Alignments for a candidate for argC in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Methylobacterium nodulans ORS 2060

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_015931791.1 MNOD_RS25255 N-acetyl-gamma-glutamyl-phosphate reductase

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



>NCBI__GCF_000022085.1:WP_015931791.1
          Length = 315

 Score =  300 bits (768), Expect = 3e-86
 Identities = 163/311 (52%), Positives = 204/311 (65%), Gaps = 10/311 (3%)

Query: 2   KPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDD 61
           +P +FIDGE GTTGL IR R+    D+ L SIP  +R++ A +  LL   D+ +LCLPDD
Sbjct: 8   RPSVFIDGEAGTTGLGIRERLEAFDDIALRSIPHEQRKDPAAKRTLLAEVDLVVLCLPDD 67

Query: 62  ASREAVAMVAG--NNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYP 119
           A+RE VAM  G      RI+D STAHRVAP W YGFAEM   Q   +R AR VANPGCYP
Sbjct: 68  AARETVAMADGLPGGGPRILDASTAHRVAPGWTYGFAEMTPDQRAALRAARRVANPGCYP 127

Query: 120 TGAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGL 178
           TGAIAL+RPL  AG++P  +PV++NAVSGY+GGG++MI   E         AP F LYGL
Sbjct: 128 TGAIALLRPLVDAGLIPADFPVSINAVSGYSGGGRKMIEAYEAGT------APAFELYGL 181

Query: 179 TLKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDH 238
              HKH+PE + +  L R P+F PSVG F QGM+V +PL+L+ L    T   +  AL   
Sbjct: 182 GFAHKHLPETQTYSRLTRRPIFIPSVGNFRQGMLVSIPLHLDALPGRPTAGDLEAALQAR 241

Query: 239 YAGQSIVEVVP-LDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGAS 297
           YAG+ +V VVP  ++ A   RI+   L  +D ++L VFG+   A   LVA LDNLGKGAS
Sbjct: 242 YAGEELVRVVPGAEDGAHRERIEPEALNDTDRLELRVFGSDAQAQAVLVARLDNLGKGAS 301

Query: 298 GAAVQNMDLML 308
           GAAVQN+ LML
Sbjct: 302 GAAVQNLRLML 312


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: 303
Number of extensions: 14
Number of successful extensions: 4
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: 315
Length adjustment: 27
Effective length of query: 283
Effective length of database: 288
Effective search space:    81504
Effective search space used:    81504
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 WP_015931791.1 MNOD_RS25255 (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.22115.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-126  405.6   0.0   8.2e-126  405.4   0.0    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015931791.1  MNOD_RS25255 N-acetyl-gamma-glut


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015931791.1  MNOD_RS25255 N-acetyl-gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.4   0.0  8.2e-126  8.2e-126       2     309 ..       9     313 ..       8     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 405.4 bits;  conditional E-value: 8.2e-126
                                 TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd 70 
                                               p vfidGeaGttGl irerl   dd+ l si +++rkd++++  ll  +d ++lclpddaare+v++ d
  lcl|NCBI__GCF_000022085.1:WP_015931791.1   9 PSVFIDGEAGTTGLGIRERLEAFDDIALRSIPHEQRKDPAAKRTLLAEVDLVVLCLPDDAARETVAMAD 77 
                                               78*****************************************************************99 PP

                                 TIGR01851  71 n...pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPad 136
                                                      +ildasta+r+a++w+yGf+e++++qr  +++a+rvanPGcy+tgaiallrPlv+aG++Pad
  lcl|NCBI__GCF_000022085.1:WP_015931791.1  78 GlpgGGPRILDASTAHRVAPGWTYGFAEMTPDQRAALRAARRVANPGCYPTGAIALLRPLVDAGLIPAD 146
                                               63225679************************************************************* PP

                                 TIGR01851 137 fPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdf 205
                                               fPv+inavsGysGGG+++i++ye       +  af  ygl + hkhlpe++++s+l+++Pif+P+vG+f
  lcl|NCBI__GCF_000022085.1:WP_015931791.1 147 FPVSINAVSGYSGGGRKMIEAYEA-----GTAPAFELYGLGFAHKHLPETQTYSRLTRRPIFIPSVGNF 210
                                               ***********************2.....334689********************************** PP

                                 TIGR01851 206 aqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfv 274
                                                qG+lv iplhl  l ++++a d+++al+  y+Ge+ v+v++ ++  +   + +++++ln+t+rlel v
  lcl|NCBI__GCF_000022085.1:WP_015931791.1 211 RQGMLVSIPLHLDALPGRPTAGDLEAALQARYAGEELVRVVPGAEDGAH-RERIEPEALNDTDRLELRV 278
                                               ******************************************9999866.5778*************** PP

                                 TIGR01851 275 fgsddgerallvarldnlGkGasGaavqnlnialG 309
                                               fgsd+  +a+lvarldnlGkGasGaavqnl ++l 
  lcl|NCBI__GCF_000022085.1:WP_015931791.1 279 FGSDAQAQAVLVARLDNLGKGASGAAVQNLRLMLD 313
                                               *********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (315 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: 7.89
//
[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