GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Sinorhizobium meliloti 1021

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate SMc01801 SMc01801 N-acetyl-gamma-glutamyl-phosphate reductase

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



>FitnessBrowser__Smeli:SMc01801
          Length = 310

 Score =  615 bits (1587), Expect = 0.0
 Identities = 310/310 (100%), Positives = 310/310 (100%)

Query: 1   MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60
           MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD
Sbjct: 1   MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60

Query: 61  DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120
           DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT
Sbjct: 61  DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120

Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180
           GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL
Sbjct: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180

Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240
           KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA
Sbjct: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240

Query: 241 GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAA 300
           GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAA
Sbjct: 241 GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAA 300

Query: 301 VQNMDLMLSA 310
           VQNMDLMLSA
Sbjct: 301 VQNMDLMLSA 310


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: 502
Number of extensions: 11
Number of successful extensions: 1
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: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
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 SMc01801 SMc01801 (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.31229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     5e-134  432.4   0.0   5.5e-134  432.3   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01801  SMc01801 N-acetyl-gamma-glutamyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01801  SMc01801 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.3   0.0  5.5e-134  5.5e-134       1     308 [.       2     308 ..       2     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 432.3 bits;  conditional E-value: 5.5e-134
                           TIGR01851   1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd.npnt 74 
                                         kpk+fidGe GttGlqir r+a+r+dlellsi e  r++a+ r +lln+ad+ailclpdda+reav++v  n+++
  lcl|FitnessBrowser__Smeli:SMc01801   2 KPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDASREAVAMVAgNNRV 76 
                                         79*****************************************************************99747789 PP

                           TIGR01851  75 kildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsGysG 149
                                         +i+d+sta+r+a+dw+yGf+e++  q+++i++a++vanPGcy+tgaial+rPl +aGilP  +Pvt+navsGy+G
  lcl|FitnessBrowser__Smeli:SMc01801  77 RIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGAIALIRPLRQAGILPDGYPVTVNAVSGYTG 151
                                         9************************************************************************** PP

                           TIGR01851 150 GGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskv 224
                                         GGk++ia+ e++++ d+  a+++ ygl+l+hkh+pem+ h+ l + P+f P+vG+faqG++v++pl l++l++ +
  lcl|FitnessBrowser__Smeli:SMc01801 152 GGKQMIAQMEDDQNPDHIGAPHFLYGLTLKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGA 226
                                         *************************************************************************** PP

                           TIGR01851 225 saedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGa 299
                                         + e ih+al+++y+G+  v+v++ld++  l    +da+ l g++ ++lfvfg++ g ++ lva+ldnlGkGasGa
  lcl|FitnessBrowser__Smeli:SMc01801 227 TLETIHRALVDHYAGQSIVEVVPLDESAKL--ARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGA 299
                                         ****************************99..89***************************************** PP

                           TIGR01851 300 avqnlnial 308
                                         avqn++++l
  lcl|FitnessBrowser__Smeli:SMc01801 300 AVQNMDLML 308
                                         ********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (310 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: 00:00:00.01
# Mc/sec: 6.87
//
[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:

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:

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