Alignments for a candidate for argC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Marinobacter adhaerens HP15

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate GFF354 HP15_352 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__Marino:GFF354
          Length = 388

 Score =  780 bits (2014), Expect = 0.0
 Identities = 388/388 (100%), Positives = 388/388 (100%)

Query: 1   MDCQKDSDNIVTVALRAAISHWFIMVDYGVKALNSDTTSLEKMVIKVGIVGGTGYTGVEL 60
           MDCQKDSDNIVTVALRAAISHWFIMVDYGVKALNSDTTSLEKMVIKVGIVGGTGYTGVEL
Sbjct: 1   MDCQKDSDNIVTVALRAAISHWFIMVDYGVKALNSDTTSLEKMVIKVGIVGGTGYTGVEL 60

Query: 61  LRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDVNVLGACDLVFFATPH 120
           LRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDVNVLGACDLVFFATPH
Sbjct: 61  LRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDVNVLGACDLVFFATPH 120

Query: 121 GVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEWAEKAVYGLPEVVRDE 180
           GVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEWAEKAVYGLPEVVRDE
Sbjct: 121 GVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEWAEKAVYGLPEVVRDE 180

Query: 181 IRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGASGAGRQGKIGMLHGEIG 240
           IRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGASGAGRQGKIGMLHGEIG
Sbjct: 181 IRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGASGAGRQGKIGMLHGEIG 240

Query: 241 ESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGIEATLYAELKNPADFDR 300
           ESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGIEATLYAELKNPADFDR
Sbjct: 241 ESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGIEATLYAELKNPADFDR 300

Query: 301 LQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQSNIVIVSSVIDNLVKG 360
           LQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQSNIVIVSSVIDNLVKG
Sbjct: 301 LQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQSNIVIVSSVIDNLVKG 360

Query: 361 AAGQAVQNMNIMFGLKETMGLEAPALLP 388
           AAGQAVQNMNIMFGLKETMGLEAPALLP
Sbjct: 361 AAGQAVQNMNIMFGLKETMGLEAPALLP 388


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: 655
Number of extensions: 18
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: 388
Length adjustment: 30
Effective length of query: 358
Effective length of database: 358
Effective search space:   128164
Effective search space used:   128164
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: 50 (23.9 bits)

Align candidate GFF354 HP15_352 (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.15497.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.1e-135  438.2   0.0   1.3e-135  438.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF354  HP15_352 N-acetyl-gamma-glutamyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF354  HP15_352 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.0   0.0  1.3e-135  1.3e-135       1     345 []      45     388 .]      45     388 .] 0.98

  Alignments for each domain:
  == domain 1  score: 438.0 bits;  conditional E-value: 1.3e-135
                          TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflAlp 76 
                                        ikv+ivG++GYtG+eLlr+la Hpev+v+ ++s++eag +++e++p+l+g++dl ++e +++ +l ++d+vf+A+p
  lcl|FitnessBrowser__Marino:GFF354  45 IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPDVN-VLGACDLVFFATP 119
                                        69***************************7777777*********************99887.678********** PP

                          TIGR01850  77 hgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaT 152
                                        hgv++++vpel+++gv+v+dlSadfRlkd +v+++wYg+ he++e++e+avYGlpE+ r+ei++a+l+anPGCy+T
  lcl|FitnessBrowser__Marino:GFF354 120 HGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPT 195
                                        **************************************************************************** PP

                          TIGR01850 153 aalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkv 228
                                        a++L+  Pll+++l++pk++i daksG SgAGr+ +  +l+ e+ e++k+Y +++HrH pEi+q l  +a+ +v v
  lcl|FitnessBrowser__Marino:GFF354 196 AVQLGFLPLLEQGLVDPKRLIADAKSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGV 271
                                        *******************************************************************99999**** PP

                          TIGR01850 229 sftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkr 304
                                        +f+phl+pm+rGi at+ya+lk++ + ++l++l+e++++depfv+v++ g+ P+t++v+g n+++++++ +e+++ 
  lcl|FitnessBrowser__Marino:GFF354 272 TFVPHLIPMIRGIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQEQSNI 347
                                        **************************************************************************** PP

                          TIGR01850 305 vvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                        v+v s+iDNLvKGaagqAvqn+N+m+g++et gLe  +llp
  lcl|FitnessBrowser__Marino:GFF354 348 VIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
                                        ***********************************998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (388 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: 10.82
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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