GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Desulfovibrio vulgaris Miyazaki F

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 8499536 DvMF_0306 acetylglutamate kinase (RefSeq)

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__Miya:8499536
          Length = 320

 Score =  330 bits (845), Expect = 3e-95
 Identities = 165/284 (58%), Positives = 219/284 (77%), Gaps = 1/284 (0%)

Query: 12  AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71
           +KVL E LPY+R+F G+T+VIKYGG+AM+ E LK  FA ++ L+K VGINPVVVHGGGPQ
Sbjct: 22  SKVLIECLPYMRQFHGQTVVIKYGGHAMKDEALKKAFALNIALLKQVGINPVVVHGGGPQ 81

Query: 72  IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131
           IG +L++L I+S F +G+RVTD ATMDVVEMVL G+VNK+IVNL+N  G  A+GL+GKD 
Sbjct: 82  IGRMLEQLHIQSQFREGLRVTDDATMDVVEMVLVGKVNKEIVNLLNLSGVKAVGLSGKDG 141

Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191
           +LIRA+K+ +         PEIID+G VGEV  V   LL  L + +F+PVIAP+GV  NG
Sbjct: 142 QLIRARKMEMIVNGGNHA-PEIIDLGKVGEVMRVETTLLRSLERDNFVPVIAPVGVDENG 200

Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251
           E+YNINAD VAG VA AL+A++L+LLT++AG++DKQ +++  L+T +  EL  DGT+ GG
Sbjct: 201 ETYNINADAVAGAVAAALRAKRLLLLTDVAGILDKQKELIRSLTTREAVELFTDGTLTGG 260

Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295
           M+PK++C LEA++ GV  A I+DGRV N +LLE+FTD G+ T I
Sbjct: 261 MIPKVKCCLEALEEGVEKAMIVDGRVENCILLELFTDKGISTEI 304


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: 321
Number of extensions: 14
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: 320
Length adjustment: 27
Effective length of query: 274
Effective length of database: 293
Effective search space:    80282
Effective search space used:    80282
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 8499536 DvMF_0306 (acetylglutamate kinase (RefSeq))
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.6927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    6.8e-83  263.7   6.8    8.1e-83  263.5   6.8    1.1  1  lcl|FitnessBrowser__Miya:8499536  DvMF_0306 acetylglutamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499536  DvMF_0306 acetylglutamate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.5   6.8   8.1e-83   8.1e-83       1     231 []      39     281 ..      39     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 263.5 bits;  conditional E-value: 8.1e-83
                         TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvli 75 
                                       t+ViK+GG+a++   l++++a +ia l+++gi++v+vHGGgp+i ++le+l i+ +f +glRvTd +t++vvemvl+
  lcl|FitnessBrowser__Miya:8499536  39 TVVIKYGGHAMKdeALKKAFALNIALLKQVGINPVVVHGGGPQIGRMLEQLHIQSQFREGLRVTDDATMDVVEMVLV 115
                                       69**********9789999********************************************************** PP

                         TIGR00761  76 gkvnkelvallekhgikavGltgkDgqlltaekldke...........dlgyvGeikkvnkelleallkagiipvia 141
                                       gkvnke+v+ll+  g+kavGl+gkDgql+ a+k++             dlg vGe+ +v++ ll++l   +++pvia
  lcl|FitnessBrowser__Miya:8499536 116 GKVNKEIVNLLNLSGVKAVGLSGKDGQLIRARKMEMIvnggnhapeiiDLGKVGEVMRVETTLLRSLERDNFVPVIA 192
                                       ********************************776666699************************************ PP

                         TIGR00761 142 slaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaa 218
                                       ++++de+g+++N+naD +A+++Aaal A++L+lLtdvaGil++ +k+li++l+++e+ +l + + ++gGmipKv+++
  lcl|FitnessBrowser__Miya:8499536 193 PVGVDENGETYNINADAVAGAVAAALRAKRLLLLTDVAGILDK-QKELIRSLTTREAVELFTDGTLTGGMIPKVKCC 268
                                       *******************************************.667****************************** PP

                         TIGR00761 219 lealesgvkkvvi 231
                                       leale+gv+k++i
  lcl|FitnessBrowser__Miya:8499536 269 LEALEEGVEKAMI 281
                                       ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (320 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: 8.59
//
[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