GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argC in Pseudomonas putida KT2440

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate PP_3633 PP_3633 putative ArgC like N-acetyl-gamma-glutamyl-phosphate reductase

Query= curated2:B1K264
         (313 letters)



>lcl|FitnessBrowser__Putida:PP_3633 PP_3633 putative ArgC like
           N-acetyl-gamma-glutamyl-phosphate reductase
          Length = 313

 Score =  434 bits (1116), Expect = e-126
 Identities = 218/312 (69%), Positives = 249/312 (79%), Gaps = 1/312 (0%)

Query: 1   MSFPTVFIDGDQGTTGLQIHARLRDRTDVRLLTLPAAERKDAARRADALNACDIAILCLP 60
           M  P VFIDGDQGTTGLQIHARL+ R+D+RLLTLP AERKD  RR +A+N+ DIA+LCLP
Sbjct: 1   MHTPVVFIDGDQGTTGLQIHARLQGRSDLRLLTLPEAERKDPQRRCEAINSADIALLCLP 60

Query: 61  DAAAREAVGFIRNPAVRVIDASSAHRTQPDWVYGFPEMADGHAHDIAHAKRVTNPGCYPT 120
           D AAREAV  I NP VRVIDASSAHRT P WVYG PE+ +  A  IA + RV+NPGCYPT
Sbjct: 61  DDAAREAVAAIHNPQVRVIDASSAHRTTPGWVYGLPELDEQQAERIAQSTRVSNPGCYPT 120

Query: 121 GAIGLLRPLLQAGLLPRDYPVSIHAVSGYSGGGRAAVDAFESGDAAARALPLQVYGLALE 180
           GAI LL PL++AGLLP DYP++IHAVSGYSGGGRAAV+  E    AA+A  LQ+YGL L 
Sbjct: 121 GAIALLHPLVKAGLLPADYPLNIHAVSGYSGGGRAAVERHEQ-PGAAKAPALQLYGLELA 179

Query: 181 HKHVPEIRQHAGLAHRPFFVPAYGAYRQGIVLTIPIELRLLPAGVTGERLHACLAHHYAD 240
           HKHVPEI+QHAGL+ RP F+P YGAYRQGI L+IP++LRLLP  V+ E L ACL  HY  
Sbjct: 180 HKHVPEIQQHAGLSARPMFMPGYGAYRQGIALSIPLQLRLLPGQVSAEHLQACLEQHYQG 239

Query: 241 ARHVDVMPLADAAAATHLDPQALNGTNDLRLGVLVNADGGQVLLSAVFDNLGKGASGAAV 300
           ARHV VMPL    AA +LDP+ALNG+NDLRL +  N + GQVLL+AVFDNLGKGASGAAV
Sbjct: 240 ARHVQVMPLHQCGAAANLDPEALNGSNDLRLALYANPEHGQVLLTAVFDNLGKGASGAAV 299

Query: 301 QNLDLMLGARHA 312
           QNLDLMLGA  A
Sbjct: 300 QNLDLMLGALQA 311


Lambda     K      H
   0.322    0.138    0.417 

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: 401
Number of extensions: 14
Number of successful extensions: 2
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: 313
Length of database: 313
Length adjustment: 27
Effective length of query: 286
Effective length of database: 286
Effective search space:    81796
Effective search space used:    81796
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 (21.9 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.5087.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.39
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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