Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pseudomonas fluorescens FW300-N1B4

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate Pf1N1B4_2559 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559
          Length = 344

 Score =  474 bits (1219), Expect = e-138
 Identities = 235/346 (67%), Positives = 277/346 (80%), Gaps = 3/346 (0%)

Query: 44  VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYD-LAFSE 102
           ++KVGIVGGTGYTGVELLR+LA HP+  V  ITSRSEAG+ VA+MYPNLRGHYD LAFS 
Sbjct: 1   MVKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDGLAFSV 60

Query: 103 PDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162
           PD+  LGACD+VFFATPHGVA  +  EL++AG +V+DLSADFRL+D D WA WYG  H +
Sbjct: 61  PDIKTLGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGA 120

Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222
           PE  E+AVYGLPEV R++I+ A+L+A PGCYPTA QLGFLPLLE GL D  RLIAD KSG
Sbjct: 121 PELLEEAVYGLPEVNREQIKQARLIAVPGCYPTATQLGFLPLLEAGLADTTRLIADCKSG 180

Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282
            SGAGR   +G L+ E  ES KAY   GHRHLPEIRQGL  AAG DVG+TFVPHL PMIR
Sbjct: 181 VSGAGRGASVGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIR 240

Query: 283 GIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQ 342
           GI +TLYA + + +    LQALFE+R+ +EPFVDVMP GSHPETRSVRGAN CR+A+HR 
Sbjct: 241 GIHSTLYATVVDRS--VDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298

Query: 343 EQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           +  ++V+V SVIDNLVKGA+GQAVQN+NI+FGL E +GL    +LP
Sbjct: 299 QDGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERLGLSHAGMLP 344


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: 24
Number of successful extensions: 3
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: 344
Length adjustment: 30
Effective length of query: 358
Effective length of database: 314
Effective search space:   112412
Effective search space used:   112412
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 Pf1N1B4_2559 (N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
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.1881525.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.6e-136  441.0   0.0   1.8e-136  440.8   0.0    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.8   0.0  1.8e-136  1.8e-136       1     345 []       2     344 .]       2     344 .] 0.98

  Alignments for each domain:
  == domain 1  score: 440.8 bits;  conditional E-value: 1.8e-136
                                  TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeilee 67 
                                                +kv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag  +++++p+l+g++d l ++  +++ +l +
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559   2 VKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDgLAFSVPDIK-TLGA 68 
                                                69***************************8888888*****************8888887777.567* PP

                                  TIGR01850  68 advvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnr 135
                                                +dvvf+A+phgv+++l+ ell++g+kvidlSadfRl+da++++kwYg++h ++elleeavYGlpE+nr
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559  69 CDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAPELLEEAVYGLPEVNR 136
                                                ******************************************************************** PP

                                  TIGR01850 136 eeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpY 203
                                                e+ik+a+lia+PGCy+Ta++L+  Pll+++l +++++i d+ksGvSgAGr as  sl++e++e++k+Y
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 137 EQIKQARLIAVPGCYPTATQLGFLPLLEAGLADTTRLIADCKSGVSGAGRGASVGSLYSETSESMKAY 204
                                                ******************************************************************** PP

                                  TIGR01850 204 kvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepf 271
                                                +v++HrH pEi+q l+++a+k+v ++f+phl+pm+rGi++t+ya++ +  ++ +l++l+e++Y++epf
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 205 AVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIRGIHSTLYATVVD--RSVDLQALFEKRYANEPF 270
                                                ***********************************************9..789*************** PP

                                  TIGR01850 272 vrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLe 339
                                                v+v+++g+ P+t++v+g n+++i+v+  ++ + vvv+s+iDNLvKGa+gqAvqnlN+ +g+de+ gL+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 271 VDVMPAGSHPETRSVRGANVCRIAVHRPQDGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERLGLS 338
                                                ******************************************************************** PP

                                  TIGR01850 340 klpllp 345
                                                + ++lp
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 339 HAGMLP 344
                                                *99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (345 nodes)
Target sequences:                          1  (344 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: 00:00:00.00
# Mc/sec: 19.23
//
[ok]

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