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_367 Acetylornithine deacetylase (EC 3.5.1.16)

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367
          Length = 385

 Score =  234 bits (598), Expect = 2e-66
 Identities = 137/373 (36%), Positives = 207/373 (55%), Gaps = 11/373 (2%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           I  +L+ F +V    N  ++ ++R  L S GI   ++    G ++N+FA+ GP++  G +
Sbjct: 8   IFERLLAFETVSSESNLALIEYVRELLLSKGIESLIVKDESGKKANLFASTGPRDLPGVL 67

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVPAA   WT   F+  V   R+YGRG+ DMKGF+A  + A+   A   L RPL
Sbjct: 68  LSGHTDVVPAAGQAWTVPAFQATVRDGRVYGRGSCDMKGFIALAIDAMLDAADHSLNRPL 127

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
            LALS+DEE GC GV  ++  L     +P   +IGEPT M+ +  HKGK + R   RG  
Sbjct: 128 QLALSHDEEIGCVGVRRLLDVLHLAPVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLE 187

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLV--GGPFEHVFEPPYSSLQIGTVKGGQAVN 243
            HSS   + +NAIH VA     A+ ++ + +   G  +  ++ PYS++ +G + GG+A+N
Sbjct: 188 AHSSLAPRSVNAIH-VACDFIAALRQSQQQLQEQGAQDADYDVPYSTVHVGQIVGGKALN 246

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALT------TLGFEVEWQELSAYPALSL 297
           I+P+ C ++FE R +   D    L  +R+ AE +       +   ++E + L+ YP L  
Sbjct: 247 IVPNLCTLDFEVRNLPDDDLDLFLEQLRERAEVIVREAKKLSSVADIEIETLNVYPGLDT 306

Query: 298 EPDAPLAALLEEL-TGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355
            P       L+   T       VS+GTE GLF QR  +  ++CGPG I +AHKPDE+I I
Sbjct: 307 HPSVEAVRFLKNFATPGTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIEI 366

Query: 356 DELMACRAMVEAL 368
            ++ A    +E L
Sbjct: 367 SQMDAGERFLEGL 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: 355
Number of extensions: 12
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: 385
Length adjustment: 30
Effective length of query: 344
Effective length of database: 355
Effective search space:   122120
Effective search space used:   122120
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 Pf6N2E2_367 (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.5272.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   8.6e-111  356.4   0.0   9.7e-111  356.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.3   0.0  9.7e-111  9.7e-111       2     363 ..       8     378 ..       7     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 356.3 bits;  conditional E-value: 9.7e-111
                                     TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsG 66 
                                                   i+++L+af++vs  sn++lieyv++ l ++g++   ++   g +k nl+a+ Gp++   g++lsG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367   8 IFERLLAFETVSSESNLALIEYVRELLLSKGIESLIVKDESG-KKANLFASTGPRD-LPGVLLSG 70 
                                                   899**********************************99999.9***********9.9******* PP

                                     TIGR01892  67 htDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDe 131
                                                   htDvvP++++aWt  +f+ t++dgr+YgrG++DmkGF+al+++a+ d a + L +Pl l+ls De
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367  71 HTDVVPAAGQAWTVPAFQATVRDGRVYGRGSCDMKGFIALAIDAMLDAADHSLNRPLQLALSHDE 135
                                                   ***************************************************************** PP

                                     TIGR01892 132 evglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsai 193
                                                   e+g+ G+++l+++l     rp l ++GePt+++ v  hkGk s +   rG e+hss + r v+ai
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 136 EIGCVGVRRLLDVLHlapVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLAPRSVNAI 200
                                                   ************9987889********************************************** PP

                                     TIGR01892 194 elaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmd 257
                                                   ++a +++a l + +++l++ + ++  +++py+t+++G++ GGka ni+++ C l +e+R +p  d
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 201 HVACDFIAALRQSQQQLQEqGAQDADYDVPYSTVHVGQIVGGKALNIVPNLCTLDFEVRNLPDDD 265
                                                   *****************996778889*************************************** PP

                                     TIGR01892 258 peellallekiaeevkekapg....fevkveelsatpaleleedaelvallekla..Gaaaevvs 316
                                                   ++  l++l++ ae ++++a +     ++++e+l+ +p+l++++  e+v++l++ a  G  +  vs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 266 LDLFLEQLRERAEVIVREAKKlssvADIEIETLNVYPGLDTHPSVEAVRFLKNFAtpGTGTAKVS 330
                                                   ********999998776654411115678999********************98744779999** PP

                                     TIGR01892 317 ygteagll.qelGieavvlGPGdidqahqpdeYveieelkrcraller 363
                                                   +gte gl+ q+l ++ vv+GPG+i+qah+pde++ei+++ +++ +le 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 331 FGTEGGLFkQRLDVPVVVCGPGSIEQAHKPDEFIEISQMDAGERFLEG 378
                                                   ******996789*******************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (385 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: 12.11
//
[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