Alignments for a candidate for argA in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Sedimenticola selenatireducens DSM 17993

Align amino-acid acetyltransferase (characterized)
to candidate WP_051301752.1 A3GO_RS0102080 amino-acid N-acetyltransferase

Query= CharProtDB::CH_024150
         (443 letters)



>NCBI__GCF_000428045.1:WP_051301752.1
          Length = 451

 Score =  450 bits (1157), Expect = e-131
 Identities = 223/440 (50%), Positives = 312/440 (70%), Gaps = 3/440 (0%)

Query: 3   KERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVV 62
           K +    V+ FR+S PYI+ HRGKT VI+ GGEA+  E+F+ +++DI L+H LGI+LV+V
Sbjct: 15  KNKHDPFVDWFRNSSPYIHAHRGKTVVILFGGEAVAEESFADLIHDISLMHGLGIKLVLV 74

Query: 63  YGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQ 122
           +GARPQI+  L  H  E  Y   +RVTD   L  VK A G ++++I ARLSM L N+P+ 
Sbjct: 75  HGARPQIEERLGLHQTEMQYINGLRVTDEAALACVKDATGAVRVEIEARLSMGLANSPMA 134

Query: 123 GAHINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTG 182
           G HI VVSGNF+ AQP+G+ +G+DY H+G +RRID DAI R +D+GAI L+  +  S TG
Sbjct: 135 GVHIRVVSGNFVTAQPIGIRNGIDYGHTGMVRRIDADAIQRVVDAGAIALVPSLGYSPTG 194

Query: 183 ESFNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGD 242
           E FNL + ++A+ +AI L A+K+I     +GVT+  G +++ + P E ++ ++ +    +
Sbjct: 195 EVFNLGAADVASAVAIALGADKLIMLIEGKGVTDTRGKVLTNVIPREVESIMQRRRSLPE 254

Query: 243 YNSGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRAT 302
                V+ L  AVKACR GV+R HLI  Q DGALL+ELF+RDG+GT +  E  E+IR A 
Sbjct: 255 E---LVQQLNCAVKACRGGVKRTHLIGRQMDGALLKELFTRDGVGTLLTAEPYEEIRGAR 311

Query: 303 INDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGE 362
           I+DIGGILEL+ PLE  G LVRRSR+ LE EI++FT+++ D T I CA+L+P+ EE+IGE
Sbjct: 312 IDDIGGILELLGPLETNGTLVRRSRDLLETEIERFTVVELDGTIIGCASLHPYVEERIGE 371

Query: 363 MACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLP 422
           +A VAVHP YR+S RG+ LL  +  +A  +G+++LFVLTT++ HWF+ERGF P  ++ LP
Sbjct: 372 LAGVAVHPAYRNSGRGDALLAHMERRALSAGINRLFVLTTQTAHWFRERGFVPTQVNTLP 431

Query: 423 ESKKQLYNYQRKSKVLMADL 442
            +K+QLYNYQR SKV +  L
Sbjct: 432 MAKQQLYNYQRNSKVFIKGL 451


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: 534
Number of extensions: 18
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: 451
Length adjustment: 33
Effective length of query: 410
Effective length of database: 418
Effective search space:   171380
Effective search space used:   171380
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_051301752.1 A3GO_RS0102080 (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.3536928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     9e-185  600.6   1.3     1e-184  600.4   1.3    1.0  1  NCBI__GCF_000428045.1:WP_051301752.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000428045.1:WP_051301752.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.4   1.3    1e-184    1e-184       1     428 [.      21     450 ..      21     451 .] 0.99

  Alignments for each domain:
  == domain 1  score: 600.4 bits;  conditional E-value: 1e-184
                             TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtth 73 
                                           fv+w+r+++Pyi+ahr+kt+v+ +gge+v+++ +++l++di+l+h lG++lvlvhGarpqieerl  ++ + +
  NCBI__GCF_000428045.1:WP_051301752.1  21 FVDWFRNSSPYIHAHRGKTVVILFGGEAVAEESFADLIHDISLMHGLGIKLVLVHGARPQIEERLGLHQTEMQ 93 
                                           8************************************************************************ PP

                             TIGR01890  74 yvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevr 146
                                           y++Glrvtdea+l +vk+a+G++r +iearlsm lan+pmag +++vvsGnfvta+PiG+ +G+dy htG+vr
  NCBI__GCF_000428045.1:WP_051301752.1  94 YINGLRVTDEAALACVKDATGAVRVEIEARLSMGLANSPMAGVHIRVVSGNFVTAQPIGIRNGIDYGHTGMVR 166
                                           ************************************************************************* PP

                             TIGR01890 147 kidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsa 219
                                           +ida++i+r +d++ i l++ lg+s+tGe+fnl + dva+ vai+l+adkli+l e +G+ d+ Gk+ +++ +
  NCBI__GCF_000428045.1:WP_051301752.1 167 RIDADAIQRVVDAGAIALVPSLGYSPTGEVFNLGAADVASAVAIALGADKLIMLIEGKGVTDTRGKVLTNVIP 239
                                           ************************************************************************* PP

                             TIGR01890 220 qeveslverlee..ettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireati 290
                                           +eves ++r ++  e   + l+ avka+rgGv+r+hl+  + dGall+elftrdG+Gtl++ e +e+ir a i
  NCBI__GCF_000428045.1:WP_051301752.1 240 REVESIMQRRRSlpEELVQQLNCAVKACRGGVKRTHLIGRQMDGALLKELFTRDGVGTLLTAEPYEEIRGARI 312
                                           *******998763344688999*************************************************** PP

                             TIGR01890 291 ddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardgg 363
                                           dd+ggilel+ Ple +G+lvrrsr+lle eie+f+v+e dG+iigca+l+py ee++gela +av+P +r++g
  NCBI__GCF_000428045.1:WP_051301752.1 313 DDIGGILELLGPLETNGTLVRRSRDLLETEIERFTVVELDGTIIGCASLHPYVEERIGELAGVAVHPAYRNSG 385
                                           ************************************************************************* PP

                             TIGR01890 364 rGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                           rG+ ll+h+e ra + G++rlfvltt+t+hWfrerGf++++v++lP+a+++lynyqr+sk+++k 
  NCBI__GCF_000428045.1:WP_051301752.1 386 RGDALLAHMERRALSAGINRLFVLTTQTAHWFRERGFVPTQVNTLPMAKQQLYNYQRNSKVFIKG 450
                                           **************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (451 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: 00:00:00.00
# Mc/sec: 21.36
//
[ok]

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