Alignments for a candidate for argC in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Nitriliruptor alkaliphilus DSM 45188

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_083441685.1 NITAL_RS16980 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000969705.1:WP_083441685.1
          Length = 365

 Score =  291 bits (746), Expect = 2e-83
 Identities = 162/351 (46%), Positives = 213/351 (60%), Gaps = 16/351 (4%)

Query: 46  KVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDV 105
           ++GIVG +GY G ELLR+ A HP   V+ + + S+AG P+ +++PNL G     F   +V
Sbjct: 23  RLGIVGASGYGGAELLRLAATHPAFEVAVVAAHSQAGTPIVDLFPNLAG--TRVFDAIEV 80

Query: 106 NVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEW 165
             L  CD+V  ATPH VA+ +  EL  AGVRVVDLSA FRL  +D +A WYG  H+ P+ 
Sbjct: 81  GALAECDVVVLATPHDVALELGAELFDAGVRVVDLSAAFRLS-VDGFATWYGGTHDRPDL 139

Query: 166 AE-------KAVYGLPEVV-RDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIA 217
           A         AVYGLPE+  R+ +R A LVANPGCYPTA  LG  PL   GL+ P  ++ 
Sbjct: 140 ATGDAAADPAAVYGLPELGHREAVRGATLVANPGCYPTATLLGLAPLA--GLLQPGTIVV 197

Query: 218 DAKSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHL 277
           DAKSG SGAGR  K  +    +     AYGA GHRH  EI + L G  G    V+F PHL
Sbjct: 198 DAKSGTSGAGRAAKDTLHFSHVHGDLSAYGAPGHRHTGEIERWLPGDLGA---VSFTPHL 254

Query: 278 IPMIRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRM 337
           +PM RG+ AT YA L +  D   +Q      + DEPFV V+  G  P T+++ G+N C++
Sbjct: 255 VPMARGLLATCYATLADGVDAAAVQDALTTAYADEPFVHVLAPGRFPHTKALAGSNGCQL 314

Query: 338 ALHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           +     ++  V V+S IDNL KGAAGQA+QN N+M G++ET GL    + P
Sbjct: 315 SAVVDGRTGRVTVTSAIDNLGKGAAGQALQNANLMLGIEETAGLTTVGVYP 365


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: 398
Number of extensions: 21
Number of successful extensions: 5
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: 365
Length adjustment: 30
Effective length of query: 358
Effective length of database: 335
Effective search space:   119930
Effective search space used:   119930
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: 50 (23.9 bits)

Align candidate WP_083441685.1 NITAL_RS16980 (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.9046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-116  375.4   0.0   1.7e-116  375.2   0.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_083441685.1  NITAL_RS16980 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_083441685.1  NITAL_RS16980 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.2   0.0  1.7e-116  1.7e-116       2     345 .]      23     365 .]      22     365 .] 0.95

  Alignments for each domain:
  == domain 1  score: 375.2 bits;  conditional E-value: 1.7e-116
                                 TIGR01850   2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 
                                               +++ivGasGY+GaeLlrl a+Hp++ev+ ++++++ag+++ +++p+l g+    ++++e+  +l+e+dv
  lcl|NCBI__GCF_000969705.1:WP_083441685.1  23 RLGIVGASGYGGAELLRLAATHPAFEVAVVAAHSQAGTPIVDLFPNLAGT--RVFDAIEVG-ALAECDV 88 
                                               689*************************9999999************997..578888886.4679*** PP

                                 TIGR01850  71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelle.......eavYGlpE 132
                                               v+lA+ph v+ el +el ++gv+v+dlSa+fRl+  + +++wYg +h++++l++        avYGlpE
  lcl|NCBI__GCF_000969705.1:WP_083441685.1  89 VVLATPHDVALELGAELFDAGVRVVDLSAAFRLS-VDGFATWYGGTHDRPDLATgdaaadpAAVYGLPE 156
                                               **********************************.668************9875333333469****** PP

                                 TIGR01850 133 ln.reeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenl 200
                                               l  re++++a+l+anPGCy+Ta+lL+laPl+  +l++p +i+vdaksG+SgAGr+a+++ +f++v++ l
  lcl|NCBI__GCF_000969705.1:WP_083441685.1 157 LGhREAVRGATLVANPGCYPTATLLGLAPLA--GLLQPGTIVVDAKSGTSGAGRAAKDTLHFSHVHGDL 223
                                               *77***************************9..999********************************* PP

                                 TIGR01850 201 kpYkvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYede 269
                                               ++Y + +HrHt Eie+ l    ++   vsftphlvpm rG+lat+ya+l+++++++ ++++++++Y+de
  lcl|NCBI__GCF_000969705.1:WP_083441685.1 224 SAYGAPGHRHTGEIERWLP---GDLGAVSFTPHLVPMARGLLATCYATLADGVDAAAVQDALTTAYADE 289
                                               ******************9...44445****************************************** PP

                                 TIGR01850 270 pfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegL 338
                                               pfv+vl  g++P+tka +gsn ++++  vd +t+rv+v+saiDNL KGaagqA+qn Nlmlg +et+gL
  lcl|NCBI__GCF_000969705.1:WP_083441685.1 290 PFVHVLAPGRFPHTKALAGSNGCQLSAVVDGRTGRVTVTSAIDNLGKGAAGQALQNANLMLGIEETAGL 358
                                               ********************************************************************* PP

                                 TIGR01850 339 eklpllp 345
                                               ++++++p
  lcl|NCBI__GCF_000969705.1:WP_083441685.1 359 TTVGVYP 365
                                               *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (365 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: 9.98
//
[ok]

This GapMind analysis is from Apr 10 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