Alignments for a candidate for argC in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Pseudomonas simiae WCS417

Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate GFF5008 PS417_25660 N-acetyl-gamma-glutamyl-phosphate reductase

Query= uniprot:E4PLW0
         (388 letters)



>FitnessBrowser__WCS417:GFF5008
          Length = 344

 Score =  475 bits (1222), Expect = e-139
 Identities = 236/346 (68%), 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 PELLEEAVYGLPEVNREQIKQARLIAVPGCYPTATQLGFLPLLEAGLADASRLIADCKSG 180

Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282
            SGAGR   +G L+ E  ES KAY   GHRHLPEIRQGL  AAG DVG+TFVPHL PMIR
Sbjct: 181 VSGAGRGAAVGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIR 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+GQAVQNMNI+FGL E +GL    +LP
Sbjct: 299 QDGDLVVVLSVIDNLVKGASGQAVQNMNILFGLDEKLGLSHAGMLP 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: 461
Number of extensions: 22
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 GFF5008 PS417_25660 (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.508336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.2e-136  440.6   0.0   2.4e-136  440.4   0.0    1.0  1  FitnessBrowser__WCS417:GFF5008  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF5008  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.4   0.0  2.4e-136  2.4e-136       1     345 []       2     344 .]       2     344 .] 0.98

  Alignments for each domain:
  == domain 1  score: 440.4 bits;  conditional E-value: 2.4e-136
                       TIGR01850   1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileeadvvflAlphg 78 
                                     +kv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag  +++++p+l+g++d l ++  +++ +l ++dvvf+A+phg
  FitnessBrowser__WCS417:GFF5008   2 VKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDgLAFSVPDIK-TLGACDVVFFATPHG 79 
                                     69***************************8888888*****************8888887777.567************ PP

                       TIGR01850  79 vsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaalLa 157
                                     v+++l+ ell++g+kvidlSadfRl+da++++kwYg++h ++elleeavYGlpE+nre+ik+a+lia+PGCy+Ta++L+
  FitnessBrowser__WCS417:GFF5008  80 VAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAPELLEEAVYGLPEVNREQIKQARLIAVPGCYPTATQLG 158
                                     ******************************************************************************* PP

                       TIGR01850 158 laPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphlvp 236
                                       Pll+++l + +++i d+ksGvSgAGr a   sl++e++e++k+Y+v++HrH pEi+q l+++a+k+v ++f+phl+p
  FitnessBrowser__WCS417:GFF5008 159 FLPLLEAGLADASRLIADCKSGVSGAGRGAAVGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTP 237
                                     ******************************************************************************* PP

                       TIGR01850 237 mtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLv 315
                                     m+rGi++t+ya++ +  ++ +l++l+e++Y++epfv+v+++g+ P+t++v+g n+++i+v+  ++ + vvv+s+iDNLv
  FitnessBrowser__WCS417:GFF5008 238 MIRGIHSTLYATVVD--RSVDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRPQDGDLVVVLSVIDNLV 314
                                     **************9..789*********************************************************** PP

                       TIGR01850 316 KGaagqAvqnlNlmlgfdetegLeklpllp 345
                                     KGa+gqAvqn+N+ +g+de+ gL++ ++lp
  FitnessBrowser__WCS417:GFF5008 315 KGASGQAVQNMNILFGLDEKLGLSHAGMLP 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: 00:00:00.00
# Mc/sec: 15.96
//
[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:

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 2024 update 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 original 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