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_1185 Acetylornithine deacetylase (EC 3.5.1.16)

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185
          Length = 413

 Score =  283 bits (723), Expect = 8e-81
 Identities = 153/376 (40%), Positives = 210/376 (55%), Gaps = 10/376 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           EI   L+GF SV    N D++ W+ GYL   G+   +LP   G ++N+FA++GP    G 
Sbjct: 28  EIARTLIGFPSVSDRSNLDLIEWVSGYLHGFGVQAQILPDASGRKANLFASLGPPRPGGI 87

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           I+SGH DVVP A   W  DPF   ++ DRLYGRG++DMKGF+A VLA VP+L A   R+ 
Sbjct: 88  ILSGHTDVVPVAGQAWAQDPFSAYLDQDRLYGRGSSDMKGFIAVVLAMVPELMASA-RQS 146

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
            HLALSYDEE G  G  H+   + +   +P G I+GEPT M  +  HKG+      V G+
Sbjct: 147 FHLALSYDEEVGAMGAKHLAPFITQAQLEPAGCIVGEPTSMALVIGHKGRHEINCCVHGK 206

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244
             HSS P++G+NAI   A V  Q    A RL  GP +  F+ PY+++Q+  V GG A N+
Sbjct: 207 VAHSSLPNEGVNAIDYAARVQMQLQHVARRLSQGPLDSGFDVPYTTVQVCRVNGGVAGNV 266

Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTAEAL-------TTLGFEVEWQELSAYPALSL 297
           IP  C  +FE R + G D  +LL  ++  A+               +E+      P L  
Sbjct: 267 IPGQCSFDFEIRYLPGCDAEQLLVQIKDDAKQAMHSETDDRAWAASIEFSHTLHTPGLDE 326

Query: 298 EPDAPLAALLEELTG-REALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
           + +   A  + E +        V+Y TEAGLFQ AGI  I+CGPG I +AHK +EY+ + 
Sbjct: 327 KGNQAFAQWVREASSMAHGRQRVAYSTEAGLFQAAGIPTIVCGPGSIKQAHKVNEYVDLA 386

Query: 357 ELMACRAMVEALGARC 372
           +L AC   +  L ARC
Sbjct: 387 QLKACEQFLRRL-ARC 401


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: 426
Number of extensions: 16
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: 413
Length adjustment: 31
Effective length of query: 343
Effective length of database: 382
Effective search space:   131026
Effective search space used:   131026
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_1185 (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.20678.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.4e-116  374.7   0.0   2.7e-116  374.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.5   0.0  2.7e-116  2.7e-116       1     364 [.      28     398 ..      28     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 374.5 bits;  conditional E-value: 2.7e-116
                                      TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 
                                                    ei + L++f+svs rsn+dlie+v +yl+  gv+++ lp a g  k nl+a+ Gp +  gg++l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185  28 EIARTLIGFPSVSDRSNLDLIEWVSGYLHGFGVQAQILPDASG-RKANLFASLGPPR-PGGIIL 89 
                                                    68899**************************************.9***********9.9***** PP

                                      TIGR01892  65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvls 128
                                                    sGhtDvvPv+++aW++Dpf     ++rLYgrG++DmkGF+a+vLa vp+l a   ++  hl+ls
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185  90 SGHTDVVPVAGQAWAQDPFSAYLDQDRLYGRGSSDMKGFIAVVLAMVPELMAS-ARQSFHLALS 152
                                                    **************************************************875.699******* PP

                                      TIGR01892 129 aDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrG 189
                                                    +Deevg +Gak+l+  ++     pa  ivGePts+  v  hkG    +  v+G+ +hss p++G
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 153 YDEEVGAMGAKHLAPFITqaqLEPAGCIVGEPTSMALVIGHKGRHEINCCVHGKVAHSSLPNEG 216
                                                    ************98777666699***************************************** PP

                                      TIGR01892 190 vsaielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpi 253
                                                    v+ai  aa++  +l + a +l +++l+++F++py+t+++ +v+GG a n+i+++C + +e+R +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 217 VNAIDYAARVQMQLQHVARRLSQGPLDSGFDVPYTTVQVCRVNGGVAGNVIPGQCSFDFEIRYL 280
                                                    **************************************************************** PP

                                      TIGR01892 254 pGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.. 310
                                                    pG d e+ll ++++ a++        +a +  ++  ++  tp+l+ + ++  ++ +++++    
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 281 PGCDAEQLLVQIKDDAKQamhseTDDRAWAASIEFSHTLHTPGLDEKGNQAFAQWVREASSMah 344
                                                    *********99998766633333445556667778888899******************99855 PP

                                      TIGR01892 311 aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                      + v+y+teagl+q +Gi+++v+GPG+i+qah+ +eYv++ +lk+c+++l+rl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 345 GRQRVAYSTEAGLFQAAGIPTIVCGPGSIKQAHKVNEYVDLAQLKACEQFLRRL 398
                                                    6789***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (413 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.53
//
[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