Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E3

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO353_29125 AO353_29125 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_29125
          Length = 382

 Score =  280 bits (716), Expect = 5e-80
 Identities = 143/374 (38%), Positives = 220/374 (58%), Gaps = 8/374 (2%)

Query: 3   AAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR 62
           + ++L +LV F +     N  ++ ++R YLE   +  + +   +  ++N+FATIGP +  
Sbjct: 4   SVDLLKQLVAFDTTSRESNLHLIDFVRDYLERFDVPCERVYNEQRSKANLFATIGPADRP 63

Query: 63  GYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLR 122
           G ++SGH DVVP     WT  PF+L     +LYGRGT DMKG++A VLA VP L   PLR
Sbjct: 64  GIVLSGHTDVVPVDGQPWTVAPFQLSERDGKLYGRGTADMKGYIACVLALVPSLVNAPLR 123

Query: 123 RPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVR 182
           RP+H+ALSYDEE GC GV  ++  L +   +P+  IIGEPT ++ +  HKGK A R  + 
Sbjct: 124 RPVHIALSYDEEVGCLGVRSLLKALEQRPVKPMLCIIGEPTELKPVLGHKGKLAMRCDIH 183

Query: 183 GRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQA 241
           G + HS+    G+NAI   A ++ +      RL V    +  F+PP+S++Q G + GG+A
Sbjct: 184 GEACHSAYAPLGVNAIEYAAELIGELGRIGHRLKVPEHHDARFDPPFSTVQTGMISGGKA 243

Query: 242 VNIIPDSCEVEFEARAISGVDPAELLAPVRKTAE-------ALTTLGFEVEWQELSAYPA 294
           +NI+P  C  +FE RA+   DP+ +   ++  AE          +   ++ + ELSAYP 
Sbjct: 244 LNIVPADCRFDFEIRALPSQDPSVVAKELKTYAEQQVLPRMRAVSDQSDIRFSELSAYPG 303

Query: 295 LSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYIL 354
           L+ +  +  A L+   +G      V++GTE GLF  AGI  ++CGPG + + HKPDE++ 
Sbjct: 304 LATDAHSEAAELIAAFSGSREFGTVAFGTEGGLFDAAGIPTVVCGPGSMDQGHKPDEFVS 363

Query: 355 IDELMACRAMVEAL 368
           +D+L  C AM++ +
Sbjct: 364 LDQLKGCDAMLQRM 377


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: 382
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: 382
Length adjustment: 30
Effective length of query: 344
Effective length of database: 352
Effective search space:   121088
Effective search space used:   121088
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 AO353_29125 AO353_29125 (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.20675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-126  407.7   0.0   2.5e-126  407.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125  AO353_29125 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125  AO353_29125 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.5   0.0  2.5e-126  2.5e-126       2     364 ..       7     377 ..       6     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 407.5 bits;  conditional E-value: 2.5e-126
                                     TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsG 66 
                                                   +l++Lvafd++s+ sn+ li++v+dyle  +v+ e++ + +   k nl+a+iGp++ + g+vlsG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125   7 LLKQLVAFDTTSRESNLHLIDFVRDYLERFDVPCERVYNEQR-SKANLFATIGPAD-RPGIVLSG 69 
                                                   799**********************************98776.************9.******** PP

                                     TIGR01892  67 htDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDe 131
                                                   htDvvPvd+++Wt  pf+L e+dg+LYgrGtaDmkG++a+vLa vp l  a+L++P+h++ls+De
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125  70 HTDVVPVDGQPWTVAPFQLSERDGKLYGRGTADMKGYIACVLALVPSLVNAPLRRPVHIALSYDE 134
                                                   ***************************************************************** PP

                                     TIGR01892 132 evglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsai 193
                                                   evg++G+++l++al     +p l i+GePt+l++v  hkGk +++  ++G   hs+++  Gv+ai
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125 135 EVGCLGVRSLLKALEqrpVKPMLCIIGEPTELKPVLGHKGKLAMRCDIHGEACHSAYAPLGVNAI 199
                                                   **********9999855567899****************************************** PP

                                     TIGR01892 194 elaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmd 257
                                                   e aa+l+++l +  ++lk  e+++  F+pp++t++ G + GGka ni++a C++ +e+R++p +d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125 200 EYAAELIGELGRIGHRLKVpEHHDARFDPPFSTVQTGMISGGKALNIVPADCRFDFEIRALPSQD 264
                                                   *****************99899999**************************************** PP

                                     TIGR01892 258 peellallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvs 316
                                                   p+ + ++l++ ae+     +++   + +++  elsa+p+l++++ +e+++l++  +G+ +  +v+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125 265 PSVVAKELKTYAEQqvlprMRAVSDQSDIRFSELSAYPGLATDAHSEAAELIAAFSGSrEFGTVA 329
                                                   **********99987776656666778889999************************9899**** PP

                                     TIGR01892 317 ygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                   +gte gl+  +Gi++vv+GPG++dq h+pde+v +++lk c+a+l+r+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_29125 330 FGTEGGLFDAAGIPTVVCGPGSMDQGHKPDEFVSLDQLKGCDAMLQRM 377
                                                   *********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (382 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: 10.59
//
[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