Alignments for a candidate for argA in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Halomonas desiderata SP1

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_086509236.1 BZY95_RS06985 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_002151265.1:WP_086509236.1
          Length = 437

 Score =  409 bits (1052), Expect = e-119
 Identities = 210/430 (48%), Positives = 283/430 (65%), Gaps = 1/430 (0%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQ 63
           +V+W R++SPYIN+HR RTFV+++ GE +       ++ DL LLH+LG RLV+V G RPQ
Sbjct: 7   FVDWFRNSSPYINAHRGRTFVILIEGEAMARGRGEQLIQDLALLHTLGVRLVVVFGIRPQ 66

Query: 64  IEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRV 123
           +E  L   G+ PR H    V D   + CV       R+ +EAR S+ +  +P+ G  L  
Sbjct: 67  VEQALNEAGIVPRRHNGRWVADEAIMACVERVAAEQRLWLEARFSLGLPNTPLHGVELTA 126

Query: 124 AGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLA 183
             GNLV A+P+GV EG+DY H+GEVRR+    +  LLD  S+VLL PLG+S TGE+F+L 
Sbjct: 127 VSGNLVMAKPLGVREGIDYDHSGEVRRVRVSAVQGLLDRGSLVLLPPLGFSSTGEVFDLD 186

Query: 184 CEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQV-PAHLQRLGNSYQAELLD 242
             +VA  AA+ L A+KLIL G E GL D +G L R+L P +  P   Q    S QA  + 
Sbjct: 187 AAEVAQHAAMALAADKLILMGEEPGLYDENGALQRQLSPDEAEPLLSQAEPGSEQARHIA 246

Query: 243 AAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIEL 302
           AA  A R GV R+H++S+ +  ALL ELFTR G GT++ + ++EQLR A + D+GGL+EL
Sbjct: 247 AACAAARHGVARTHLLSWHDHDALLGELFTRDGVGTMITRHRYEQLRPAELGDIGGLLEL 306

Query: 303 IRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPEY 362
           + PLE +G+LV RSRE LE EI+ + ++ER+G+II CAAL+  A+++ GELACLA++  Y
Sbjct: 307 LEPLERRGMLVPRSRERLEHEIDDYLVIERDGMIIGCAALHRFAEADMGELACLAIHVGY 366

Query: 363 RHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNFQ 422
           R G RG  LL  IE RAR LGL +LFVLTT TAHWF E GF+PS +E LP  +   YN  
Sbjct: 367 RGGARGSLLLSGIERRARRLGLASLFVLTTHTAHWFVEHGFRPSDIESLPPLKRDTYNHA 426

Query: 423 RNSQVFEKSL 432
           R S++  K L
Sbjct: 427 RKSKILVKPL 436


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: 580
Number of extensions: 30
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: 432
Length of database: 437
Length adjustment: 32
Effective length of query: 400
Effective length of database: 405
Effective search space:   162000
Effective search space used:   162000
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_086509236.1 BZY95_RS06985 (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.11895.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-161  521.6   0.0   9.6e-161  521.4   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509236.1  BZY95_RS06985 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509236.1  BZY95_RS06985 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.4   0.0  9.6e-161  9.6e-161       1     429 []       7     436 ..       7     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 521.4 bits;  conditional E-value: 9.6e-161
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               fv+w+r+++Pyinahr++t+v+ ++ge+++ +  ++l++d+allh+lGvrlv+v G rpq+e+ l++ g
  lcl|NCBI__GCF_002151265.1:WP_086509236.1   7 FVDWFRNSSPYINAHRGRTFVILIEGEAMARGRGEQLIQDLALLHTLGVRLVVVFGIRPQVEQALNEAG 75 
                                               8******************************************************************** PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                               + ++ ++G  v+dea + +v+ +a e rl +ear+s  l+ntp  g +l+ vsGn+v+a+P+Gv eG+d
  lcl|NCBI__GCF_002151265.1:WP_086509236.1  76 IVPRRHNGRWVADEAIMACVERVAAEQRLWLEARFSLGLPNTPLHGVELTAVSGNLVMAKPLGVREGID 144
                                               ********************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                               y h+Gevr++ + +++ lld +s+vll+Plgfs tGe+f+l++ +va ++a++l adklil++ee+G+ 
  lcl|NCBI__GCF_002151265.1:WP_086509236.1 145 YDHSGEVRRVRVSAVQGLLDRGSLVLLPPLGFSSTGEVFDLDAAEVAQHAAMALAADKLILMGEEPGLY 213
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslverleeet.tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGt 275
                                               d++G l+++ls++e+e+l+ ++e +  +ar + aa +a r Gvar+hl+s+    all elftrdG+Gt
  lcl|NCBI__GCF_002151265.1:WP_086509236.1 214 DENGALQRQLSPDEAEPLLSQAEPGSeQARHIAAACAAARHGVARTHLLSWHDHDALLGELFTRDGVGT 282
                                               *********************99876689**************************************** PP

                                 TIGR01890 276 lvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyae 344
                                               +++++ +e++r a+++d+gg+lel++Ple  G+lv+rsre le+ei+++ vie+dG+iigcaal+ +ae
  lcl|NCBI__GCF_002151265.1:WP_086509236.1 283 MITRHRYEQLRPAELGDIGGLLELLEPLERRGMLVPRSRERLEHEIDDYLVIERDGMIIGCAALHRFAE 351
                                               ********************************************************************* PP

                                 TIGR01890 345 eevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearr 413
                                               +++gelacla++  +r+g rG  ll+ ie rar +Gl  lfvltt+t+hWf e+Gf ++++++lP  +r
  lcl|NCBI__GCF_002151265.1:WP_086509236.1 352 ADMGELACLAIHVGYRGGARGSLLLSGIERRARRLGLASLFVLTTHTAHWFVEHGFRPSDIESLPPLKR 420
                                               ********************************************************************* PP

                                 TIGR01890 414 klynyqrrskilvkkl 429
                                                 yn+ r+skilvk+l
  lcl|NCBI__GCF_002151265.1:WP_086509236.1 421 DTYNHARKSKILVKPL 436
                                               *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (437 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: 10.68
//
[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