Alignments for a candidate for argC in Sinorhizobium meliloti 1021

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.30111.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 4.87
//
[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:

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