GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Escherichia coli BW25113

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 17998 b3959 acetylglutamate kinase (RefSeq)

Query= BRENDA::A0A140NEG9
         (258 letters)



>FitnessBrowser__Keio:17998
          Length = 258

 Score =  499 bits (1285), Expect = e-146
 Identities = 258/258 (100%), Positives = 258/258 (100%)

Query: 1   MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK 60
           MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK
Sbjct: 1   MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK 60

Query: 61  KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG 120
           KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG
Sbjct: 61  KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG 120

Query: 121 HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS 180
           HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS
Sbjct: 121 HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS 180

Query: 181 DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA 240
           DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA
Sbjct: 181 DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA 240

Query: 241 EQLPALFNGMPMGTRILA 258
           EQLPALFNGMPMGTRILA
Sbjct: 241 EQLPALFNGMPMGTRILA 258


Lambda     K      H
   0.317    0.136    0.381 

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: 375
Number of extensions: 5
Number of successful extensions: 1
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate 17998 b3959 (acetylglutamate kinase (RefSeq))
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))

# 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/TIGR00761.hmm
# target sequence database:        /tmp/gapView.20603.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00761  [M=231]
Accession:   TIGR00761
Description: argB: acetylglutamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    3.2e-82  261.5   2.0    3.7e-82  261.3   2.0    1.0  1  lcl|FitnessBrowser__Keio:17998  b3959 acetylglutamate kinase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17998  b3959 acetylglutamate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   2.0   3.7e-82   3.7e-82       2     231 .]       5     234 ..       4     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 3.7e-82
                       TIGR00761   2 iViKiGGaais..elleelakdiaklrkegik.lvivHGGgpeinelleklgievefvnglRvTdketlevvemvligk 77 
                                     ++iK+GG++++  e+le+l+++++++r+++++ lvivHGGg+ ++el++ l+++v+++nglRvT ++++++++ +l+g+
  lcl|FitnessBrowser__Keio:17998   5 LIIKLGGVLLDseEALERLFSALVNYRESHQRpLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGT 83 
                                     69********9999******************889******************************************** PP

                       TIGR00761  78 vnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllNvna 156
                                     +nk+l+a+ +kh+i+avGl+ +Dg+ +++++ld+e lg+vG ++  +++l+++ll++g++pv++s+++++egql+Nvna
  lcl|FitnessBrowser__Keio:17998  84 ANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEE-LGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNA 161
                                     **********************************9.******************************************* PP

                       TIGR00761 157 DtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231
                                     D+aA++lAa+l+A+ L+lL+dv+Gil+g+++ +i+e++++++eqli+q++i++Gmi Kv+aal+a++++ + v i
  lcl|FitnessBrowser__Keio:17998 162 DQAATALAATLGAD-LILLSDVSGILDGKGQ-RIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDI 234
                                     **************.*************555.*************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (258 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: 00:00:00.00
# Mc/sec: 8.86
//
[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:

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:

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:

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:

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