAL 63

Query: 73  -GGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTK 131
            GG++L+GHTD VP D   WT +PF LTE DGK +G GTADMKG+ A +L A+     + 
Sbjct: 64  PGGVVLSGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 123

Query: 132 LKKPLYILATADEETSMAGARYFAETTALR---PDCAIIGEPTSLQPVRAHKGHISNAIR 188
           L++P+++  + DEE    G R   E    R   P   +IGEPT LQPV  HKG ++    
Sbjct: 124 LRRPVHLAFSYDEEVGCLGVRSLLEVLPQRIAQPALCLIGEPTELQPVLGHKGKLAMRCH 183

Query: 189 IQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKE-RYHYEAFTVPYPTLNLGHIHGG 247
           ++G + HS+    GVNAIE     IG + ++   L E   H   F   + T+ +G +HGG
Sbjct: 184 VKGAACHSAYAPYGVNAIEQAARLIGRLGEIGAQLAEPSRHDPRFDPAFSTVQVGVVHGG 243

Query: 248 DASNRICACCELHMDIRPLPG----MTLNELNGLLNDALAPVSERWPGRLTVD-ELHPPI 302
            A N + A C    ++R LP     +   +L G     L P  +   G   +  E     
Sbjct: 244 TALNIVPADCRFDFEVRALPDFDPLVVAEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSAY 303

Query: 303 PGYECPPNHQLVEVVEKLLGAKT-EVVNYCTEAP-FIQTLCPTLVLGPGSINQAHQPDEY 360
           PG    P+    ++V +L G+     V + TE   F Q   PT+V GPGS++Q H+PDEY
Sbjct: 304 PGLATSPDSAAAQLVARLCGSDAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEY 363

Query: 361 LETRFIKPTRELITQVIHHFC 381
           +    +     L+ ++  + C
Sbjct: 364 VSVEQMAACDRLMDRLASYLC 384


Lambda     K      H
   0.320    0.139    0.430 

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: 370
Number of extensions: 19
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: 383
Length of database: 389
Length adjustment: 30
Effective length of query: 353
Effective length of database: 359
Effective search space:   126727
Effective search space used:   126727
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate AO356_25400 AO356_25400 (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.5383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.3e-125  405.2   0.0   1.4e-125  405.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  AO356_25400 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  AO356_25400 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.1   0.0  1.4e-125  1.4e-125       2     364 ..       9     379 ..       8     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.1 bits;  conditional E-value: 1.4e-125
                                       TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 
                                                     +la+Lv+f +vs+ sn++lie+v+dyl+ lgv+ e + +a+  +k nlla+iGp+   gg+vl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400   9 LLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAER-TKANLLASIGPAL-PGGVVL 69 
                                                     689*************************************99.************9.9***** PP

                                       TIGR01892  65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvl 127
                                                     sGhtDvvPvd++aWt +pf Lte dg+ +grGtaDmkG+la vLaavp     +L++P+hl++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400  70 SGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSPLRRPVHLAF 132
                                                     *************************************************************** PP

                                       TIGR01892 128 saDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpd 187
                                                     s+Deevg++G+++l+e+l+    +pal ++GePt+l++v  hkGk +++ +v+G   hs+++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 133 SYDEEVGCLGVRSLLEVLPqriAQPALCLIGEPTELQPVLGHKGKLAMRCHVKGAACHSAYAP 195
                                                     ******************988889*************************************** PP

                                       TIGR01892 188 rGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvle 249
                                                      Gv+aie+aa+l++rl +   +l + + ++  F+p ++t+++G+v+GG+a ni++a C++ +e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 196 YGVNAIEQAARLIGRLGEIGAQLAEpSRHDPRFDPAFSTVQVGVVHGGTALNIVPADCRFDFE 258
                                                     ************************98999********************************** PP

                                       TIGR01892 250 lRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvallekl 307
                                                     +R++p  dp  + ++l+  ae+     +++ a ++ ++ e lsa+p+l++ +d+ +++l+++l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 259 VRALPDFDPLVVAEQLQGYAEQtllpaMQAVAGDTAIRFEPLSAYPGLATSPDSAAAQLVARL 321
                                                     ****************99998877765555566677788999********************* PP

                                       TIGR01892 308 aGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                      G+ a  +v++gte gl+ ++G+++vv+GPG++dq h+pdeYv +e++ +c+ l+ rl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 322 CGSdAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRL 379
                                                     **9999*************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (389 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: 11.07
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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