Alignments for a candidate for argC in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Escherichia coli BW25113

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 17997 b3958 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI)

Query= BRENDA::P11446
         (334 letters)



>FitnessBrowser__Keio:17997
          Length = 334

 Score =  672 bits (1735), Expect = 0.0
 Identities = 334/334 (100%), Positives = 334/334 (100%)

Query: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60
           MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL
Sbjct: 1   MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60

Query: 61  QPMSDISEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGF 120
           QPMSDISEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGF
Sbjct: 61  QPMSDISEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGF 120

Query: 121 THQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVI 180
           THQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVI
Sbjct: 121 THQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVI 180

Query: 181 NATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRGIL 240
           NATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRGIL
Sbjct: 181 NATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRGIL 240

Query: 241 ETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIGFAVQGEHL 300
           ETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIGFAVQGEHL
Sbjct: 241 ETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIGFAVQGEHL 300

Query: 301 IIVATEDNLLKGAAAQAVQCANIRFGYAETQSLI 334
           IIVATEDNLLKGAAAQAVQCANIRFGYAETQSLI
Sbjct: 301 IIVATEDNLLKGAAAQAVQCANIRFGYAETQSLI 334


Lambda     K      H
   0.321    0.136    0.409 

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: 592
Number of extensions: 10
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 17997 b3958 (N-acetyl-gamma-glutamyl-phosphate reductase (NCBI))
to HMM TIGR01850 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))

# 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/TIGR01850.hmm
# target sequence database:        /tmp/gapView.12131.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01850  [M=345]
Accession:   TIGR01850
Description: argC: N-acetyl-gamma-glutamyl-phosphate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.1e-129  416.1   0.0   6.8e-129  415.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:17997  b3958 N-acetyl-gamma-glutamyl-ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17997  b3958 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.9   0.0  6.8e-129  6.8e-129       2     338 ..       3     333 ..       2     334 .] 0.98

  Alignments for each domain:
  == domain 1  score: 415.9 bits;  conditional E-value: 6.8e-129
                       TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvdlkleelee.eeileeadvvflAlp 76 
                                     ++ ivGasGY+GaeL+ ++++Hp++++t+l++s +   agk +s++hp+lkg+vdl l+++++ +e++  +dvvflA++
  lcl|FitnessBrowser__Keio:17997   3 NTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQsndAGKLISDLHPQLKGIVDLPLQPMSDiSEFSPGVDVVFLATA 81 
                                     578*************************9888877789**********************9999999************ PP

                       TIGR01850  77 hgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaal 155
                                     h+vs++l+p++le+g++v+dlS++fR++da++Yek+Yg++h+++elle+a+YGl+E+  +++k+a+lia+PGCy+Taa+
  lcl|FitnessBrowser__Keio:17997  82 HEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQ 160
                                     ******************************************************************************* PP

                       TIGR01850 156 LalaPllkekliepks.iivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftph 233
                                     Lal+Pl++++l++ ++ ++++a sGvSgAGrka  +++f+ev  +l+pY v++HrH+pEi+++l+      + v+ftph
  lcl|FitnessBrowser__Keio:17997 161 LALKPLIDADLLDLNQwPVINATSGVSGAGRKAAISNSFCEV--SLQPYGVFTHRHQPEIATHLG------ADVIFTPH 231
                                     ******************************************..*********************......78****** PP

                       TIGR01850 234 lvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiD 312
                                     l ++ rGil ti+++lk+++t+++++++++++Y+++p+vr+++ + +P++k+v+g  f+dig+av+   +++++v++ D
  lcl|FitnessBrowser__Keio:17997 232 LGNFPRGILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYD-KGVPALKNVVGLPFCDIGFAVQG--EHLIIVATED 307
                                     ******************************************9.89********************9..8********* PP

                       TIGR01850 313 NLvKGaagqAvqnlNlmlgfdetegL 338
                                     NL+KGaa+qAvq+ N+++g++et++L
  lcl|FitnessBrowser__Keio:17997 308 NLLKGAAAQAVQCANIRFGYAETQSL 333
                                     ***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (334 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.92
//
[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