Alignments for a candidate for argC in Azoarcus olearius BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for argC in Azoarcus olearius BH72

Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_011767638.1 AZO_RS19650 N-acetyl-gamma-glutamyl-phosphate reductase

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



>NCBI__GCF_000061505.1:WP_011767638.1
          Length = 307

 Score =  275 bits (703), Expect = 1e-78
 Identities = 151/312 (48%), Positives = 197/312 (63%), Gaps = 14/312 (4%)

Query: 3   PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62
           PK+FIDGE GTTGLQIR ++     +EL+SI    R++   + +L+   D+ ILCL DDA
Sbjct: 2   PKVFIDGEAGTTGLQIRDQLQQMPQIELVSIAPELRKDVGAKRELMAGVDLVILCLHDDA 61

Query: 63  SREAVAMVAG--NNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120
           +RE+VA++ G    R RIID STAHRV+P W YGF E+     Q +  A  VANPGCY T
Sbjct: 62  ARESVALIDGLPGKRPRIIDASTAHRVSPGWVYGFPELTAGHAQAVAGAERVANPGCYAT 121

Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180
           GAIALIRPL  AG+LP G+PV++ +VSGY+GGG+ MI   E    P      H  Y L L
Sbjct: 122 GAIALIRPLIDAGLLPAGFPVSLPSVSGYSGGGRSMIEAYEAGTAP-----LHEAYALGL 176

Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240
           KHKH+PE+  +  LE  P+F P+VG F QGM+VQ+PL+L+ L        +  A   HYA
Sbjct: 177 KHKHIPEIMQYTGLECRPLFIPAVGNFRQGMLVQLPLHLDALPGKPRAADLEAAYAAHYA 236

Query: 241 ----GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGA 296
                +  V+V+P  E  KL   DA  L  ++ +++ VF  +   H  L+A LDNLGKGA
Sbjct: 237 KSNTPEQFVQVLPATEDGKL---DALALNDTNRLEIRVFANEEYRHAVLIARLDNLGKGA 293

Query: 297 SGAAVQNMDLML 308
           SGAAVQN+ LML
Sbjct: 294 SGAAVQNLKLML 305


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: 311
Number of extensions: 11
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: 307
Length adjustment: 27
Effective length of query: 283
Effective length of database: 280
Effective search space:    79240
Effective search space used:    79240
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_011767638.1 AZO_RS19650 (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.3413427.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-122  393.4   0.0   4.1e-122  393.3   0.0    1.0  1  NCBI__GCF_000061505.1:WP_011767638.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000061505.1:WP_011767638.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.3   0.0  4.1e-122  4.1e-122       2     310 .]       2     307 .]       1     307 [] 0.95

  Alignments for each domain:
  == domain 1  score: 393.3 bits;  conditional E-value: 4.1e-122
                             TIGR01851   2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdn... 71 
                                           pkvfidGeaGttGlqir++l++   +el+si+++ rkd  ++ +l+  +d +ilcl+ddaare+v+l+d    
  NCBI__GCF_000061505.1:WP_011767638.1   2 PKVFIDGEAGTTGLQIRDQLQQMPQIELVSIAPELRKDVGAKRELMAGVDLVILCLHDDAARESVALIDGlpg 74 
                                           8*******************************************************************96322 PP

                             TIGR01851  72 pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinav 144
                                            + +i+dasta+r++++wvyGfpel+a+  + +a a+rvanPGcyatgaial+rPl++aG+lPa fPv++ +v
  NCBI__GCF_000061505.1:WP_011767638.1  75 KRPRIIDASTAHRVSPGWVYGFPELTAGHAQAVAGAERVANPGCYATGAIALIRPLIDAGLLPAGFPVSLPSV 147
                                           5779********************************************************************* PP

                             TIGR01851 145 sGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhl 217
                                           sGysGGG+++i++ye ++a       + +y+l l+hkh+pe+++++gl  +P+f+PavG+f qG+lv++plhl
  NCBI__GCF_000061505.1:WP_011767638.1 148 SGYSGGGRSMIEAYEAGTAPL-----HEAYALGLKHKHIPEIMQYTGLECRPLFIPAVGNFRQGMLVQLPLHL 215
                                           ***************555544.....478******************************************** PP

                             TIGR01851 218 aeldskvsaedihkalaeyykG....ekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallv 286
                                             l +k+ a+d+++a a +y+     e+fv+v ++ +        lda +ln+tnrle+ vf++++ ++a+l+
  NCBI__GCF_000061505.1:WP_011767638.1 216 DALPGKPRAADLEAAYAAHYAKsntpEQFVQVLPATEDG-----KLDALALNDTNRLEIRVFANEEYRHAVLI 283
                                           ********************74333489*****988765.....67*************************** PP

                             TIGR01851 287 arldnlGkGasGaavqnlnialGl 310
                                           arldnlGkGasGaavqnl+++lGl
  NCBI__GCF_000061505.1:WP_011767638.1 284 ARLDNLGKGASGAAVQNLKLMLGL 307
                                           ***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (310 nodes)
Target sequences:                          1  (307 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 18.06
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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