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_26745 AO356_26745 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26745
          Length = 385

 Score =  238 bits (607), Expect = 2e-67
 Identities = 134/373 (35%), Positives = 205/373 (54%), Gaps = 9/373 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           +IL +L+ F +V    N  ++ ++R  L + GI   ++    G ++N+FA+ GP++  G 
Sbjct: 7   DILKRLMAFDTVSSESNMALIEYVRDLLLTKGIESLIVQDESGKKANLFASTGPRDVPGI 66

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVPAA   WT   F   V+  R+YGRG+ DMKGF+A  + A+ +    PL RP
Sbjct: 67  LLSGHTDVVPAAGQAWTFPAFEATVQDGRIYGRGSCDMKGFIALAVDAMLEATEQPLSRP 126

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           L LALS+DEE GC GV  ++  L     +P   +IGEPT M+ +  HKGK + R   RG 
Sbjct: 127 LQLALSHDEEIGCVGVRRLLDVLHLAPVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGL 186

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243
             HSS   + +NAIH     +        +L   G  +  ++ PYS++ +G + GG+A+N
Sbjct: 187 EAHSSLAPRSVNAIHVACDFIAALRLSQQQLQEQGARDTDYDVPYSTVHVGQIVGGKALN 246

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

Query: 298 EPDAPLAALLEELTGREALPA-VSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355
            P       L+     +   A VS+GTE GLF QR  +  ++CGPG I +AHKPDE+I I
Sbjct: 307 HPSVEAVRFLKNFAAPDTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIEI 366

Query: 356 DELMACRAMVEAL 368
            ++ A    ++ L
Sbjct: 367 SQMDAGERFLQGL 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: 348
Number of extensions: 15
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 AO356_26745 AO356_26745 (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.4029438.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-108  348.9   0.0   1.9e-108  348.7   0.0    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_26745  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_26745  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.7   0.0  1.9e-108  1.9e-108       1     364 [.       7     379 ..       7     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 348.7 bits;  conditional E-value: 1.9e-108
                                   TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGh 67 
                                                 +il++L+afd+vs  sn++lieyv+d l  +g++   ++   g +k nl+a+ Gp++   g++lsGh
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745   7 DILKRLMAFDTVSSESNMALIEYVRDLLLTKGIESLIVQDESG-KKANLFASTGPRD-VPGILLSGH 71 
                                                 79*******************************9999988888.9***********9.9******** PP

                                   TIGR01892  68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevg 134
                                                 tDvvP++++aWt  +f  t++dgr+YgrG++DmkGF+al+++a+ +   ++L +Pl l+ls Dee+g
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745  72 TDVVPAAGQAWTFPAFEATVQDGRIYGRGSCDMKGFIALAVDAMLEATEQPLSRPLQLALSHDEEIG 138
                                                 ********************************************9999******************* PP

                                   TIGR01892 135 laGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaak 198
                                                 + G+++l+++l     rp l ++GePt+++ v  hkGk s +   rG e+hss + r v+ai++a +
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745 139 CVGVRRLLDVLHlapVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLAPRSVNAIHVACD 205
                                                 *********9987889*************************************************** PP

                                   TIGR01892 199 llarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellal 264
                                                 ++a l   +++l++ +  +  +++py+t+++G++ GGka ni+++ C l +e+R +p  d++  l++
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745 206 FIAALRLSQQQLQEqGARDTDYDVPYSTVHVGQIVGGKALNIVPNLCTLDFEVRNLPADDLDGFLEQ 272
                                                 ************996788999********************************************** PP

                                   TIGR01892 265 lekiaeevkeka....pgfevkveelsatpaleleedaelvalleklaGa..aaevvsygteagll. 324
                                                 +++ ae ++ +a        +++e+l+ +p+l++++  e+v++l++ a     +  vs+gte gl+ 
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745 273 MRERAELIVGEArklsSVAAIEIETLNVYPGLDTHPSVEAVRFLKNFAAPdtGTAKVSFGTEGGLFk 339
                                                 *9999986544311103456789999********************9887567889********996 PP

                                   TIGR01892 325 qelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                 q+l ++ vv+GPG+i+qah+pde++ei+++ +++ +l+ l
  FitnessBrowser__pseudo5_N2C3_1:AO356_26745 340 QRLDVPVVVCGPGSIEQAHKPDEFIEISQMDAGERFLQGL 379
                                                 789*******************************999876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 17.11
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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