Alignments for a candidate for argC in Thiomicrospira pelophila DSM 1534

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Thiomicrospira pelophila DSM 1534

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_029935993.1 N746_RS0109310 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000711195.1:WP_029935993.1
          Length = 347

 Score =  480 bits (1235), Expect = e-140
 Identities = 234/344 (68%), Positives = 276/344 (80%)

Query: 45  IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPD 104
           I+VGIVGGTGYTGVELLR+LA HP   V  ITSRSEAGM VAEM+PNLRGHYDLAFSEPD
Sbjct: 4   IQVGIVGGTGYTGVELLRLLANHPHAEVKVITSRSEAGMKVAEMFPNLRGHYDLAFSEPD 63

Query: 105 VNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPE 164
           ++ L +CDLVFFATPHGVAM + PEL+ AGVRV+DL+ADFRL DL VW NWYGMAH  PE
Sbjct: 64  MSTLTSCDLVFFATPHGVAMSLTPELVQAGVRVIDLAADFRLNDLQVWENWYGMAHTCPE 123

Query: 165 WAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGAS 224
             ++ VYGLPE  R++I+ A+++ANPGCYPTAVQLGF PLL+ GLVD   LIAD KSG S
Sbjct: 124 IMDEVVYGLPEFNREKIKTAKVIANPGCYPTAVQLGFQPLLKAGLVDIDHLIADGKSGVS 183

Query: 225 GAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGI 284
           GAGR  K+G L  E  E FKAYG +GHRHLPEI +GL   AG  V +TFVPHL+PMIRGI
Sbjct: 184 GAGRGAKVGSLSAETSEGFKAYGINGHRHLPEIAEGLNHMAGSRVNLTFVPHLVPMIRGI 243

Query: 285 EATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQ 344
           EATLY +L      ++LQ LFE+ +  EPFVDVMP GS P+TR V+G+N CRMA++R   
Sbjct: 244 EATLYGKLNQDWSQEQLQELFEKHYAQEPFVDVMPAGSLPDTRMVKGSNMCRMAVYRPAG 303

Query: 345 SNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
            ++V+V+SVIDNLVKGA+GQAVQNMN+MFGL+ET GLE  AL+P
Sbjct: 304 GDVVVVTSVIDNLVKGASGQAVQNMNLMFGLEETCGLEQVALMP 347


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: 441
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: 388
Length of database: 347
Length adjustment: 30
Effective length of query: 358
Effective length of database: 317
Effective search space:   113486
Effective search space used:   113486
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_029935993.1 N746_RS0109310 (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.14608.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-137  444.5   0.0   1.5e-137  444.3   0.0    1.0  1  lcl|NCBI__GCF_000711195.1:WP_029935993.1  N746_RS0109310 N-acetyl-gamma-gl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711195.1:WP_029935993.1  N746_RS0109310 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.3   0.0  1.5e-137  1.5e-137       1     345 []       4     347 .]       4     347 .] 0.98

  Alignments for each domain:
  == domain 1  score: 444.3 bits;  conditional E-value: 1.5e-137
                                 TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 
                                               i+v+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag k++e++p+l+g++dl ++e ++++ l+++d
  lcl|NCBI__GCF_000711195.1:WP_029935993.1   4 IQVGIVGGTGYTGVELLRLLANHPHAEVKVITSRSEAGMKVAEMFPNLRGHYDLAFSEPDMST-LTSCD 71 
                                               68***************************8888888*********************999985.569** PP

                                 TIGR01850  70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138
                                               +vf+A+phgv+++l pel+++gv+vidl+adfRl+d +v+e+wYg+ h+ +e+++e+vYGlpE+nre+i
  lcl|NCBI__GCF_000711195.1:WP_029935993.1  72 LVFFATPHGVAMSLTPELVQAGVRVIDLAADFRLNDLQVWENWYGMAHTCPEIMDEVVYGLPEFNREKI 140
                                               ********************************************************************* PP

                                 TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207
                                               k+ak+ianPGCy+Ta++L+  Pllk++l++ +++i d+ksGvSgAGr a+  sl ae++e +k+Y +++
  lcl|NCBI__GCF_000711195.1:WP_029935993.1 141 KTAKVIANPGCYPTAVQLGFQPLLKAGLVDIDHLIADGKSGVSGAGRGAKVGSLSAETSEGFKAYGING 209
                                               ********************************************************************* PP

                                 TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276
                                               HrH pEi++ l+++a+++v+++f+phlvpm+rGi at+y kl++++++e+l++l+e+ Y++epfv+v++
  lcl|NCBI__GCF_000711195.1:WP_029935993.1 210 HRHLPEIAEGLNHMAGSRVNLTFVPHLVPMIRGIEATLYGKLNQDWSQEQLQELFEKHYAQEPFVDVMP 278
                                               ********************************************************************* PP

                                 TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                               +g+lP+t+ v gsn+++++v      + vvv+s+iDNLvKGa+gqAvqn+Nlm+g++et gLe+++l+p
  lcl|NCBI__GCF_000711195.1:WP_029935993.1 279 AGSLPDTRMVKGSNMCRMAVYRPAGGDVVVVTSVIDNLVKGASGQAVQNMNLMFGLEETCGLEQVALMP 347
                                               *****************************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (347 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.63
//
[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