Alignments for a candidate for argC in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Thioalkalivibrio denitrificans ALJD

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_077277213.1 B1C78_RS00050 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_002000365.1:WP_077277213.1
          Length = 343

 Score =  448 bits (1153), Expect = e-131
 Identities = 219/345 (63%), Positives = 264/345 (76%), Gaps = 2/345 (0%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103
           +I+ G+VG TGYTGVELLR+L  HP+     +TSR  AG P+A M+PNLRGH DL F+EP
Sbjct: 1   MIRAGVVGATGYTGVELLRLLLSHPQAQPVVVTSRGNAGEPLAAMFPNLRGHTDLTFTEP 60

Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163
           D   L  CD+VFFATPHGVA  +  EL+S G RV+DLSADFRL+D ++WA WYG  H +P
Sbjct: 61  DAGRLADCDVVFFATPHGVAHGLAGELLSRGTRVIDLSADFRLRDPELWARWYGQPHGAP 120

Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223
           E  + AVYGLPE+ R  I  A+L+A PGCYPTAV LGF+PLLEQGLVD  RL+ADAKSG 
Sbjct: 121 ELLDAAVYGLPEINRASIPKARLIAVPGCYPTAVILGFIPLLEQGLVDTGRLVADAKSGV 180

Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283
           SGAGR+ ++G L  E  E+FKAYG  GHRHLPEI Q L   AG   G+TFVPHL+PMIRG
Sbjct: 181 SGAGRKAQVGTLLCEASETFKAYGVPGHRHLPEILQTLAQVAGAQPGLTFVPHLLPMIRG 240

Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343
           I ATLYA L +P     +QAL+E R+ DEPFVDVMP GSHPETRSVRG N+CR+A+HR +
Sbjct: 241 IHATLYATLSDPG--TDVQALYETRYRDEPFVDVMPAGSHPETRSVRGTNRCRLAVHRPQ 298

Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
             + V+V SVIDNLVKGA+GQA+QN+N+MFGL ET GL+  A+LP
Sbjct: 299 DGDTVVVLSVIDNLVKGASGQAIQNLNLMFGLAETTGLDGIAVLP 343


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: 462
Number of extensions: 12
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: 343
Length adjustment: 30
Effective length of query: 358
Effective length of database: 313
Effective search space:   112054
Effective search space used:   112054
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_077277213.1 B1C78_RS00050 (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.960.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-133  429.4   0.0   5.9e-133  429.3   0.0    1.0  1  lcl|NCBI__GCF_002000365.1:WP_077277213.1  B1C78_RS00050 N-acetyl-gamma-glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077277213.1  B1C78_RS00050 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.3   0.0  5.9e-133  5.9e-133       1     345 []       2     343 .]       2     343 .] 0.97

  Alignments for each domain:
  == domain 1  score: 429.3 bits;  conditional E-value: 5.9e-133
                                 TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileea 68 
                                               i++++vGa+GYtG+eLlrll +Hp+++ + +v+sr  ag++l++++p+l+g++dl+++e ++ + l+++
  lcl|NCBI__GCF_002000365.1:WP_077277213.1   2 IRAGVVGATGYTGVELLRLLLSHPQAQPV-VVTSRGnAGEPLAAMFPNLRGHTDLTFTEPDAGR-LADC 68 
                                               5899***********************99.6666656*********************998874.67** PP

                                 TIGR01850  69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137
                                               dvvf+A+phgv++ l+ ell++g++vidlSadfRl+d+e++++wYg++h ++ell+ avYGlpE+nr +
  lcl|NCBI__GCF_002000365.1:WP_077277213.1  69 DVVFFATPHGVAHGLAGELLSRGTRVIDLSADFRLRDPELWARWYGQPHGAPELLDAAVYGLPEINRAS 137
                                               ********************************************************************* PP

                                 TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206
                                               i ka+lia+PGCy+Ta++L+ +Pll+++l+++ +++ daksGvSgAGrka+  +l++e++e +k+Y v 
  lcl|NCBI__GCF_002000365.1:WP_077277213.1 138 IPKARLIAVPGCYPTAVILGFIPLLEQGLVDTGRLVADAKSGVSGAGRKAQVGTLLCEASETFKAYGVP 206
                                               ********************************************************************* PP

                                 TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275
                                               +HrH pEi q+l ++a+++  ++f+phl+pm+rGi+at+ya+l++    +++++lye++Y+depfv+v+
  lcl|NCBI__GCF_002000365.1:WP_077277213.1 207 GHRHLPEILQTLAQVAGAQPGLTFVPHLLPMIRGIHATLYATLSD--PGTDVQALYETRYRDEPFVDVM 273
                                               *********************************************..5699****************** PP

                                 TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344
                                               ++g+ P+t++v+g+n ++++v+  ++ ++vvv+s+iDNLvKGa+gqA+qnlNlm+g++et+gL+ +++l
  lcl|NCBI__GCF_002000365.1:WP_077277213.1 274 PAGSHPETRSVRGTNRCRLAVHRPQDGDTVVVLSVIDNLVKGASGQAIQNLNLMFGLAETTGLDGIAVL 342
                                               ***************************************************************999887 PP

                                 TIGR01850 345 p 345
                                               p
  lcl|NCBI__GCF_002000365.1:WP_077277213.1 343 P 343
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (343 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: 8.90
//
[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