Alignments for a candidate for argB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Herbaspirillum seropedicae SmR1

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate HSERO_RS21495 HSERO_RS21495 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__HerbieS:HSERO_RS21495
          Length = 297

 Score =  335 bits (860), Expect = 6e-97
 Identities = 164/285 (57%), Positives = 218/285 (76%), Gaps = 5/285 (1%)

Query: 12  AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71
           A++L+EALPYIR+F GKT+V+KYGGNAM  E LK GFARDV+L+K VG+NPVVVHGGGPQ
Sbjct: 14  AEILAEALPYIRKFHGKTIVVKYGGNAMTEESLKHGFARDVILLKLVGMNPVVVHGGGPQ 73

Query: 72  IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131
           I   LK++  +  F+ GMR+TD  TM+VVE VLGG+V +DIV LIN +GG A+GLTGKD 
Sbjct: 74  IDAALKKIGKQGTFVQGMRITDEETMEVVEWVLGGEVQQDIVMLINHYGGQAVGLTGKDG 133

Query: 132 ELIRAKKLTVTRQTPEMTKP-EIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190
            LIRA+K+    Q P+   P   +DIG+VGE+  +N  ++  L    FIP+I+PIG G +
Sbjct: 134 GLIRARKM----QMPDKEHPGAFLDIGYVGEIEAINPAVVKALQDDAFIPIISPIGFGDD 189

Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250
           G++YNINAD+VAGK+AE L AEKL+++TNIAG+ DK G +LT LS  +++E+ ADGTI G
Sbjct: 190 GQAYNINADVVAGKIAEILHAEKLIMMTNIAGVQDKAGNLLTDLSAREIDEMFADGTISG 249

Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           GMLPKI  AL+A + GV + HIIDGR+ +++LLE+ T+   GT+I
Sbjct: 250 GMLPKISSALDAAKSGVNTVHIIDGRIEHSLLLEVLTEQAFGTMI 294


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: 338
Number of extensions: 11
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: 297
Length adjustment: 27
Effective length of query: 274
Effective length of database: 270
Effective search space:    73980
Effective search space used:    73980
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 HSERO_RS21495 HSERO_RS21495 (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.21840.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.1e-76  242.5   4.1    2.5e-76  242.2   4.1    1.1  1  lcl|FitnessBrowser__HerbieS:HSERO_RS21495  HSERO_RS21495 acetylglutamate ki


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS21495  HSERO_RS21495 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.2   4.1   2.5e-76   2.5e-76       1     231 []      31     271 ..      31     271 .. 0.97

  Alignments for each domain:
  == domain 1  score: 242.2 bits;  conditional E-value: 2.5e-76
                                  TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdket 66 
                                                tiV+K+GG+a++   l++ +a+d++ l+ +g+++v+vHGGgp+i+++l+k+g +  fv+g+R+Td+et
  lcl|FitnessBrowser__HerbieS:HSERO_RS21495  31 TIVVKYGGNAMTeeSLKHGFARDVILLKLVGMNPVVVHGGGPQIDAALKKIGKQGTFVQGMRITDEET 98 
                                                69*********988899*************************************************** PP

                                  TIGR00761  67 levvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeikkvnk 125
                                                +evve vl g+v++ +v l+++ g +avGltgkDg l+ a+k++           d+gyvGei+++n+
  lcl|FitnessBrowser__HerbieS:HSERO_RS21495  99 MEVVEWVLGGEVQQDIVMLINHYGGQAVGLTGKDGGLIRARKMQMPdkehpgaflDIGYVGEIEAINP 166
                                                *****************************************77655568******************* PP

                                  TIGR00761 126 elleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193
                                                ++++al +  +ip+i+++++ ++gq++N+naD++A+++A+ l+AekL+++t++aG+ ++ + +l++ l
  lcl|FitnessBrowser__HerbieS:HSERO_RS21495 167 AVVKALQDDAFIPIISPIGFGDDGQAYNINADVVAGKIAEILHAEKLIMMTNIAGVQDK-AGNLLTDL 233
                                                **********************************************************9.666***** PP

                                  TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231
                                                +++ei+++   + i gGm pK+++al+a++sgv+ v+i
  lcl|FitnessBrowser__HerbieS:HSERO_RS21495 234 SAREIDEMFADGTISGGMLPKISSALDAAKSGVNTVHI 271
                                                ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (297 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: 11.49
//
[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