Alignments for a candidate for argB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Dyella japonica UNC79MFTsu3.2

Align N-acetylglutamate synthase; N-acetylglutamate kinase (EC 2.3.1.1; EC 2.7.2.8) (characterized)
to candidate N515DRAFT_3768 N515DRAFT_3768 N-acetylglutamate kinase

Query= reanno::Dyella79:N515DRAFT_3768
         (438 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3768
          Length = 438

 Score =  860 bits (2221), Expect = 0.0
 Identities = 438/438 (100%), Positives = 438/438 (100%)

Query: 1   MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60
           MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL
Sbjct: 1   MEAHKHTRKTIVRLLSSMGSAKEIQQYLKRFSQLDAKRFAVVKVGGAVLRDDLPALTSSL 60

Query: 61  TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120
           TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV
Sbjct: 61  TFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKALAIVRKVFQEQNLRLV 120

Query: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180
           EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET
Sbjct: 121 EALQGMDTRATSVPSGVFTSEYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGET 180

Query: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240
           AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW
Sbjct: 181 AEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPW 240

Query: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300
           INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE
Sbjct: 241 INGGMRVKIEQIADLLSSLPLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLRYESWE 300

Query: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360
           GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD
Sbjct: 301 GIDLARMRELIESSFGRKVVADYFERTRPYRIYVSENYRAAMILTQEEGLAYLDKFAVLD 360

Query: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420
           DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG
Sbjct: 361 DAQGEGLGRAVWQVMREENPQLFWRSRHGNQVNIFYYAESDGCFKQERWKVFWYGLKNFG 420

Query: 421 EIERCVAHCAVRPATLMD 438
           EIERCVAHCAVRPATLMD
Sbjct: 421 EIERCVAHCAVRPATLMD 438


Lambda     K      H
   0.319    0.135    0.389 

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: 712
Number of extensions: 16
Number of successful extensions: 1
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: 438
Length of database: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
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: 51 (24.3 bits)

Align candidate N515DRAFT_3768 N515DRAFT_3768 (N-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.30323.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.4e-60  190.8   0.0    1.8e-60  190.3   0.0    1.1  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3768  N515DRAFT_3768 N-acetylglutamate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3768  N515DRAFT_3768 N-acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   1.8e-60   1.8e-60       1     225 [.      39     259 ..      39     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 1.8e-60
                                    TIGR00761   1 tiViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdket 66 
                                                  ++V+K+GGa++++ l +l + + +l+++g+ ++++HG gp+ +e l++ gi+ ++vnglRvT  ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3768  39 FAVVKVGGAVLRDDLPALTSSLTFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLRVTSPKA 104
                                                  58**************************************************************** PP

                                    TIGR00761  67 levvemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleall 132
                                                  l++v++v+ + +n +lv++l+  + +a  + ++   ++t e+ld++ +g+vG+++++n + +ea+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 105 LAIVRKVFQE-QNLRLVEALQGMDTRATSVPSG---VFTSEYLDRDVYGLVGKVSSINLAPIEASL 166
                                                  ********99.9****************99999...****************************** PP

                                    TIGR00761 133 kagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliselel.ee 197
                                                   ag ipviasl+ ++egq+lN+naD aA el ++l++ k+v+Lt + G+l++ k ++i++++l  e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 167 RAGSIPVIASLGETAEGQILNINADFAANELVRVLQPYKIVFLTGTGGLLDD-KGRIIDSINLsTE 231
                                                  ***************************************************9.666*******889 PP

                                    TIGR00761 198 ieqlikqavikgGmipKveaalealesg 225
                                                  +e+l+ q +i+gGm  K+e++++ l+s+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3768 232 YEHLMAQPWINGGMRVKIEQIADLLSSL 259
                                                  **********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (438 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: 12.67
//
[ok]

This GapMind analysis is from Apr 09 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