Alignments for a candidate for argC in Nocardioides dokdonensis FR1436

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Nocardioides dokdonensis FR1436

Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_068111444.1 I601_RS15140 N-acetyl-gamma-glutamyl-phosphate reductase

Query= BRENDA::P9WPZ9
         (352 letters)



>NCBI__GCF_001653335.1:WP_068111444.1
          Length = 345

 Score =  425 bits (1093), Expect = e-124
 Identities = 211/346 (60%), Positives = 258/346 (74%), Gaps = 9/346 (2%)

Query: 11  KVAVAGASGYAGGEILRLLLGHPAYADGRLRIGALTAATSAGSTLGEHHPHLTPLAHRVV 70
           +VAVAGASGYAGGE+LRLLL HP      + IGALT A++AG  LG   PHL PLA RV+
Sbjct: 5   RVAVAGASGYAGGEVLRLLLSHP-----EVEIGALTGASNAGQPLGALQPHLVPLADRVL 59

Query: 71  EPTEAAVLGGHDAVFLALPHGHSAVLAQQLSPETLIIDCGADFRLTDAAVWERFYGSSHA 130
           EPT   VL GHD VFLALPHG S  +A QL  +T++IDCGADFRL DA  W +FYG  HA
Sbjct: 60  EPTTIEVLSGHDVVFLALPHGQSGEVAAQLGDDTVVIDCGADFRLRDAGEWAKFYGGEHA 119

Query: 131 GSWPYGLPELPGARDQLRGTRRIAVPGCYPTAALLALFPALAADLIEPAVTVVAVSGTSG 190
           G+WPYGLPELPG R +LRG RRIAVPGCYPT + L+L PA+AA ++EP V++VA SGTSG
Sbjct: 120 GTWPYGLPELPGQRQELRGARRIAVPGCYPTVSTLSLAPAVAAGIVEPRVSIVAASGTSG 179

Query: 191 AGRAATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAVTDRDVSVSFTPVLIPASRGI 250
           AG+AA + LLG+E++G+A AY + G HRHTPEI Q L A+ D  V+VSFTP+L+P SRGI
Sbjct: 180 AGKAAKSHLLGSEIMGNASAYGVGGDHRHTPEITQNLSALVDETVAVSFTPLLVPMSRGI 239

Query: 251 LATCTARTRS----PLSQLRAAYEKAYHAEPFIYLMPEGQLPRTGAVIGSNAAHIAVAVD 306
           LATC+A  R+       +  A Y +AY  EPF++++P GQ P+T +VIGSNA H+ V VD
Sbjct: 240 LATCSADLRAGHEVDAEEAHAIYAQAYAHEPFVHVLPRGQWPQTKSVIGSNALHLQVTVD 299

Query: 307 EDAQTFVAIAAIDNLVKGTAGAAVQSMNLALGWPETDGLSVVGVAP 352
           E A   VA+ A+DNL KGTAGAAVQ MNLALG  E  GL+ +G+AP
Sbjct: 300 EVAGRLVAVGAVDNLAKGTAGAAVQCMNLALGLDEGTGLTTIGLAP 345


Lambda     K      H
   0.318    0.133    0.393 

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: 446
Number of extensions: 31
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: 352
Length of database: 345
Length adjustment: 29
Effective length of query: 323
Effective length of database: 316
Effective search space:   102068
Effective search space used:   102068
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: 49 (23.5 bits)

Align candidate WP_068111444.1 I601_RS15140 (N-acetyl-gamma-glutamyl-phosphate reductase)
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.1188930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-119  384.9   0.0   2.1e-119  384.7   0.0    1.0  1  NCBI__GCF_001653335.1:WP_068111444.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068111444.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.7   0.0  2.1e-119  2.1e-119       1     345 []       4     345 .]       4     345 .] 0.97

  Alignments for each domain:
  == domain 1  score: 384.7 bits;  conditional E-value: 2.1e-119
                             TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 
                                           ++va+ GasGY+G+e+lrll +Hpeve+ +l++ ++ag++l ++ phl  l+d  le++++e +l+ +dvvfl
  NCBI__GCF_001653335.1:WP_068111444.1   4 VRVAVAGASGYAGGEVLRLLLSHPEVEIGALTGASNAGQPLGALQPHLVPLADRVLEPTTIE-VLSGHDVVFL 75 
                                           58*******************************************************99998.678******* PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpEln..reeikkakli 144
                                           Alphg+s e++++ l  +++vid++adfRl+da +++k+Yg +h+      ++ YGlpEl   r+e+++a++i
  NCBI__GCF_001653335.1:WP_068111444.1  76 ALPHGQSGEVAAQ-LGDDTVVIDCGADFRLRDAGEWAKFYGGEHAG-----TWPYGLPELPgqRQELRGARRI 142
                                           **********966.67889*************************99.....8********988********** PP

                             TIGR01850 145 anPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieq 216
                                           a+PGCy+T ++L+laP+++++++ep+ + + a sG+SgAG++a+ + l +e+++n ++Y v  +HrHtpEi q
  NCBI__GCF_001653335.1:WP_068111444.1 143 AVPGCYPTVSTLSLAPAVAAGIVEPR-VSIVAASGTSGAGKAAKSHLLGSEIMGNASAYGVGgDHRHTPEITQ 214
                                           ************************96.9999******************************999********* PP

                             TIGR01850 217 elsklaekkvkvsftphlvpmtrGilatiyaklkke..lteeelrklyeevYedepfvrvlkegelPstkavl 287
                                           +ls+l +++v vsftp lvpm+rGilat++a l+++  +++ee +++y+++Y++epfv+vl+ g++P+tk+v+
  NCBI__GCF_001653335.1:WP_068111444.1 215 NLSALVDETVAVSFTPLLVPMSRGILATCSADLRAGheVDAEEAHAIYAQAYAHEPFVHVLPRGQWPQTKSVI 287
                                           ******************************9998765599********************************* PP

                             TIGR01850 288 gsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           gsn+ +++v+vde ++r+v v a+DNL KG+ag Avq++Nl+lg+de +gL++++l+p
  NCBI__GCF_001653335.1:WP_068111444.1 288 GSNALHLQVTVDEVAGRLVAVGAVDNLAKGTAGAAVQCMNLALGLDEGTGLTTIGLAP 345
                                           ******************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (345 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: 00:00:00.00
# Mc/sec: 16.57
//
[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