GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Ruegeria conchae TW15

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_029621561.1 G7G_RS0100260 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>NCBI__GCF_000192475.1:WP_029621561.1
          Length = 287

 Score =  281 bits (719), Expect = 1e-80
 Identities = 147/289 (50%), Positives = 197/289 (68%), Gaps = 13/289 (4%)

Query: 7   DAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVH 66
           D    A  L+ ALPY++R+ G  +VIK GG+AM S+E    FARDVVLM+ VG+NPVVVH
Sbjct: 9   DWIATAATLNSALPYLQRYDGAIVVIKLGGHAMGSDEAMESFARDVVLMRQVGVNPVVVH 68

Query: 67  GGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGL 126
           GGGP I  +L +L I+S F+ G RVTD AT++VVEMVL G VNK IV  IN  GGSA+GL
Sbjct: 69  GGGPMINAMLGKLDIQSEFVGGKRVTDKATVEVVEMVLSGLVNKRIVQAINGQGGSAVGL 128

Query: 127 TGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIG 186
           +GKDA L+            + T P    +G VG  + +N  +L+ L   D IPVIAP+G
Sbjct: 129 SGKDANLM----------VCDQTDP---SLGFVGSPSKMNPKVLHDLFSHDVIPVIAPLG 175

Query: 187 VGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADG 246
            G NGE++N+N D  AG +A ALKA++L+LLT+++G+ +  G+V+T L   Q+ E+  +G
Sbjct: 176 AGQNGETFNVNGDTAAGAIASALKADRLLLLTDVSGVKNAAGEVVTELKAGQIREMTLEG 235

Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           TI GGM+PK   AL+A+  GV +  I+DGR PNAVLLE+FT+ G G+LI
Sbjct: 236 TIAGGMIPKTETALDALHSGVRAVVILDGRAPNAVLLELFTEHGAGSLI 284


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: 286
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: 301
Length of database: 287
Length adjustment: 26
Effective length of query: 275
Effective length of database: 261
Effective search space:    71775
Effective search space used:    71775
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_029621561.1 G7G_RS0100260 (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.3823926.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.2e-80  253.5   5.3    1.1e-79  253.2   5.3    1.1  1  NCBI__GCF_000192475.1:WP_029621561.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_029621561.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.2   5.3   1.1e-79   1.1e-79       2     231 .]      32     261 ..      31     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: 253.2 bits;  conditional E-value: 1.1e-79
                             TIGR00761   2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvem 72 
                                           +ViK+GG+a+   e++e++a+d++ +r++g+++v+vHGGgp+in++l kl+i+ efv+g RvTdk+t+evvem
  NCBI__GCF_000192475.1:WP_029621561.1  32 VVIKLGGHAMGsdEAMESFARDVVLMRQVGVNPVVVHGGGPMINAMLGKLDIQSEFVGGKRVTDKATVEVVEM 104
                                           8*********8889*********************************************************** PP

                             TIGR00761  73 vligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslal 145
                                           vl g vnk++v++++ +g +avGl+gkD++l++ ++ d + lg+vG+ +k+n+++l++l  +++ipvia+l++
  NCBI__GCF_000192475.1:WP_029621561.1 105 VLSGLVNKRIVQAINGQGGSAVGLSGKDANLMVCDQTDPS-LGFVGSPSKMNPKVLHDLFSHDVIPVIAPLGA 176
                                           ***************************************9.******************************** PP

                             TIGR00761 146 deegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaa 218
                                            ++g+++Nvn+DtaA+++A+al+A++L+lLtdv+G+ +  + ++++el++ +i+++  ++ i+gGmipK e a
  NCBI__GCF_000192475.1:WP_029621561.1 177 GQNGETFNVNGDTAAGAIASALKADRLLLLTDVSGVKNA-AGEVVTELKAGQIREMTLEGTIAGGMIPKTETA 248
                                           ***************************************.777****************************** PP

                             TIGR00761 219 lealesgvkkvvi 231
                                           l+al+sgv++vvi
  NCBI__GCF_000192475.1:WP_029621561.1 249 LDALHSGVRAVVI 261
                                           ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (287 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: 14.93
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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