Alignments for a candidate for argA in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Klebsiella variicola At-22

Align amino-acid acetyltransferase (characterized)
to candidate WP_004149616.1 KVAR_RS04235 amino-acid N-acetyltransferase

Query= CharProtDB::CH_024150
         (443 letters)



>NCBI__GCF_000025465.1:WP_004149616.1
          Length = 443

 Score =  818 bits (2114), Expect = 0.0
 Identities = 417/442 (94%), Positives = 427/442 (96%)

Query: 1   MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLV 60
           MVKER+TELVEGFRHSVPYIN HRGKTFVIMLGGEAIEHENFS+IVNDIGLLHSLGIRLV
Sbjct: 1   MVKERRTELVEGFRHSVPYINAHRGKTFVIMLGGEAIEHENFSNIVNDIGLLHSLGIRLV 60

Query: 61  VVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTP 120
           VVYGARPQIDANLA HHHEP+YHK  RVTDAKTLELVKQAAG LQL+ITARLSMSLNNTP
Sbjct: 61  VVYGARPQIDANLAEHHHEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTP 120

Query: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSV 180
           LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDE+AIHRQLDSGAIVLMGPVAVSV
Sbjct: 121 LQGAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEEAIHRQLDSGAIVLMGPVAVSV 180

Query: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEK 240
           TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGV N  G+IVSELFPNEAQARVE  E  
Sbjct: 181 TGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQAGEIVSELFPNEAQARVEELEAD 240

Query: 241 GDYNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR 300
            DYNSGTVRFLRGAVKACRSGVRRCHLISYQE+GALLQELFSRDGIGTQIVMESAEQIRR
Sbjct: 241 EDYNSGTVRFLRGAVKACRSGVRRCHLISYQENGALLQELFSRDGIGTQIVMESAEQIRR 300

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

Query: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDL 420
           GEMACVAVHPDYRSSSRGEVLLERIAAQA+Q GLSKLFVLTTRSIHWFQERGFTPVDIDL
Sbjct: 361 GEMACVAVHPDYRSSSRGEVLLERIAAQARQMGLSKLFVLTTRSIHWFQERGFTPVDIDL 420

Query: 421 LPESKKQLYNYQRKSKVLMADL 442
           LPESKKQ+YNYQR+SKVLMADL
Sbjct: 421 LPESKKQMYNYQRRSKVLMADL 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: 775
Number of extensions: 12
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 WP_004149616.1 KVAR_RS04235 (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.26868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-202  657.0   1.2   7.6e-202  656.8   1.2    1.0  1  lcl|NCBI__GCF_000025465.1:WP_004149616.1  KVAR_RS04235 amino-acid N-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_004149616.1  KVAR_RS04235 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.8   1.2  7.6e-202  7.6e-202       1     429 []       9     442 ..       9     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 656.8 bits;  conditional E-value: 7.6e-202
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               +v+++r++ Pyinahr+kt+v++lgge++e++n++++v+di+llhslG+rlv+v+Garpqi+ +la+++
  lcl|NCBI__GCF_000025465.1:WP_004149616.1   9 LVEGFRHSVPYINAHRGKTFVIMLGGEAIEHENFSNIVNDIGLLHSLGIRLVVVYGARPQIDANLAEHH 77 
                                               699****************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                                ++ y++  rvtd+ +lelvk+aaG l+l+i+arlsmsl+ntp +g++++vvsGnf++a+P+Gv++Gvd
  lcl|NCBI__GCF_000025465.1:WP_004149616.1  78 HEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVD 146
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                               y+h+G++r+id e+i+r+ld++ ivl++P++ svtGe fnl++e++at+ aiklka+k+i +++++G+ 
  lcl|NCBI__GCF_000025465.1:WP_004149616.1 147 YCHSGRIRRIDEEAIHRQLDSGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVY 215
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslverleeet.....tarllsaavkalrgGvarshlvsyaedGallqelftrd 271
                                               ++ G++v el+++e+++ ve+le +      t r+l+ avka+r+Gv+r+hl+sy+e+Gallqelf+rd
  lcl|NCBI__GCF_000025465.1:WP_004149616.1 216 NQAGEIVSELFPNEAQARVEELEADEdynsgTVRFLRGAVKACRSGVRRCHLISYQENGALLQELFSRD 284
                                               **********************9998899*9************************************** PP

                                 TIGR01890 272 GiGtlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaaly 340
                                               GiGt++++e++e+ir+ati+d+ggileli+Ple+qGilvrrsre+le ei++f++i++d + i+caaly
  lcl|NCBI__GCF_000025465.1:WP_004149616.1 285 GIGTQIVMESAEQIRRATINDIGGILELISPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALY 353
                                               ********************************************************************* PP

                                 TIGR01890 341 pyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelP 409
                                               p++ee++ge+ac+av+P++r + rGe ll++i ++arq+Gl++lfvlttr+ hWf+erGf+++++d lP
  lcl|NCBI__GCF_000025465.1:WP_004149616.1 354 PFPEEKIGEMACVAVHPDYRSSSRGEVLLERIAAQARQMGLSKLFVLTTRSIHWFQERGFTPVDIDLLP 422
                                               ********************************************************************* PP

                                 TIGR01890 410 earrklynyqrrskilvkkl 429
                                               e+++++ynyqrrsk+l+  l
  lcl|NCBI__GCF_000025465.1:WP_004149616.1 423 ESKKQMYNYQRRSKVLMADL 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.11
//
[ok]

This GapMind analysis is from Apr 10 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis