GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pseudomonas stutzeri RCH2

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF3738 Psest_3807 acetylglutamate kinase

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__psRCH2:GFF3738
          Length = 300

 Score =  523 bits (1347), Expect = e-153
 Identities = 271/300 (90%), Positives = 281/300 (93%)

Query: 1   MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60
           MTLSR+ A Q AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELK GFARD+VLMKAVGI
Sbjct: 1   MTLSREAATQFAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKTGFARDIVLMKAVGI 60

Query: 61  NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120
           NPVVVHGGGPQIGDLLKRL+IESHFIDGMRVTD+ TMDVVEMVLGGQVNK IV+LIN+HG
Sbjct: 61  NPVVVHGGGPQIGDLLKRLNIESHFIDGMRVTDSQTMDVVEMVLGGQVNKSIVSLINQHG 120

Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180
           GSAIGLTGKDA LIRAKKL  TRQTPEMTKPEIIDIGHVGEVTGVN  LL MLVKG+FIP
Sbjct: 121 GSAIGLTGKDAGLIRAKKLKATRQTPEMTKPEIIDIGHVGEVTGVNAELLEMLVKGNFIP 180

Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240
           VIAPIGVG NGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQG VLTGLST QV+
Sbjct: 181 VIAPIGVGENGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGSVLTGLSTAQVD 240

Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300
            LIADGTIYGGMLPKIRCALEAVQGGV SAHIIDGRVPNAVLLEIFTD GVGTLI+N +R
Sbjct: 241 ALIADGTIYGGMLPKIRCALEAVQGGVNSAHIIDGRVPNAVLLEIFTDVGVGTLITNGQR 300


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: 449
Number of extensions: 11
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: 300
Length adjustment: 27
Effective length of query: 274
Effective length of database: 273
Effective search space:    74802
Effective search space used:    74802
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 GFF3738 Psest_3807 (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.2633.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.6e-83  265.8   7.4    1.9e-83  265.6   7.4    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3738  Psest_3807 acetylglutamate kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3738  Psest_3807 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.6   7.4   1.9e-83   1.9e-83       1     231 []      29     272 ..      29     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 1.9e-83
                           TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemv 73 
                                         t+ViK+GG+a++  el++ +a+di+ ++++gi++v+vHGGgp+i  ll++l+ie +f++g+RvTd +t++vvemv
  lcl|FitnessBrowser__psRCH2:GFF3738  29 TLVIKYGGNAMEseELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLNIESHFIDGMRVTDSQTMDVVEMV 103
                                         68*********9999************************************************************ PP

                           TIGR00761  74 ligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvnkelleallkagi 136
                                         l g+vnk +v l+++hg +a+GltgkD+ l+ a+kl+              d+g+vGe++ vn+elle l+k ++
  lcl|FitnessBrowser__psRCH2:GFF3738 104 LGGQVNKSIVSLINQHGGSAIGLTGKDAGLIRAKKLKATrqtpemtkpeiiDIGHVGEVTGVNAELLEMLVKGNF 178
                                         **********************************8888888999******************************* PP

                           TIGR00761 137 ipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGm 211
                                         ipvia++++ e+g+ +N+naD +A+++A+al+AekL+lLt++aG++++ + s+++ l++++++ li  + i+gGm
  lcl|FitnessBrowser__psRCH2:GFF3738 179 IPVIAPIGVGENGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDK-QGSVLTGLSTAQVDALIADGTIYGGM 252
                                         ************************************************.666*********************** PP

                           TIGR00761 212 ipKveaalealesgvkkvvi 231
                                          pK+++alea+++gv++++i
  lcl|FitnessBrowser__psRCH2:GFF3738 253 LPKIRCALEAVQGGVNSAHI 272
                                         ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (300 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.11
//
[ok]

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

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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