GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Klebsiella michiganensis M5al

Align amino-acid acetyltransferase (characterized)
to candidate BWI76_RS23220 BWI76_RS23220 amino-acid N-acetyltransferase

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__Koxy:BWI76_RS23220
          Length = 443

 Score =  811 bits (2095), Expect = 0.0
 Identities = 412/442 (93%), Positives = 425/442 (96%)

Query: 1   MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV 60
           MVKER+TELVEGFRHSVPYIN HRGKTFVIMLGGEAIEH+NFSSIVNDIGLLHSLGIRLV
Sbjct: 1   MVKERRTELVEGFRHSVPYINAHRGKTFVIMLGGEAIEHDNFSSIVNDIGLLHSLGIRLV 60

Query: 61  VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP 120
           VVYGARPQIDANLA H HEP+YHK  RVTDAKTLELVKQAAG LQL+ITARLSMSLNNTP
Sbjct: 61  VVYGARPQIDANLAEHRHEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTP 120

Query: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV 180
           LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDE+AIHRQLD+GAIVLMGPVAVSV
Sbjct: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEEAIHRQLDNGAIVLMGPVAVSV 180

Query: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK 240
           TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGV N DG+IV ELFPNEAQARVE  E  
Sbjct: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQDGEIVPELFPNEAQARVEEIEAD 240

Query: 241 GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR 300
            DY+SGTVRFLRGAVKACRSGVRRCHLISYQE+G LLQELFSRDGIGTQIVMESAEQIRR
Sbjct: 241 EDYSSGTVRFLRGAVKACRSGVRRCHLISYQENGTLLQELFSRDGIGTQIVMESAEQIRR 300

Query: 301 ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360
           ATINDIGGILELI PLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI
Sbjct: 301 ATINDIGGILELISPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKI 360

Query: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL 420
           GEMACVAVHPDYRSSSRGEVLLERIAAQAKQ GLSKLFVLTTRSIHWFQERGFTPVD+DL
Sbjct: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQMGLSKLFVLTTRSIHWFQERGFTPVDVDL 420

Query: 421 LPESKKQLYNYQRKSKVLMADL 442
           LPESKK++YNYQR+SKVLMADL
Sbjct: 421 LPESKKEMYNYQRRSKVLMADL 442


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: 772
Number of extensions: 15
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: 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 BWI76_RS23220 BWI76_RS23220 (amino-acid N-acetyltransferase)
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.2804.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.7e-201  655.0   0.7   3.1e-201  654.8   0.7    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS23220  BWI76_RS23220 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS23220  BWI76_RS23220 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  654.8   0.7  3.1e-201  3.1e-201       1     429 []       9     442 ..       9     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 654.8 bits;  conditional E-value: 3.1e-201
                               TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrt 71 
                                             +v+++r++ Pyinahr+kt+v++lgge++e++n++ +v+di+llhslG+rlv+v+Garpqi+ +la+++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS23220   9 LVEGFRHSVPYINAHRGKTFVIMLGGEAIEHDNFSSIVNDIGLLHSLGIRLVVVYGARPQIDANLAEHRHE 79 
                                             699******************************************************************** PP

                               TIGR01890  72 thyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyeht 142
                                             + y++  rvtd+ +lelvk+aaG l+l+i+arlsmsl+ntp +g++++vvsGnf++a+P+Gv++Gvdy+h+
  lcl|FitnessBrowser__Koxy:BWI76_RS23220  80 PVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVDYCHS 150
                                             *********************************************************************** PP

                               TIGR01890 143 GevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGkl 213
                                             G++r+id e+i+r+ld++ ivl++P++ svtGe fnl++e++at+ aiklka+k+i +++++G+ ++dG++
  lcl|FitnessBrowser__Koxy:BWI76_RS23220 151 GRIRRIDEEAIHRQLDNGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQDGEI 221
                                             *********************************************************************** PP

                               TIGR01890 214 vaelsaqeveslverleeet.....tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvsk 279
                                             v el+++e+++ ve++e +      t r+l+ avka+r+Gv+r+hl+sy+e+G+llqelf+rdGiGt++++
  lcl|FitnessBrowser__Koxy:BWI76_RS23220 222 VPELFPNEAQARVEEIEADEdyssgTVRFLRGAVKACRSGVRRCHLISYQENGTLLQELFSRDGIGTQIVM 292
                                             ****************998888**9********************************************** PP

                               TIGR01890 280 ealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgel 350
                                             e++e+ir+ati+d+ggileli+Ple+qGilvrrsre+le ei++f++i++d + i+caalyp++ee++ge+
  lcl|FitnessBrowser__Koxy:BWI76_RS23220 293 ESAEQIRRATINDIGGILELISPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEM 363
                                             *********************************************************************** PP

                               TIGR01890 351 aclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrr 421
                                             ac+av+P++r + rGe ll++i ++a+q+Gl++lfvlttr+ hWf+erGf++++vd lPe+++++ynyqrr
  lcl|FitnessBrowser__Koxy:BWI76_RS23220 364 ACVAVHPDYRSSSRGEVLLERIAAQAKQMGLSKLFVLTTRSIHWFQERGFTPVDVDLLPESKKEMYNYQRR 434
                                             *********************************************************************** PP

                               TIGR01890 422 skilvkkl 429
                                             sk+l+  l
  lcl|FitnessBrowser__Koxy:BWI76_RS23220 435 SKVLMADL 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.58
//
[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