Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E2

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339
          Length = 394

 Score =  195 bits (496), Expect = 2e-54
 Identities = 133/381 (34%), Positives = 191/381 (50%), Gaps = 15/381 (3%)

Query: 13  RALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGA 72
           RAL+A     AT      SN  LI  + D+ + LG N E+      R K N+LASIG   
Sbjct: 12  RALLAELVSFATVSR--DSNLALIEFVRDYLQGLGVNSELI-YNAERTKANLLASIGPAV 68

Query: 73  -GGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTK 131
            GG++L+GHTD VP D   WT DPF LTE DGK +G GTADMKG+ A +L A+     + 
Sbjct: 69  PGGVVLSGHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 128

Query: 132 LKKPLYILATADEETSMAGARYFAETTALR---PDCAIIGEPTSLQPVRAHKGHISNAIR 188
           L++P+++  + DEE    G     E    R   P   +IGEPT L+PV  HKG ++    
Sbjct: 129 LRRPVHLAFSYDEEVGCLGVHSLLEVLVRRIAQPALCLIGEPTQLRPVLGHKGKLAMRCH 188

Query: 189 IQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKE-RYHYEAFTVPYPTLNLGHIHGG 247
           ++G + HS+    GVNAIE     IG + ++   L E   H   F     T+ +G +HGG
Sbjct: 189 VRGAACHSAYAPYGVNAIEQAARLIGRLGEIGAQLAEPSRHDPRFDPACSTVQVGVVHGG 248

Query: 248 DASNRICACCELHMDIRPLPG----MTLNELNGLLNDALAPVSERWPGRLTVD-ELHPPI 302
            A N + A C    ++R LP     + + +L G     L P  +   G   +  E     
Sbjct: 249 TALNIVPADCRFDFEVRALPDFDPLVVVEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSAY 308

Query: 303 PGYECPPNHQLVEVVEKLLGAKT-EVVNYCTEAP-FIQTLCPTLVLGPGSINQAHQPDEY 360
           PG    P+     ++ +L G+     V + TE   F Q   PT+V GPGS++Q H+PDEY
Sbjct: 309 PGLATSPDSAAARLIAQLCGSDAFGTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEY 368

Query: 361 LETRFIKPTRELITQVIHHFC 381
           +    +     L+ ++  + C
Sbjct: 369 VSVEQMAACDRLMDRLASYLC 389


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: 378
Number of extensions: 20
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: 394
Length adjustment: 30
Effective length of query: 353
Effective length of database: 364
Effective search space:   128492
Effective search space used:   128492
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 Pf6N2E2_1339 (Acetylornithine deacetylase (EC 3.5.1.16))
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.6414.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.7e-125  404.8   0.0   1.9e-125  404.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.6   0.0  1.9e-125  1.9e-125       2     364 ..      14     384 ..      13     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 404.6 bits;  conditional E-value: 1.9e-125
                                      TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvls 65 
                                                    +la+Lv+f +vs+ sn++lie+v+dyl+ lgv+ e + +a+  +k nlla+iGp++  gg+vls
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339  14 LLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAER-TKANLLASIGPAV-PGGVVLS 75 
                                                    689*************************************99.************9.9****** PP

                                      TIGR01892  66 GhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsa 129
                                                    GhtDvvPvd++aWt Dpf Lte dg+ +grGtaDmkG+la vLaavp     +L++P+hl++s+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339  76 GHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSPLRRPVHLAFSY 139
                                                    **************************************************************** PP

                                      TIGR01892 130 DeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGv 190
                                                    Deevg++G+++l+e+l     +pal ++GePt+l++v  hkGk +++ +vrG   hs+++  Gv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 140 DEEVGCLGVHSLLEVLVrriAQPALCLIGEPTQLRPVLGHKGKLAMRCHVRGAACHSAYAPYGV 203
                                                    ***************9977789****************************************** PP

                                      TIGR01892 191 saielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpi 253
                                                    +aie+aa+l++rl +   +l + + ++  F+p  +t+++G+v+GG+a ni++a C++ +e+R++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 204 NAIEQAARLIGRLGEIGAQLAEpSRHDPRFDPACSTVQVGVVHGGTALNIVPADCRFDFEVRAL 267
                                                    *********************98999************************************** PP

                                      TIGR01892 254 pGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.a 311
                                                    p  dp  + ++l+  ae+     +++ a ++ ++ e lsa+p+l++ +d+ +++l+++l G+ a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 268 PDFDPLVVVEQLQGYAEQtllpaMQAVAGDTAIRFEPLSAYPGLATSPDSAAARLIAQLCGSdA 331
                                                    ********999999998877765555566677788999***********************989 PP

                                      TIGR01892 312 aevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                      +v++gte gl+ ++G+++vv+GPG++dq h+pdeYv +e++ +c+ l+ rl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 332 FGTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRL 384
                                                    9*************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (394 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: 9.61
//
[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