Alignments for a candidate for argC in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Sinorhizobium fredii NGR234

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate YP_002825561.1 NGR_c10190 N-acetyl-gamma-glutamyl-phosphate reductase

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



>NCBI__GCF_000018545.1:YP_002825561.1
          Length = 308

 Score =  560 bits (1443), Expect = e-164
 Identities = 280/310 (90%), Positives = 294/310 (94%), Gaps = 2/310 (0%)

Query: 1   MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60
           MKPKIFIDGEHGTTGLQIR RMAGR+DLELLSIPEAERRNAA+REDLLN ADIAILCLPD
Sbjct: 1   MKPKIFIDGEHGTTGLQIRARMAGRSDLELLSIPEAERRNAALREDLLNGADIAILCLPD 60

Query: 61  DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120
           DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQP +IRDARHV+NPGCYPT
Sbjct: 61  DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPAKIRDARHVSNPGCYPT 120

Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180
           GAI +IRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQ+ED+ + DHI APHFLYGL L
Sbjct: 121 GAIGVIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQIEDENHADHISAPHFLYGLPL 180

Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240
           KHKHVPEMKMHG+LERAP+FSPSVGKF QGMIVQVPLYL+DLA GATLE+IH ALV+HYA
Sbjct: 181 KHKHVPEMKMHGMLERAPIFSPSVGKFPQGMIVQVPLYLDDLAPGATLESIHAALVEHYA 240

Query: 241 GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAA 300
           GQSIVEVVPL  SA+LARIDATELAG D MKLFVFGT GGAHVNLVALLDNLGKGASGAA
Sbjct: 241 GQSIVEVVPL--SAQLARIDATELAGKDTMKLFVFGTPGGAHVNLVALLDNLGKGASGAA 298

Query: 301 VQNMDLMLSA 310
           VQNMDLMLSA
Sbjct: 299 VQNMDLMLSA 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: 462
Number of extensions: 12
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: 310
Length of database: 308
Length adjustment: 27
Effective length of query: 283
Effective length of database: 281
Effective search space:    79523
Effective search space used:    79523
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 YP_002825561.1 NGR_c10190 (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.32561.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-129  416.1   0.0   5.4e-129  415.9   0.0    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002825561.1  NGR_c10190 N-acetyl-gamma-glutam


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002825561.1  NGR_c10190 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.9   0.0  5.4e-129  5.4e-129       1     308 [.       2     306 ..       2     308 .] 0.98

  Alignments for each domain:
  == domain 1  score: 415.9 bits;  conditional E-value: 5.4e-129
                                 TIGR01851   1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 
                                               kpk+fidGe GttGlqir r+a+r+dlellsi e  r++a+ r +lln ad+ailclpdda+reav++v
  lcl|NCBI__GCF_000018545.1:YP_002825561.1   2 KPKIFIDGEHGTTGLQIRARMAGRSDLELLSIPEAERRNAALREDLLNGADIAILCLPDDASREAVAMV 70 
                                               79*****************************************************************99 PP

                                 TIGR01851  70 d.npntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadf 137
                                                 n++++i+d+sta+r+a+dw+yGf+e++  q+ ki++a++v+nPGcy+tgai ++rPl +aGilP  +
  lcl|NCBI__GCF_000018545.1:YP_002825561.1  71 AgNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPAKIRDARHVSNPGCYPTGAIGVIRPLRQAGILPDGY 139
                                               7477899************************************************************** PP

                                 TIGR01851 138 PvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfa 206
                                               Pvt+navsGy+GGGk++ia+ e+e+ +d+ +a+++ ygl l+hkh+pem+ h+ l + Pif P+vG+f 
  lcl|NCBI__GCF_000018545.1:YP_002825561.1 140 PVTVNAVSGYTGGGKQMIAQIEDENHADHISAPHFLYGLPLKHKHVPEMKMHGMLERAPIFSPSVGKFP 208
                                               ********************************************************************* PP

                                 TIGR01851 207 qGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvf 275
                                               qG++v++pl l +l+  ++ e ih+al+e+y+G+  v+v++l+ +       +da+ l g ++++lfvf
  lcl|NCBI__GCF_000018545.1:YP_002825561.1 209 QGMIVQVPLYLDDLAPGATLESIHAALVEHYAGQSIVEVVPLSAQL----ARIDATELAGKDTMKLFVF 273
                                               ******************************************9776....569**************** PP

                                 TIGR01851 276 gsddgerallvarldnlGkGasGaavqnlnial 308
                                               g+  g ++ lva+ldnlGkGasGaavqn++++l
  lcl|NCBI__GCF_000018545.1:YP_002825561.1 274 GTPGGAHVNLVALLDNLGKGASGAAVQNMDLML 306
                                               ********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (308 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.95
//
[ok]

This GapMind analysis is from Apr 10 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