Alignments for a candidate for argB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Dechlorosoma suillum PS

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Dsui_1309 Dsui_1309 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__PS:Dsui_1309
          Length = 293

 Score =  358 bits (918), Expect = e-103
 Identities = 180/290 (62%), Positives = 231/290 (79%), Gaps = 5/290 (1%)

Query: 9   AQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGG 68
           AQ A +L+EALPYI+RF G+T+V+KYGGNAM  E LK  FARDVVL+K VG+N VVVHGG
Sbjct: 7   AQQAAILAEALPYIKRFHGRTIVVKYGGNAMTDEHLKQCFARDVVLLKLVGMNVVVVHGG 66

Query: 69  GPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTG 128
           GPQI ++L R+  +  FI GMRVTDA TM+VVEMVLGGQVNKD+VNLINR GG A+GLTG
Sbjct: 67  GPQIENMLGRVGKKGEFIQGMRVTDAETMEVVEMVLGGQVNKDVVNLINRAGGKAVGLTG 126

Query: 129 KDAELIRAKKLTV-TRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGV 187
           KD  +IRAKKL +  ++ P+    ++ID+G VG++  ++  L+  L    FIPVIAPIGV
Sbjct: 127 KDGGMIRAKKLLLPNKENPD----DLIDVGQVGDIVQIDPSLIGNLEGAGFIPVIAPIGV 182

Query: 188 GSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGT 247
           G +GE+YNINAD+VAGKVAE LKAEKL+LLTN  G++DK GQ++TG++ +Q+++++ DGT
Sbjct: 183 GKDGETYNINADVVAGKVAEVLKAEKLVLLTNTPGVLDKAGQLITGITPKQIDDMVEDGT 242

Query: 248 IYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISN 297
           + GGMLPKI  AL+A + GV S HIIDGRV +A+LLEI TD GVGT+I +
Sbjct: 243 LSGGMLPKISSALDAARNGVKSVHIIDGRVEHALLLEILTDHGVGTMIKS 292


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: 379
Number of extensions: 19
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: 301
Length of database: 293
Length adjustment: 26
Effective length of query: 275
Effective length of database: 267
Effective search space:    73425
Effective search space used:    73425
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 Dsui_1309 Dsui_1309 (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.859.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.5e-77  246.3   7.7    1.8e-77  246.0   7.7    1.1  1  lcl|FitnessBrowser__PS:Dsui_1309  Dsui_1309 acetylglutamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1309  Dsui_1309 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.0   7.7   1.8e-77   1.8e-77       1     231 []      27     267 ..      27     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 246.0 bits;  conditional E-value: 1.8e-77
                         TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvli 75 
                                       tiV+K+GG+a++  +l++ +a+d++ l+ +g+++v+vHGGgp+i+++l ++g + ef++g+RvTd+et+evvemvl 
  lcl|FitnessBrowser__PS:Dsui_1309  27 TIVVKYGGNAMTdeHLKQCFARDVVLLKLVGMNVVVVHGGGPQIENMLGRVGKKGEFIQGMRVTDAETMEVVEMVLG 103
                                       69*********98889999********************************************************** PP

                         TIGR00761  76 gkvnkelvallekhgikavGltgkDgqlltae..kldke.......dlgyvGeikkvnkelleallkagiipviasl 143
                                       g+vnk +v+l++++g kavGltgkDg ++ a+   l ++       d+g vG+i +++++l+ +l  ag+ipvia++
  lcl|FitnessBrowser__PS:Dsui_1309 104 GQVNKDVVNLINRAGGKAVGLTGKDGGMIRAKklLLPNKenpddliDVGQVGDIVQIDPSLIGNLEGAGFIPVIAPI 180
                                       ********************************652222258999********************************* PP

                         TIGR00761 144 aldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaale 220
                                       ++ ++g+++N+naD++A+++A++l+AekLvlLt+++G+l++ + +li+ +++++i+++++ + + gGm pK+++al+
  lcl|FitnessBrowser__PS:Dsui_1309 181 GVGKDGETYNINADVVAGKVAEVLKAEKLVLLTNTPGVLDK-AGQLITGITPKQIDDMVEDGTLSGGMLPKISSALD 256
                                       *****************************************.555******************************** PP

                         TIGR00761 221 alesgvkkvvi 231
                                       a+++gvk+v+i
  lcl|FitnessBrowser__PS:Dsui_1309 257 AARNGVKSVHI 267
                                       *********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (293 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: 00:00:00.00
# Mc/sec: 10.55
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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