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.5197.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.34
//
[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