Alignments for a candidate for argA in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Pseudomonas benzenivorans DSM 8628

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_090443859.1 BLS63_RS11100 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_900100495.1:WP_090443859.1
          Length = 432

 Score =  753 bits (1943), Expect = 0.0
 Identities = 382/432 (88%), Positives = 400/432 (92%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           M DYVNWLRHASPYIN+HRD TFVVMLPGEGV HPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MHDYVNWLRHASPYINAHRDCTFVVMLPGEGVAHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARLAARGL  R+HRDLRVTD PTLECVIDAVG LRIAIEARLSMDMAASPMQGAR
Sbjct: 61  RPQIEARLAARGLTARFHRDLRVTDGPTLECVIDAVGQLRIAIEARLSMDMAASPMQGAR 120

Query: 121 LRVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIF 180
           LRVA GN VTARPIGVVEG+DYHHTGEVRR+DRKGIGRLLDERSIVLLS LGYSPTGEIF
Sbjct: 121 LRVASGNFVTARPIGVVEGIDYHHTGEVRRVDRKGIGRLLDERSIVLLSSLGYSPTGEIF 180

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL A+KL+L+ AE+GLLD  GKLVRELRPQQVPA+L RLGNSYQ EL
Sbjct: 181 NLACEDVATRAAIDLGADKLLLFSAERGLLDEQGKLVRELRPQQVPAYLARLGNSYQGEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAAQACRAGVKR+HIVSY +DG+LL+ELFTR G GTLV QEQFE LREA IEDVGGLI
Sbjct: 241 LDAAAQACRAGVKRAHIVSYADDGSLLTELFTRDGGGTLVDQEQFESLREASIEDVGGLI 300

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           ELI PLEEQGILVRRSREVLEREIEQFSIVER+GLIIACAALY IADS+ GELACLAVNP
Sbjct: 301 ELISPLEEQGILVRRSREVLEREIEQFSIVERDGLIIACAALYQIADSDYGELACLAVNP 360

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
            YRHGGRGDELLERIEERAR  GLK LFVLTTRTAHWFRERGF PSSV+RLPAARASLYN
Sbjct: 361 AYRHGGRGDELLERIEERARAQGLKHLFVLTTRTAHWFRERGFVPSSVDRLPAARASLYN 420

Query: 421 FQRNSQVFEKSL 432
           +QRNSQVFEK+L
Sbjct: 421 YQRNSQVFEKAL 432


Lambda     K      H
   0.321    0.138    0.398 

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: 760
Number of extensions: 18
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: 432
Length of database: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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_090443859.1 BLS63_RS11100 (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.15578.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-216  703.8   0.2   4.7e-216  703.6   0.2    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090443859.1  BLS63_RS11100 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090443859.1  BLS63_RS11100 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.6   0.2  4.7e-216  4.7e-216       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 703.6 bits;  conditional E-value: 4.7e-216
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               +v+wlr+a+Pyinahrd+t+vv+l+ge+v+++n+g++v+d++llhslGvrlvlvhG+rpqie rla+rg
  lcl|NCBI__GCF_900100495.1:WP_090443859.1   4 YVNWLRHASPYINAHRDCTFVVMLPGEGVAHPNFGNIVHDLVLLHSLGVRLVLVHGSRPQIEARLAARG 72 
                                               8******************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                               +t++++r lrvtd  +le+v++a+G+lr aiearlsm++a++pm+g+rl+v+sGnfvtarPiGvveG+d
  lcl|NCBI__GCF_900100495.1:WP_090443859.1  73 LTARFHRDLRVTDGPTLECVIDAVGQLRIAIEARLSMDMAASPMQGARLRVASGNFVTARPIGVVEGID 141
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                               y+htGevr++d++gi rlldersivlls lg+s+tGeifnla+edvat++ai+l+adkl+l+++e G+l
  lcl|NCBI__GCF_900100495.1:WP_090443859.1 142 YHHTGEVRRVDRKGIGRLLDERSIVLLSSLGYSPTGEIFNLACEDVATRAAIDLGADKLLLFSAERGLL 210
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslverleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtl 276
                                               d++Gklv+el++q+v + + rl++ ++ +ll+aa++a+r+Gv+r+h+vsya dG+ll+elftrdG Gtl
  lcl|NCBI__GCF_900100495.1:WP_090443859.1 211 DEQGKLVRELRPQQVPAYLARLGNSYQGELLDAAAQACRAGVKRAHIVSYADDGSLLTELFTRDGGGTL 279
                                               ********************************************************************* PP

                                 TIGR01890 277 vskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaee 345
                                               v +e++es+rea i+dvgg++eli+PleeqGilvrrsre+lereie+fs++e+dGlii+caaly +a++
  lcl|NCBI__GCF_900100495.1:WP_090443859.1 280 VDQEQFESLREASIEDVGGLIELISPLEEQGILVRRSREVLEREIEQFSIVERDGLIIACAALYQIADS 348
                                               ********************************************************************* PP

                                 TIGR01890 346 evgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrk 414
                                               + gelaclav+P +r+ggrG++ll++ie+rar+ Glk+lfvlttrt+hWfrerGf+++svd+lP+ar++
  lcl|NCBI__GCF_900100495.1:WP_090443859.1 349 DYGELACLAVNPAYRHGGRGDELLERIEERARAQGLKHLFVLTTRTAHWFRERGFVPSSVDRLPAARAS 417
                                               ********************************************************************* PP

                                 TIGR01890 415 lynyqrrskilvkkl 429
                                               lynyqr+s++++k l
  lcl|NCBI__GCF_900100495.1:WP_090443859.1 418 LYNYQRNSQVFEKAL 432
                                               ***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (432 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.07
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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