Alignments for a candidate for argC in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Desulfovibrio oxyclinae DSM 11498

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_018125987.1 B149_RS0114990 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000375485.1:WP_018125987.1
          Length = 351

 Score =  308 bits (789), Expect = 2e-88
 Identities = 163/350 (46%), Positives = 223/350 (63%), Gaps = 3/350 (0%)

Query: 42  KMVIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRG--HYDLA 99
           K  I  G+VG TGY G+EL R++  HP + +  +TSR+EAG  ++++YP L+G    +L 
Sbjct: 2   KGTIAAGLVGVTGYAGMELARLMTSHPSMELVRVTSRAEAGKKLSDLYPFLQGLGPGELE 61

Query: 100 FSEPDVNVLG-ACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGM 158
            +EPD   L  +CD+VF A PH  AM +   L+  GV+VVDLSADFRL+D   +  WY +
Sbjct: 62  VTEPDPRDLATSCDVVFLAVPHKAAMEIAAVLLEEGVKVVDLSADFRLRDRCTYEQWYDV 121

Query: 159 AHESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIAD 218
            H  PE  E+AVYGLPE+  D I  A L+ANPGCYPTA  LG  P L+ GLV+   +I D
Sbjct: 122 PHTRPELLEQAVYGLPELYADRIPLANLIANPGCYPTASVLGLAPALKNGLVETDGVIID 181

Query: 219 AKSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLI 278
           AKSGASGAGR  K+  L  E+ +SF+AYG   HRH PEI Q     AG D+ ++F  HL+
Sbjct: 182 AKSGASGAGRGAKVPNLFCEVHDSFRAYGLPKHRHTPEIEQEAGLLAGTDMVLSFNTHLL 241

Query: 279 PMIRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMA 338
           P+ RGI AT+Y  LK+    + ++  +E  + D+P+V V+P G  PETR VRG   C + 
Sbjct: 242 PIDRGILATIYTSLKDGVTMEAVREAYESFYADKPYVRVLPEGKFPETRFVRGTMFCDIG 301

Query: 339 LHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           L    ++  +I+ S IDNL +GA+GQA+ N N+M GL  ++GL    L+P
Sbjct: 302 LVTDPRTGRLIILSAIDNLCRGASGQALANANLMCGLDISLGLPTAPLMP 351


Lambda     K      H
   0.321    0.137    0.412 

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: 391
Number of extensions: 14
Number of successful extensions: 2
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: 388
Length of database: 351
Length adjustment: 30
Effective length of query: 358
Effective length of database: 321
Effective search space:   114918
Effective search space used:   114918
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 WP_018125987.1 B149_RS0114990 (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.2610637.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-131  424.2   0.0   2.4e-131  424.0   0.0    1.0  1  NCBI__GCF_000375485.1:WP_018125987.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000375485.1:WP_018125987.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.0   0.0  2.4e-131  2.4e-131       3     345 .]       7     351 .]       5     351 .] 0.98

  Alignments for each domain:
  == domain 1  score: 424.0 bits;  conditional E-value: 2.4e-131
                             TIGR01850   3 vaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd..lkleeleeeeileeadvvfl 73 
                                           +++vG +GY+G+eL rl+++Hp++e+++++s+ eagkkls+++p l+gl    l+++e + +++++++dvvfl
  NCBI__GCF_000375485.1:WP_018125987.1   7 AGLVGVTGYAGMELARLMTSHPSMELVRVTSRAEAGKKLSDLYPFLQGLGPgeLEVTEPDPRDLATSCDVVFL 79 
                                           799************************9999999**************98754666666779999******** PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           A+ph++++e+++ lle+gvkv+dlSadfRl+d+ +Ye+wY  +h+++elle+avYGlpEl+ ++i  a+lian
  NCBI__GCF_000375485.1:WP_018125987.1  80 AVPHKAAMEIAAVLLEEGVKVVDLSADFRLRDRCTYEQWYDVPHTRPELLEQAVYGLPELYADRIPLANLIAN 152
                                           ************************************************************************* PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGCy+Ta++L+laP+lk++l+e++ +i+daksG SgAGr a+  +lf+ev++++++Y + kHrHtpEieqe +
  NCBI__GCF_000375485.1:WP_018125987.1 153 PGCYPTASVLGLAPALKNGLVETDGVIIDAKSGASGAGRGAKVPNLFCEVHDSFRAYGLPKHRHTPEIEQEAG 225
                                           ***********************99************************************************ PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292
                                            la++++++sf +hl+p+ rGilatiy+ lk+++t e +r++ye++Y+d+p+vrvl+eg++P+t+ v+g+ f+
  NCBI__GCF_000375485.1:WP_018125987.1 226 LLAGTDMVLSFNTHLLPIDRGILATIYTSLKDGVTMEAVREAYESFYADKPYVRVLPEGKFPETRFVRGTMFC 298
                                           ***99******************************************************************** PP

                             TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           dig+ +d +t+r++++saiDNL +Ga+gqA+ n Nlm+g+d + gL++ pl+p
  NCBI__GCF_000375485.1:WP_018125987.1 299 DIGLVTDPRTGRLIILSAIDNLCRGASGQALANANLMCGLDISLGLPTAPLMP 351
                                           **************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (351 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 14.03
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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