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.3949276.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 12.39
//
[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:

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:

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:

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:

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