GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Sinorhizobium meliloti 1021

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate SMc01726 SMc01726 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__Smeli:SMc01726
          Length = 295

 Score =  291 bits (744), Expect = 2e-83
 Identities = 141/293 (48%), Positives = 209/293 (71%)

Query: 3   LSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINP 62
           +S  ++   A++L++ALPY++R+  KT+V+KYGG+AM + EL   FA D+ L+K  G+NP
Sbjct: 1   MSASESEIQARLLAQALPYMQRYEHKTIVVKYGGHAMGNAELGRAFASDIALLKQSGVNP 60

Query: 63  VVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGS 122
           +VVHGGGPQIG +L R+ IES F  G+RVTD  T+++VEMVL G +NK+IV LIN+ G  
Sbjct: 61  IVVHGGGPQIGAMLNRMGIESKFEGGLRVTDEKTVEIVEMVLAGSINKEIVALINQTGEW 120

Query: 123 AIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVI 182
           AIGL GKD  ++ A+K   T + P+     ++D+G VG+V  V+  LL++L + + IPVI
Sbjct: 121 AIGLCGKDGNMVFAEKAKKTIRDPDSNIERVLDLGFVGDVVEVDRTLLDLLARSEMIPVI 180

Query: 183 APIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNEL 242
           AP+  G +G +YNINAD  AG +A AL A +L+ LT++ G+++K+G+++  LS  +   L
Sbjct: 181 APVAPGRDGHTYNINADTFAGAIAGALNATRLLFLTDVPGVLNKKGELIKQLSVAEARAL 240

Query: 243 IADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           IADGTI GGM+PK+   +EA++ GV    I++G+  ++VLLEIFT+ G GTLI
Sbjct: 241 IADGTISGGMIPKVETCIEAIKAGVQGVVILNGKTAHSVLLEIFTEHGAGTLI 293


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: 252
Number of extensions: 15
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: 301
Length of database: 295
Length adjustment: 26
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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 SMc01726 SMc01726 (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.3097.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    7.9e-81  257.0   2.8    9.3e-81  256.7   2.8    1.0  1  lcl|FitnessBrowser__Smeli:SMc01726  SMc01726 acetylglutamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01726  SMc01726 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.7   2.8   9.3e-81   9.3e-81       1     231 []      27     270 ..      27     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.7 bits;  conditional E-value: 9.3e-81
                           TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemv 73 
                                         tiV+K+GG+a+   el +++a+dia l+++g+++++vHGGgp+i ++l+++gie +f +glRvTd++t+e+vemv
  lcl|FitnessBrowser__Smeli:SMc01726  27 TIVVKYGGHAMGnaELGRAFASDIALLKQSGVNPIVVHGGGPQIGAMLNRMGIESKFEGGLRVTDEKTVEIVEMV 101
                                         69*********988899********************************************************** PP

                           TIGR00761  74 ligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvnkelleallkagi 136
                                         l+g++nke+val+++ g  a+Gl+gkDg+++ aek +k             dlg+vG++ +v++ ll+ l  +++
  lcl|FitnessBrowser__Smeli:SMc01726 102 LAGSINKEIVALINQTGEWAIGLCGKDGNMVFAEKAKKTirdpdsniervlDLGFVGDVVEVDRTLLDLLARSEM 176
                                         **********************************998888999******************************** PP

                           TIGR00761 137 ipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGm 211
                                         ipvia++a   +g+++N+naDt A+++A al+A +L++Ltdv+G+l++ k +li++l+++e++ li  + i gGm
  lcl|FitnessBrowser__Smeli:SMc01726 177 IPVIAPVAPGRDGHTYNINADTFAGAIAGALNATRLLFLTDVPGVLNK-KGELIKQLSVAEARALIADGTISGGM 250
                                         ************************************************.667*********************** PP

                           TIGR00761 212 ipKveaalealesgvkkvvi 231
                                         ipKve ++ea++ gv+ vvi
  lcl|FitnessBrowser__Smeli:SMc01726 251 IPKVETCIEAIKAGVQGVVI 270
                                         ****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (295 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: 7.51
//
[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:

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