GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Shewanella amazonensis SB2B

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 6936060 Sama_0257 acetylglutamate kinase (RefSeq)

Query= BRENDA::A0A140NEG9
         (258 letters)



>FitnessBrowser__SB2B:6936060
          Length = 262

 Score =  224 bits (571), Expect = 1e-63
 Identities = 117/252 (46%), Positives = 167/252 (66%), Gaps = 1/252 (0%)

Query: 5   LIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNG 64
           L++K+GG LL  E  + RL        E  ++ +V+VHGGGC+VDE +K   +   K +G
Sbjct: 8   LVLKVGGALLQCEMGMARLMDTARQLLEKGEQ-VVLVHGGGCLVDEQLKANGMETVKLDG 66

Query: 65  LRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGL 124
           LRVTPA+Q+ II GALAGT+NK L   A K  + ++G+ L D + V     DE LG VG 
Sbjct: 67  LRVTPAEQMPIIAGALAGTSNKLLQGAAAKAGVVSMGMSLCDANMVTAVIKDERLGMVGE 126

Query: 125 AQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSG 184
             P   K +  +L  G+LP++SSI + ++G+L+NVNADQAA+ LA  LG  L+LLSDVSG
Sbjct: 127 VSPKDAKALEFILAQGWLPIISSIAMGEDGELLNVNADQAASVLAKLLGGKLVLLSDVSG 186

Query: 185 ILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLP 244
           +LDGKG+ I  + + + ++L++ G+I  GM VKV AAL+ A+ LG+PV +ASWR + Q+ 
Sbjct: 187 VLDGKGKLIPSLNSQEIDELVKLGVIEKGMKVKVEAALEVAQWLGQPVQVASWRDSGQMA 246

Query: 245 ALFNGMPMGTRI 256
           AL  G  +GT+I
Sbjct: 247 ALIKGEAVGTQI 258


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: 218
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: 262
Length adjustment: 24
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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 6936060 Sama_0257 (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.23426.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    6.5e-61  191.8   5.9    7.5e-61  191.6   5.9    1.0  1  lcl|FitnessBrowser__SB2B:6936060  Sama_0257 acetylglutamate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936060  Sama_0257 acetylglutamate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.6   5.9   7.5e-61   7.5e-61       2     229 ..       8     234 ..       7     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 7.5e-61
                         TIGR00761   2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 
                                       +V+K+GGa+++    + +l++ + +l ++g ++v+vHGGg+ ++e l++ g+e+ +++glRvT +e++ ++  +l+g
  lcl|FitnessBrowser__SB2B:6936060   8 LVLKVGGALLQceMGMARLMDTARQLLEKGEQVVLVHGGGCLVDEQLKANGMETVKLDGLRVTPAEQMPIIAGALAG 84 
                                       79*********944478999********************************************************* PP

                         TIGR00761  77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllN 153
                                       + nk l  + +k+g+  +G++  D++++ta   d+ +lg+vGe++  ++++le +l++g +p+i+s+a+ e+g+llN
  lcl|FitnessBrowser__SB2B:6936060  85 TSNKLLQGAAAKAGVVSMGMSLCDANMVTAVIKDE-RLGMVGEVSPKDAKALEFILAQGWLPIISSIAMGEDGELLN 160
                                       ***************************99976555.5**************************************** PP

                         TIGR00761 154 vnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkv 229
                                       vnaD+aA+ lA+ l+ + LvlL+dv+G+l+g k +li +l+ +ei++l+k +vi++Gm+ Kveaale ++ + + v
  lcl|FitnessBrowser__SB2B:6936060 161 VNADQAASVLAKLLGGK-LVLLSDVSGVLDG-KGKLIPSLNSQEIDELVKLGVIEKGMKVKVEAALEVAQWLGQPV 234
                                       ***************99.*************.666********************************998777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (262 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: 10.95
//
[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