Alignments for a candidate for argA in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Sulfurivirga caldicuralii DSM 17737

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_074200765.1 BUQ81_RS02290 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_900141795.1:WP_074200765.1
          Length = 426

 Score =  283 bits (723), Expect = 9e-81
 Identities = 178/431 (41%), Positives = 249/431 (57%), Gaps = 15/431 (3%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGV-EHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           ++  LR ASPYI  HRD+T VV L  E V +     + + DL+LLH++G +LVL  G R 
Sbjct: 7   FITALRQASPYILGHRDKTCVVYLASELVADEKALRDTLADLLLLHNMGLKLVLAVGLRE 66

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           Q    L  +GL   +    RVT A  L  +    G +   ++A  S     S ++     
Sbjct: 67  QFTHALQEKGLQCDFCGQQRVTPAEALPILAGVSGRVATQLQALASCRCPVSDLRTLPPV 126

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           +  GN V A+P GV+ G D+ HTG VR++    +   L+   I +L+ +  S TGE+FNL
Sbjct: 127 ITLGNWVIAQPRGVLNGTDFQHTGRVRKVQVDMLRHALNSGQIPMLTAVTPSFTGELFNL 186

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAH-LQRLGNSYQAELL 241
              + A   A  L ++KLI+   +  L            P+Q+ A  LQ+  N  + +LL
Sbjct: 187 NAFEQACAVASALRSDKLIVLLPQDQL---------PTLPKQLNARELQK--NQSKHQLL 235

Query: 242 DAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIE 301
              A+   A V+R H++     GALL ELFTR G GTL+  +Q+ ++R+A I+DVGG++ 
Sbjct: 236 PQLAEVSGA-VRRIHLLDAFAPGALLKELFTRDGVGTLIFADQYHEIRQATIDDVGGILA 294

Query: 302 LIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPE 361
           LI PLEE GILVRR RE LE EI  F +V R+G II CAALYP+ D  A E+AC AV+P 
Sbjct: 295 LIEPLEEAGILVRREREKLEAEIANFLVVVRDGHIIGCAALYPL-DEHAAEVACFAVDPA 353

Query: 362 YRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNF 421
           YR  G G  LL  IE RA  LGL+ L++LTT+T HWF + GF   + E LP +R +LYN+
Sbjct: 354 YRGQGIGVSLLHAIEARACSLGLQRLYLLTTQTQHWFTQHGFVEVNPEDLPESRQALYNW 413

Query: 422 QRNSQVFEKSL 432
           QR S+V+ K++
Sbjct: 414 QRRSRVYAKAV 424


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: 432
Number of extensions: 15
Number of successful extensions: 4
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: 426
Length adjustment: 32
Effective length of query: 400
Effective length of database: 394
Effective search space:   157600
Effective search space used:   157600
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_074200765.1 BUQ81_RS02290 (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.2152751.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-125  405.5   0.1   1.7e-125  405.2   0.1    1.1  1  NCBI__GCF_900141795.1:WP_074200765.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900141795.1:WP_074200765.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   0.1  1.7e-125  1.7e-125       1     427 [.       7     422 ..       7     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 1.7e-125
                             TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelved.knlgklvadiallhslGvrlvlvhGarpqieerlakrgrtt 72 
                                           f+  lr+a+Pyi  hrdkt vv l  elv+d k l + +ad+ llh++G++lvl  G r+q  + l+++g++ 
  NCBI__GCF_900141795.1:WP_074200765.1   7 FITALRQASPYILGHRDKTCVVYLASELVADeKALRDTLADLLLLHNMGLKLVLAVGLREQFTHALQEKGLQC 79 
                                           7889*************************862679************************************** PP

                             TIGR01890  73 hyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGev 145
                                           +++   rvt + +l     ++G++ ++++a  s   + +        +  Gn+v+a+P Gv++G+d++htG+v
  NCBI__GCF_900141795.1:WP_074200765.1  80 DFCGQQRVTPAEALPILAGVSGRVATQLQALASCRCPVSDLRTLPPVITLGNWVIAQPRGVLNGTDFQHTGRV 152
                                           ********************************999999988887777888*********************** PP

                             TIGR01890 146 rkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaels 218
                                           rk+ ++ +r+ l++++i +l+ ++ s tGe fnl++ + a+ va +l++dkli+l ++d +     +l ++l+
  NCBI__GCF_900141795.1:WP_074200765.1 153 RKVQVDMLRHALNSGQIPMLTAVTPSFTGELFNLNAFEQACAVASALRSDKLIVLLPQDQL----PTLPKQLN 221
                                           *********************************************************9766....57788888 PP

                             TIGR01890 219 aqeveslverleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatid 291
                                           a+e+++     ++  +++ll + ++ + g v+r hl++  + Gall+elftrdG+Gtl+  +++ +ir+atid
  NCBI__GCF_900141795.1:WP_074200765.1 222 ARELQK----NQS--KHQLLPQ-LAEVSGAVRRIHLLDAFAPGALLKELFTRDGVGTLIFADQYHEIRQATID 287
                                           555443....222..2356655.56689********************************************* PP

                             TIGR01890 292 dvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggr 364
                                           dvggil+li+Plee Gilvrr+re le ei++f v+ +dG iigcaalyp+ +e+++e+ac+av+P +r+ g 
  NCBI__GCF_900141795.1:WP_074200765.1 288 DVGGILALIEPLEEAGILVRREREKLEAEIANFLVVVRDGHIIGCAALYPL-DEHAAEVACFAVDPAYRGQGI 359
                                           **************************************************8.6789***************** PP

                             TIGR01890 365 GerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvk 427
                                           G  ll+ ie+ra ++Gl+rl+ ltt+t+hWf+++Gf+e++ ++lPe+r+ lyn+qrrs+++ k
  NCBI__GCF_900141795.1:WP_074200765.1 360 GVSLLHAIEARACSLGLQRLYLLTTQTQHWFTQHGFVEVNPEDLPESRQALYNWQRRSRVYAK 422
                                           ************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (426 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.11
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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