GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Shewanella loihica PV-4

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 5207681 Shew_0203 acetylglutamate kinase (RefSeq)

Query= BRENDA::A0A140NEG9
         (258 letters)



>FitnessBrowser__PV4:5207681
          Length = 261

 Score =  237 bits (605), Expect = 2e-67
 Identities = 126/253 (49%), Positives = 171/253 (67%), Gaps = 1/253 (0%)

Query: 5   LIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNG 64
           L++K+GG L+  E  L RL ++  N  +S Q  +++VHGGGC+VDE +K   +   K +G
Sbjct: 8   LVLKVGGALMQCEMGLARLMASAANIIKSGQS-VILVHGGGCLVDEQLKANGMETVKLDG 66

Query: 65  LRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGL 124
           LRVTP +Q+ I+ GALAGT+NK L A A K  I +VG+ L DG  V  +  DE+LG VG 
Sbjct: 67  LRVTPEEQVPIVVGALAGTSNKILQASAIKAGITSVGMSLCDGAIVNGSIKDEQLGFVGE 126

Query: 125 AQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSG 184
             P  P  +N LL  G++P+VSSI V D G L+NVNADQAAT +A  +   L+LLSDVSG
Sbjct: 127 VSPNDPTYLNFLLAQGWMPIVSSIAVDDAGNLLNVNADQAATVIAKLVEGQLVLLSDVSG 186

Query: 185 ILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLP 244
           +LDGKGQ I  +  A A++L + G+I  GM VKV AAL+ A+ +G+PV +ASWR AEQL 
Sbjct: 187 VLDGKGQLIKTLDKAHADELTKLGVIEKGMKVKVEAALEVAQWMGQPVQVASWRDAEQLS 246

Query: 245 ALFNGMPMGTRIL 257
           AL  G  +GT+++
Sbjct: 247 ALEKGESIGTQVM 259


Lambda     K      H
   0.317    0.136    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: 217
Number of extensions: 8
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: 258
Length of database: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate 5207681 Shew_0203 (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.25126.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    1.9e-60  190.3   6.6    2.2e-60  190.1   6.6    1.0  1  lcl|FitnessBrowser__PV4:5207681  Shew_0203 acetylglutamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207681  Shew_0203 acetylglutamate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   6.6   2.2e-60   2.2e-60       1     228 [.       7     233 ..       7     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 2.2e-60
                        TIGR00761   1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 
                                      t+V+K+GGa+++    l +l++ +a++ k+g+++++vHGGg+ ++e l++ g+e+ +++glRvT +e++ +v  +l+g
  lcl|FitnessBrowser__PV4:5207681   7 TLVLKVGGALMQceMGLARLMASAANIIKSGQSVILVHGGGCLVDEQLKANGMETVKLDGLRVTPEEQVPIVVGALAG 84 
                                      589*********9555899*********************************************************** PP

                        TIGR00761  77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllNv 154
                                      + nk l a   k+gi  vG++  Dg ++ +   d++ lg+vGe++  ++  l+ ll++g +p+++s+a+d++g+llNv
  lcl|FitnessBrowser__PV4:5207681  85 TSNKILQASAIKAGITSVGMSLCDGAIVNGSIKDEQ-LGFVGEVSPNDPTYLNFLLAQGWMPIVSSIAVDDAGNLLNV 161
                                      **************************9999766665.***************************************** PP

                        TIGR00761 155 naDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkk 228
                                      naD+aA+ +A+ +e + LvlL+dv+G+l+g+++ li+ l+ +++++l k +vi++Gm+ Kveaale ++   + 
  lcl|FitnessBrowser__PV4:5207681 162 NADQAATVIAKLVEGQ-LVLLSDVSGVLDGKGQ-LIKTLDKAHADELTKLGVIEKGMKVKVEAALEVAQWMGQP 233
                                      ***************9.*************555.*******************************998866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (261 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: 8.45
//
[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