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.20476.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.36
//
[ok]

This GapMind analysis is from Apr 09 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:

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