Alignments for a candidate for argC in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pseudomonas putida KT2440

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate PP_0432 PP_0432 N-acetyl-gamma-glutamyl-phosphate reductase 1

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__Putida:PP_0432
          Length = 344

 Score =  472 bits (1214), Expect = e-138
 Identities = 238/346 (68%), Positives = 274/346 (79%), Gaps = 3/346 (0%)

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

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

Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222
           PE  + AVYGLPEV R++IR A+L+A PGCYPTA QLGFLPLLE GL DP RLIAD KSG
Sbjct: 121 PELLKDAVYGLPEVNREKIRQARLIAVPGCYPTATQLGFLPLLEAGLADPSRLIADCKSG 180

Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282
            SGAGR   +G L  E GES KAY   GHRHLPEI QGL  AAG D+G+TFVPHL PMIR
Sbjct: 181 VSGAGRGAAVGSLFCEAGESMKAYAVKGHRHLPEISQGLRLAAGKDIGLTFVPHLTPMIR 240

Query: 283 GIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQ 342
           GI ATLYA + + +    LQALFE+R+ DEPFVDVMP GSHPETRSVRGAN CR+A+HR 
Sbjct: 241 GIHATLYANVVDTS--VDLQALFEKRYADEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298

Query: 343 EQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388
           +  ++V+V SVIDNLVKGA+GQAVQN+NI+FGL E MGL    LLP
Sbjct: 299 QGGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERMGLSHAGLLP 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: 453
Number of extensions: 19
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 PP_0432 PP_0432 (N-acetyl-gamma-glutamyl-phosphate reductase 1)
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.24747.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-135  437.9   0.0   1.5e-135  437.8   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0432  PP_0432 N-acetyl-gamma-glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0432  PP_0432 N-acetyl-gamma-glutamyl-phosphate reductase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.8   0.0  1.5e-135  1.5e-135       1     345 []       2     344 .]       2     344 .] 0.97

  Alignments for each domain:
  == domain 1  score: 437.8 bits;  conditional E-value: 1.5e-135
                           TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileeadvvflA 74 
                                         ikv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag  +++++p+l+g++d l ++   ++++l ++dvvf+A
  lcl|FitnessBrowser__Putida:PP_0432   2 IKVGIVGGTGYTGVELLRLLAQHPQAEVAVITSRSEAGVAVADMYPNLRGHYDgLAFSVP-DSKALGACDVVFFA 75 
                                         69***************************8888888*****************7777755.555778******** PP

                           TIGR01850  75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGC 149
                                         +phgv+++l+ ell++g+kvidlSadfRl+da+++ kwYg++h ++ell++avYGlpE+nre+i++a+lia+PGC
  lcl|FitnessBrowser__Putida:PP_0432  76 TPHGVAHALAGELLAAGTKVIDLSADFRLQDATEWGKWYGQPHGAPELLKDAVYGLPEVNREKIRQARLIAVPGC 150
                                         *************************************************************************** PP

                           TIGR01850 150 yaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaek 224
                                         y+Ta++L+  Pll+++l +p+++i d+ksGvSgAGr a   slf+e+ e++k+Y+v++HrH pEi+q l+ +a+k
  lcl|FitnessBrowser__Putida:PP_0432 151 YPTATQLGFLPLLEAGLADPSRLIADCKSGVSGAGRGAAVGSLFCEAGESMKAYAVKGHRHLPEISQGLRLAAGK 225
                                         **********************************************************************99999 PP

                           TIGR01850 225 kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavd 299
                                         ++ ++f+phl+pm+rGi+at+ya++ +  t+ +l++l+e++Y+depfv+v+++g+ P+t++v+g n+++i+v+  
  lcl|FitnessBrowser__Putida:PP_0432 226 DIGLTFVPHLTPMIRGIHATLYANVVD--TSVDLQALFEKRYADEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298
                                         9**************************..89******************************************** PP

                           TIGR01850 300 eetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345
                                         +  + vvv+s+iDNLvKGa+gqAvqnlN+ +g+de+ gL++ +llp
  lcl|FitnessBrowser__Putida:PP_0432 299 QGGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERMGLSHAGLLP 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.46
//
[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:

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