GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Escherichia coli BW25113

Align amino-acid acetyltransferase (characterized)
to candidate 16899 b2818 N-acetylglutamate synthase (NCBI)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__Keio:16899
          Length = 443

 Score =  869 bits (2245), Expect = 0.0
 Identities = 443/443 (100%), Positives = 443/443 (100%)

Query: 1   MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV 60
           MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV
Sbjct: 1   MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV 60

Query: 61  VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP 120
           VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP
Sbjct: 61  VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP 120

Query: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV 180
           LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV
Sbjct: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV 180

Query: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK 240
           TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK
Sbjct: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK 240

Query: 241 GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR 300
           GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR
Sbjct: 241 GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR 300

Query: 301 ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360
           ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI
Sbjct: 301 ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360

Query: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL 420
           GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL
Sbjct: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL 420

Query: 421 LPESKKQLYNYQRKSKVLMADLG 443
           LPESKKQLYNYQRKSKVLMADLG
Sbjct: 421 LPESKKQLYNYQRKSKVLMADLG 443


Lambda     K      H
   0.319    0.136    0.384 

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: 811
Number of extensions: 17
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: 443
Length of database: 443
Length adjustment: 32
Effective length of query: 411
Effective length of database: 411
Effective search space:   168921
Effective search space used:   168921
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 16899 b2818 (N-acetylglutamate synthase (NCBI))
to HMM TIGR01890 (argA: amino-acid N-acetyltransferase (EC 2.3.1.1))

# 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/TIGR01890.hmm
# target sequence database:        /tmp/gapView.15561.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01890  [M=429]
Accession:   TIGR01890
Description: N-Ac-Glu-synth: amino-acid N-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.4e-201  654.3   0.8     5e-201  654.1   0.8    1.0  1  lcl|FitnessBrowser__Keio:16899  b2818 N-acetylglutamate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16899  b2818 N-acetylglutamate synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  654.1   0.8    5e-201    5e-201       1     429 []       9     442 ..       9     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 654.1 bits;  conditional E-value: 5e-201
                       TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrGlr 79 
                                     +v+++r++ Pyin+hr+kt+v++lgge++e++n++ +v+di+llhslG+rlv+v+Garpqi+ +la+++ ++ y++ +r
  lcl|FitnessBrowser__Keio:16899   9 LVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYGARPQIDANLAAHHHEPLYHKNIR 87 
                                     699**************************************************************************** PP

                       TIGR01890  80 vtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrlld 158
                                     vtd+ +lelvk+aaG+l+l+i+arlsmsl+ntp +g++++vvsGnf++a+P+Gv++Gvdy+h+G++r+id ++i+r+ld
  lcl|FitnessBrowser__Keio:16899  88 VTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLD 166
                                     ******************************************************************************* PP

                       TIGR01890 159 ersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverleeet.... 233
                                     ++ ivl++P++ svtGe fnl++e++at+ aiklka+k+i +++++G+ + dG +v el+++e+++ ve  ee+     
  lcl|FitnessBrowser__Keio:16899 167 SGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGdyns 245
                                     ********************************************************************98877667799 PP

                       TIGR01890 234 .tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPleeqGilvr 311
                                      t r+l+ avka+r+Gv+r+hl+sy+edGallqelf+rdGiGt++++e++e+ir+ati+d+ggilelirPle+qGilvr
  lcl|FitnessBrowser__Keio:16899 246 gTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATINDIGGILELIRPLEQQGILVR 324
                                     9****************************************************************************** PP

                       TIGR01890 312 rsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttr 390
                                     rsre+le ei++f++i++d + i+caalyp++ee++ge+ac+av+P++r + rGe ll++i ++a+q Gl++lfvlttr
  lcl|FitnessBrowser__Keio:16899 325 RSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTR 403
                                     ******************************************************************************* PP

                       TIGR01890 391 tehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                     + hWf+erGf+++++d lPe++++lynyqr+sk+l+  l
  lcl|FitnessBrowser__Keio:16899 404 SIHWFQERGFTPVDIDLLPESKKQLYNYQRKSKVLMADL 442
                                     ***********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (443 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.82
//
[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