Alignments for a candidate for argC in Methylococcus capsulatus str. Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Methylococcus capsulatus str. Bath

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_010960038.1 MCA_RS03455 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>NCBI__GCF_000008325.1:WP_010960038.1
          Length = 348

 Score =  441 bits (1135), Expect = e-128
 Identities = 217/345 (62%), Positives = 266/345 (77%), Gaps = 4/345 (1%)

Query: 45  IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPD 104
           I+VGIVGGTGYTGVELLR+LA+HP V +  +TSR++AG  VA++YPNLRGH D+ F+ P+
Sbjct: 7   IEVGIVGGTGYTGVELLRLLALHPGVRIRAVTSRADAGKAVADLYPNLRGHVDVVFTGPE 66

Query: 105 VNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPE 164
           V  LG CD+VFFATPHG+AM+  P L+  G+ V+DLSADFRLKD D WA+WYG  H  P 
Sbjct: 67  VENLGGCDVVFFATPHGIAMQSAPALLEQGIVVIDLSADFRLKDADEWAHWYGQEHACPG 126

Query: 165 WAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGAS 224
              +AVYGLPEV R+ +R+A+L+ANPGCYPTAVQLG LPLLE  LV   RLIAD KSG S
Sbjct: 127 LLSEAVYGLPEVRREAVRSARLIANPGCYPTAVQLGLLPLLENRLVAADRLIADVKSGVS 186

Query: 225 GAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGI 284
           GAGR+ ++ +L  E GESFKAY  +GHRH PEI QGL   AG  VG+TFVPHL+PMIRGI
Sbjct: 187 GAGRKAEVPLLMSETGESFKAYAVAGHRHWPEIVQGLVELAGEPVGLTFVPHLLPMIRGI 246

Query: 285 EATLYA-ELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343
            ATLYA  +  P D   +Q L+E+R+ DEPFVDV+P GSHP+TR VRG+N+C++A+    
Sbjct: 247 HATLYAVPVGEPGD---IQRLYEERYCDEPFVDVLPPGSHPDTRDVRGSNRCQIAVFELR 303

Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           +S  ++V SVIDNLVKGAAGQAVQNMN+ FG  ET GL+A  L P
Sbjct: 304 RSGQIVVLSVIDNLVKGAAGQAVQNMNLRFGFAETTGLQAIGLYP 348


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: 449
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: 348
Length adjustment: 30
Effective length of query: 358
Effective length of database: 318
Effective search space:   113844
Effective search space used:   113844
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_010960038.1 MCA_RS03455 (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.3944950.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-134  432.0   0.0   9.8e-134  431.8   0.0    1.0  1  NCBI__GCF_000008325.1:WP_010960038.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010960038.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.8   0.0  9.8e-134  9.8e-134       1     345 []       7     348 .]       7     348 .] 0.97

  Alignments for each domain:
  == domain 1  score: 431.8 bits;  conditional E-value: 9.8e-134
                             TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 
                                           i+v+ivG++GYtG+eLlrlla Hp v++ +++s+  agk +++++p+l+g+vd+ ++  e+e++   +dvvf+
  NCBI__GCF_000008325.1:WP_010960038.1   7 IEVGIVGGTGYTGVELLRLLALHPGVRIRAVTSRADAGKAVADLYPNLRGHVDVVFTGPEVENL-GGCDVVFF 78 
                                           589**************************6555555*********************9999865.6******* PP

                             TIGR01850  74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146
                                           A+phg++++ +p+lle+g++vidlSadfRlkda+++++wYg++h+ + ll+eavYGlpE++re++++a+lian
  NCBI__GCF_000008325.1:WP_010960038.1  79 ATPHGIAMQSAPALLEQGIVVIDLSADFRLKDADEWAHWYGQEHACPGLLSEAVYGLPEVRREAVRSARLIAN 151
                                           ************************************************************************* PP

                             TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219
                                           PGCy+Ta++L+l Pll+++l+  +++i d+ksGvSgAGrka+   l++e+ e++k+Y+v++HrH pEi+q l 
  NCBI__GCF_000008325.1:WP_010960038.1 152 PGCYPTAVQLGLLPLLENRLVAADRLIADVKSGVSGAGRKAEVPLLMSETGESFKAYAVAGHRHWPEIVQGLV 224
                                           ************************************************************************* PP

                             TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292
                                           +la++ v ++f+phl+pm+rGi+at+ya      +  ++++lyee+Y depfv+vl+ g+ P+t++v+gsn +
  NCBI__GCF_000008325.1:WP_010960038.1 225 ELAGEPVGLTFVPHLLPMIRGIHATLYAVPVG--EPGDIQRLYEERYCDEPFVDVLPPGSHPDTRDVRGSNRC 295
                                           ***************************99888..78************************************* PP

                             TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                           +i+v   ++++++vv+s+iDNLvKGaagqAvqn+Nl++gf+et+gL+ ++l+p
  NCBI__GCF_000008325.1:WP_010960038.1 296 QIAVFELRRSGQIVVLSVIDNLVKGAAGQAVQNMNLRFGFAETTGLQAIGLYP 348
                                           ***999999*****************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (348 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.38
//
[ok]

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