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-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate PP_3633 PP_3633 putative ArgC like N-acetyl-gamma-glutamyl-phosphate reductase

Query= reanno::Smeli:SMc01801
         (310 letters)



>FitnessBrowser__Putida:PP_3633
          Length = 313

 Score =  303 bits (775), Expect = 5e-87
 Identities = 155/309 (50%), Positives = 206/309 (66%), Gaps = 5/309 (1%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           P +FIDG+ GTTGLQI  R+ GR+DL LL++PEAER++   R + +NSADIA+LCLPDDA
Sbjct: 4   PVVFIDGDQGTTGLQIHARLQGRSDLRLLTLPEAERKDPQRRCEAINSADIALLCLPDDA 63

Query: 63  SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122
           +REAVA +  N +VR+ID S+AHR  P W YG  E+D+ Q +RI  +  V+NPGCYPTGA
Sbjct: 64  AREAVAAIH-NPQVRVIDASSAHRTTPGWVYGLPELDEQQAERIAQSTRVSNPGCYPTGA 122

Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181
           IAL+ PL +AG+LP  YP+ ++AVSGY+GGG+   A +E  + P    AP   LYGL L 
Sbjct: 123 IALLHPLVKAGLLPADYPLNIHAVSGYSGGGR---AAVERHEQPGAAKAPALQLYGLELA 179

Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241
           HKHVPE++ H  L   P+F P  G + QG+ + +PL L  L    + E +   L  HY G
Sbjct: 180 HKHVPEIQQHAGLSARPMFMPGYGAYRQGIALSIPLQLRLLPGQVSAEHLQACLEQHYQG 239

Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301
              V+V+PL +    A +D   L GS+ ++L ++       V L A+ DNLGKGASGAAV
Sbjct: 240 ARHVQVMPLHQCGAAANLDPEALNGSNDLRLALYANPEHGQVLLTAVFDNLGKGASGAAV 299

Query: 302 QNMDLMLSA 310
           QN+DLML A
Sbjct: 300 QNLDLMLGA 308


Lambda     K      H
   0.319    0.136    0.395 

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: 340
Number of extensions: 15
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: 310
Length of database: 313
Length adjustment: 27
Effective length of query: 283
Effective length of database: 286
Effective search space:    80938
Effective search space used:    80938
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: 48 (23.1 bits)

Align candidate PP_3633 PP_3633 (putative ArgC like N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm
# target sequence database:        /tmp/gapView.21945.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01851  [M=310]
Accession:   TIGR01851
Description: argC_other: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.4e-126  405.4   0.0   9.7e-126  405.2   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3633  PP_3633 putative ArgC like N-ace


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3633  PP_3633 putative ArgC like N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   0.0  9.7e-126  9.7e-126       2     309 ..       4     307 ..       3     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 9.7e-126
                           TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdnpntki 76 
                                         p vfidG++GttGlqi+ rl++r+dl+ll++ e  rkd++ r + +n+ad+a+lclpddaareav+ ++np++++
  lcl|FitnessBrowser__Putida:PP_3633   4 PVVFIDGDQGTTGLQIHARLQGRSDLRLLTLPEAERKDPQRRCEAINSADIALLCLPDDAAREAVAAIHNPQVRV 78 
                                         679************************************************************************ PP

                           TIGR01851  77 ldastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsGysGGG 151
                                         +das+a+rt+++wvyG+pel+ +q e+ia++ rv+nPGcy+tgaiall+Plv+aG+lPad+P++i+avsGysGGG
  lcl|FitnessBrowser__Putida:PP_3633  79 IDASSAHRTTPGWVYGLPELDEQQAERIAQSTRVSNPGCYPTGAIALLHPLVKAGLLPADYPLNIHAVSGYSGGG 153
                                         *************************************************************************** PP

                           TIGR01851 152 kaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskvsa 226
                                         +a ++++e+   +++k  a + ygl+l hkh+pe+++h+gl  +P+f+P  G + qG+++ ipl+l  l ++vsa
  lcl|FitnessBrowser__Putida:PP_3633 154 RAAVERHEQP--GAAKAPALQLYGLELAHKHVPEIQQHAGLSARPMFMPGYGAYRQGIALSIPLQLRLLPGQVSA 226
                                         ********55..44556899******************************************************* PP

                           TIGR01851 227 edihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaav 301
                                         e++++ l ++y+G ++v+v++l++  +     ld+++lng+n l l ++++ + +++ll+a +dnlGkGasGaav
  lcl|FitnessBrowser__Putida:PP_3633 227 EHLQACLEQHYQGARHVQVMPLHQCGAA--ANLDPEALNGSNDLRLALYANPEHGQVLLTAVFDNLGKGASGAAV 299
                                         ************************9966..88******************************************* PP

                           TIGR01851 302 qnlnialG 309
                                         qnl+++lG
  lcl|FitnessBrowser__Putida:PP_3633 300 QNLDLMLG 307
                                         *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (313 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: 9.03
//
[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