Alignments for a candidate for argA in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Methylosarcina fibrata AML-C10

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_020562316.1 A3OW_RS0104920 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000372865.1:WP_020562316.1
          Length = 438

 Score =  417 bits (1073), Expect = e-121
 Identities = 218/433 (50%), Positives = 296/433 (68%), Gaps = 6/433 (1%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQ 63
           +VNW R +SPYI+SHR++TFV+   GE +  P+F ++VHD  LL SLG RLVLVHG RPQ
Sbjct: 7   FVNWFRDSSPYIHSHRNKTFVINFGGEALLDPDFDHLVHDFALLKSLGIRLVLVHGIRPQ 66

Query: 64  IEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRV 123
           I+ RL        +H++LR+T    L+CV +A G+ R+ IEA LS+ +A +PM G  LRV
Sbjct: 67  IDERLQKLDAPALFHKNLRITSDLALQCVKEAAGTARVEIEALLSLGLANTPMAGYGLRV 126

Query: 124 AGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLA 183
           A GN VTA+PIGV++GVDY HTGEVRRID   I R LD+ +IVL+SP+GYSP+GE+FNL+
Sbjct: 127 ASGNFVTAKPIGVIDGVDYGHTGEVRRIDGAAISRQLDQDAIVLISPIGYSPSGEVFNLS 186

Query: 184 CEDVAMRAAIDLEAEKLILYGAEQGL-LDASGKLVRELRPQQVPAHLQR---LGNSYQAE 239
            E VA + AI L+AEKLI +  EQG     SG+ ++++   +  + L     L N+    
Sbjct: 187 AEQVATQVAISLKAEKLI-FLTEQGFNYPESGEPIQQMTTAEARSFLDHHPDLPNTVSLP 245

Query: 240 LLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGL 299
            L AA Q+  AGV R H++    DGALL ELFTR G GTLV++  FE +R A ++D+GG+
Sbjct: 246 -LKAAIQSSNAGVGRIHLIDRRTDGALLLELFTRNGIGTLVSEAPFEDIRSATLDDIGGI 304

Query: 300 IELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVN 359
           +ELI+PLE QGIL +R+RE +E EI  + ++ER+GLII C AL+       G +ACLAV+
Sbjct: 305 LELIKPLELQGILAKRTREKIETEIADYIVIERDGLIIGCTALHAHRHGHFGAIACLAVH 364

Query: 360 PEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLY 419
           P YR G RG+ +LE    +A+ L LK L+VL+T+TAHWF ERGFQP+    LP     LY
Sbjct: 365 PGYRGGARGNRMLEHAYRKAKKLALKKLYVLSTQTAHWFIERGFQPTDFNHLPEPLKILY 424

Query: 420 NFQRNSQVFEKSL 432
           N +RNS++  + +
Sbjct: 425 NPERNSKILVRDI 437


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: 535
Number of extensions: 15
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: 438
Length adjustment: 32
Effective length of query: 400
Effective length of database: 406
Effective search space:   162400
Effective search space used:   162400
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_020562316.1 A3OW_RS0104920 (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.3855590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-167  543.3   0.0   2.5e-167  543.1   0.0    1.0  1  NCBI__GCF_000372865.1:WP_020562316.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000372865.1:WP_020562316.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.1   0.0  2.5e-167  2.5e-167       1     428 [.       7     436 ..       7     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 543.1 bits;  conditional E-value: 2.5e-167
                             TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtth 73 
                                           fv+w+r+++Pyi++hr+kt+v+ +gge++ d+ +++lv+d all+slG+rlvlvhG rpqi+erl+k +  + 
  NCBI__GCF_000372865.1:WP_020562316.1   7 FVNWFRDSSPYIHSHRNKTFVINFGGEALLDPDFDHLVHDFALLKSLGIRLVLVHGIRPQIDERLQKLDAPAL 79 
                                           8************************************************************************ PP

                             TIGR01890  74 yvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevr 146
                                           +++ lr+t + +l++vkeaaG+ r +iea ls  lantpmag  l+v+sGnfvta+PiGv++Gvdy htGevr
  NCBI__GCF_000372865.1:WP_020562316.1  80 FHKNLRITSDLALQCVKEAAGTARVEIEALLSLGLANTPMAGYGLRVASGNFVTAKPIGVIDGVDYGHTGEVR 152
                                           ************************************************************************* PP

                             TIGR01890 147 kidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsa 219
                                           +id ++i+r+ld+  ivl+sP+g+s++Ge+fnl++e+vat+vai+lka+kli+lte+     ++G+ ++++++
  NCBI__GCF_000372865.1:WP_020562316.1 153 RIDGAAISRQLDQDAIVLISPIGYSPSGEVFNLSAEQVATQVAISLKAEKLIFLTEQGFNYPESGEPIQQMTT 225
                                           *******************************************************988888999********* PP

                             TIGR01890 220 qeveslverlee..ettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireati 290
                                            e++s +++  +  +t +  l+aa+++ ++Gv r hl++ ++dGall+elftr+GiGtlvs++ +e ir at+
  NCBI__GCF_000372865.1:WP_020562316.1 226 AEARSFLDHHPDlpNTVSLPLKAAIQSSNAGVGRIHLIDRRTDGALLLELFTRNGIGTLVSEAPFEDIRSATL 298
                                           *******99876223355669**************************************************** PP

                             TIGR01890 291 ddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardgg 363
                                           dd+ggileli+Ple qGil +r re +e ei+++ vie+dGliigc+al+++ + + g +aclav+P +r+g 
  NCBI__GCF_000372865.1:WP_020562316.1 299 DDIGGILELIKPLELQGILAKRTREKIETEIADYIVIERDGLIIGCTALHAHRHGHFGAIACLAVHPGYRGGA 371
                                           ************************************************************************* PP

                             TIGR01890 364 rGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                           rG+r+l+h   +a+++ lk+l+vl+t+t+hWf erGf++++ ++lPe  + lyn +r+skilv+ 
  NCBI__GCF_000372865.1:WP_020562316.1 372 RGNRMLEHAYRKAKKLALKKLYVLSTQTAHWFIERGFQPTDFNHLPEPLKILYNPERNSKILVRD 436
                                           **************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (438 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.97
//
[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