Alignments for a candidate for argB in Methylococcus capsulatus str. Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Methylococcus capsulatus str. Bath

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_010961983.1 MCA_RS13615 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>NCBI__GCF_000008325.1:WP_010961983.1
          Length = 300

 Score =  395 bits (1014), Expect = e-115
 Identities = 196/291 (67%), Positives = 244/291 (83%), Gaps = 2/291 (0%)

Query: 8   AAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHG 67
           A ++A VL+EALPYIRRF G+T+V+KYGGNAM  + LK  FARDVVL+K VGINPVVVHG
Sbjct: 12  ANRIAHVLTEALPYIRRFKGRTIVVKYGGNAMIDDHLKNSFARDVVLLKLVGINPVVVHG 71

Query: 68  GGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLT 127
           GGPQIG+LL+RL   S F+ GMRVTDA TMDVVEMVLGG VNK+IVNLINR GG+A+GL+
Sbjct: 72  GGPQIGNLLQRLGKTSEFVQGMRVTDAETMDVVEMVLGGLVNKEIVNLINRQGGAAVGLS 131

Query: 128 GKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGV 187
           GKD +LIRA+K+ +++  P    PEIID+GHVGEV  ++  +++MLV GDFIPVIAPIGV
Sbjct: 132 GKDGDLIRARKIRMSQ--PLSDAPEIIDLGHVGEVASIDPAVVDMLVNGDFIPVIAPIGV 189

Query: 188 GSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGT 247
           G +G SYNINADLVAGK+AE LKAEKL+LLTN  G++ + G +LTGLS ++V+ LI DGT
Sbjct: 190 GEDGCSYNINADLVAGKMAEVLKAEKLILLTNTQGILGRDGALLTGLSLKEVDALIEDGT 249

Query: 248 IYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298
           I GGM+PK+RCA++A++GGV SAHIIDGR+ +AVLLE+FTD G+GTL+  R
Sbjct: 250 ISGGMIPKVRCAMDALRGGVNSAHIIDGRIDHAVLLELFTDQGIGTLLLRR 300


Lambda     K      H
   0.318    0.138    0.381 

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: 357
Number of extensions: 18
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: 301
Length of database: 300
Length adjustment: 27
Effective length of query: 274
Effective length of database: 273
Effective search space:    74802
Effective search space used:    74802
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_010961983.1 MCA_RS13615 (acetylglutamate kinase)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))

# 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/TIGR00761.hmm
# target sequence database:        /tmp/gapView.3797083.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00761  [M=231]
Accession:   TIGR00761
Description: argB: acetylglutamate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-80  255.5   3.9    2.6e-80  255.3   3.9    1.0  1  NCBI__GCF_000008325.1:WP_010961983.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010961983.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.3   3.9   2.6e-80   2.6e-80       1     231 []      33     274 ..      33     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.3 bits;  conditional E-value: 2.6e-80
                             TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevve 71 
                                           tiV+K+GG+a+   +l++++a+d++ l+ +gi++v+vHGGgp+i +ll++lg   efv+g+RvTd+et++vve
  NCBI__GCF_000008325.1:WP_010961983.1  33 TIVVKYGGNAMIddHLKNSFARDVVLLKLVGINPVVVHGGGPQIGNLLQRLGKTSEFVQGMRVTDAETMDVVE 105
                                           69*********988899******************************************************** PP

                             TIGR00761  72 mvligkvnkelvallekhgikavGltgkDgqlltaekldke..........dlgyvGeikkvnkelleallka 134
                                           mvl g vnke+v+l++++g +avGl+gkDg+l+ a+k+  +          dlg+vGe+ ++++++++ l++ 
  NCBI__GCF_000008325.1:WP_010961983.1 106 MVLGGLVNKEIVNLINRQGGAAVGLSGKDGDLIRARKIRMSqplsdapeiiDLGHVGEVASIDPAVVDMLVNG 178
                                           ************************************8888778999*************************** PP

                             TIGR00761 135 giipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavi 207
                                           ++ipvia++++ e+g  +N+naD +A+++A++l+AekL+lLt+++Gil +d++ l++ l+l+e++ li+ + i
  NCBI__GCF_000008325.1:WP_010961983.1 179 DFIPVIAPIGVGEDGCSYNINADLVAGKMAEVLKAEKLILLTNTQGILGRDGA-LLTGLSLKEVDALIEDGTI 250
                                           **************************************************888.******************* PP

                             TIGR00761 208 kgGmipKveaalealesgvkkvvi 231
                                            gGmipKv++a++al++gv++++i
  NCBI__GCF_000008325.1:WP_010961983.1 251 SGGMIPKVRCAMDALRGGVNSAHI 274
                                           **********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (300 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: 22.10
//
[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