Alignments for a candidate for argC in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Archaeoglobus veneficus SNP6

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_013683323.1 ARCVE_RS03110 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000194625.1:WP_013683323.1
          Length = 333

 Score =  268 bits (685), Expect = 2e-76
 Identities = 153/345 (44%), Positives = 210/345 (60%), Gaps = 12/345 (3%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103
           ++KVGIVGG+GYTG ELLR+L  HP+  V  +TSR   G PV E +P L+G  DL F  P
Sbjct: 1   MVKVGIVGGSGYTGSELLRLLYKHPKAEVVAVTSRKWEGKPVWECHPFLKGFCDLTFVSP 60

Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163
           ++     CD+VF A PHG AM+ VP+L+  G++VVDLSAD+RL+  DV+   YG+ HE+ 
Sbjct: 61  EIKNFDGCDIVFTAVPHGEAMKYVPQLLDVGIKVVDLSADYRLQK-DVYEKAYGLEHEA- 118

Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223
               +AVYGLPE+ RDE+  A LVANPGCYPT   L   PL + GL++  R++ D+KSG 
Sbjct: 119 --YREAVYGLPELHRDEVAKADLVANPGCYPTGCILAAAPLAKAGLIE--RVVFDSKSGI 174

Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283
           +GAG +      +  + E+   Y  + HRH  E+ Q + G     V V+F P + P  RG
Sbjct: 175 TGAGIKPTEFTHYPNLHEAIVPYKVTNHRHYYEMVQEI-GELQDGVKVSFTPQVFPGSRG 233

Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343
           I    +  LK     + ++ ++E+ + D  FV +    +      VRG+N C +A+   E
Sbjct: 234 ILTNAHIFLKENVSLEEVRRIYEEFYKDCYFVRMQ---NMVRLSWVRGSNFCDIAVFAGE 290

Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
               V+VSS IDNLVKGA+GQA+QNMNIM G  E  GL+ P L P
Sbjct: 291 DR--VVVSSAIDNLVKGASGQAIQNMNIMLGFDEKEGLDFPPLFP 333


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: 386
Number of extensions: 20
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: 333
Length adjustment: 29
Effective length of query: 359
Effective length of database: 304
Effective search space:   109136
Effective search space used:   109136
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_013683323.1 ARCVE_RS03110 (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.20384.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-127  411.5   0.0   1.6e-127  411.4   0.0    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013683323.1  ARCVE_RS03110 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013683323.1  ARCVE_RS03110 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.4   0.0  1.6e-127  1.6e-127       1     345 []       2     333 .]       2     333 .] 0.97

  Alignments for each domain:
  == domain 1  score: 411.4 bits;  conditional E-value: 1.6e-127
                                 TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileea 68 
                                               +kv+ivG+sGYtG eLlrll kHp++ev+ +v+sr+ +gk++ e+hp lkg+ dl++ + e+++  + +
  lcl|NCBI__GCF_000194625.1:WP_013683323.1   2 VKVGIVGGSGYTGSELLRLLYKHPKAEVV-AVTSRKwEGKPVWECHPFLKGFCDLTFVSPEIKN-FDGC 68 
                                               69***************************.7777777*********************999986.57** PP

                                 TIGR01850  69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137
                                               d+vf+A+phg ++++vp+ll+ g+kv+dlSad+Rl+ ++vYek Yg +he+   ++eavYGlpEl+r+e
  lcl|NCBI__GCF_000194625.1:WP_013683323.1  69 DIVFTAVPHGEAMKYVPQLLDVGIKVVDLSADYRLQ-KDVYEKAYGLEHEA---YREAVYGLPELHRDE 133
                                               ************************************.77********9999...89************* PP

                                 TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206
                                               ++ka+l+anPGCy+T+ +La aPl+k++lie+  +++d+ksG++gAG k++e +++++++e + pYkvt
  lcl|NCBI__GCF_000194625.1:WP_013683323.1 134 VAKADLVANPGCYPTGCILAAAPLAKAGLIER--VVFDSKSGITGAGIKPTEFTHYPNLHEAIVPYKVT 200
                                               ******************************96..8********************************** PP

                                 TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275
                                               +HrH  E++qe+++l+ + vkvsftp+++p +rGil+ +++ lk++++ ee+r++yee+Y+d  fvr++
  lcl|NCBI__GCF_000194625.1:WP_013683323.1 201 NHRHYYEMVQEIGELQ-DGVKVSFTPQVFPGSRGILTNAHIFLKENVSLEEVRRIYEEFYKDCYFVRMQ 268
                                               *************887.6899**********************************************98 PP

                                 TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344
                                               +   + ++++v+gsnf+di+v   e  +rvvv saiDNLvKGa+gqA+qn+N+mlgfde+egL++ pl+
  lcl|NCBI__GCF_000194625.1:WP_013683323.1 269 N---MVRLSWVRGSNFCDIAVFAGE--DRVVVSSAIDNLVKGASGQAIQNMNIMLGFDEKEGLDFPPLF 332
                                               7...789*************99988..8***************************************99 PP

                                 TIGR01850 345 p 345
                                               p
  lcl|NCBI__GCF_000194625.1:WP_013683323.1 333 P 333
                                               8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (333 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: 00:00:00.01
# Mc/sec: 6.99
//
[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