Alignments for a candidate for argA in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Methylovulum miyakonense HT12

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_029151571.1 METMI_RS0108775 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000384075.1:WP_029151571.1
          Length = 437

 Score =  422 bits (1085), Expect = e-122
 Identities = 212/432 (49%), Positives = 299/432 (69%), Gaps = 3/432 (0%)

Query: 3   DYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRP 62
           ++VNW R +SPYI++HR++TFV+   GE V   +F + VHD  LL+SLG RLVLVHG RP
Sbjct: 6   EFVNWFRSSSPYIHAHRNKTFVISFGGEAVLAADFEHHVHDFALLNSLGIRLVLVHGIRP 65

Query: 63  QIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLR 122
           QI+ RL      PR+H  LR+TD   L+ V +A G +R+ IEA LS+ +A SPM GA+++
Sbjct: 66  QIDQRLH-NSAPPRFHNHLRITDDLALQAVKEAAGLVRVEIEALLSLGLANSPMAGAKIK 124

Query: 123 VAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNL 182
           VA GN VTA+P+GV++G+DY HTGEVRRID + I + LD+ ++VL+SP+GYSP+GEIFNL
Sbjct: 125 VASGNFVTAKPLGVIDGIDYCHTGEVRRIDSEAIHQQLDQDNVVLISPIGYSPSGEIFNL 184

Query: 183 ACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQ--AEL 240
           + E VA   AI L+AEKL+L   +      SGK ++++   ++ A L +  N ++  ++ 
Sbjct: 185 SAEQVATAVAIALKAEKLVLLTEQSCCHPDSGKPIQQMTTAEISAFLDKHPNLHETMSQP 244

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           L AA  AC +G+ R H++  T++GALL ELFTR G GTL++   FE LR A + D+GG++
Sbjct: 245 LKAAIHACNSGIARVHLIDRTQNGALLLELFTRDGIGTLISSNPFEDLRPASLHDIGGIL 304

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           ELI+PLE+QG+L +RSRE +E EI  + I+ER+GLII C AL+       G +ACLAV+P
Sbjct: 305 ELIKPLEQQGVLAKRSREKIEMEIADYFIIERDGLIIGCIALHADLQRHFGVIACLAVHP 364

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           +YR   R + LL+    +A+ L LK +FVL+T+T HWF ERGF  S +  LP    +LYN
Sbjct: 365 DYRRSARANRLLDYASRKAKQLNLKKIFVLSTQTVHWFIERGFLSSDITNLPEPLKALYN 424

Query: 421 FQRNSQVFEKSL 432
            QRNS++  K +
Sbjct: 425 PQRNSKILCKDI 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: 519
Number of extensions: 16
Number of successful extensions: 3
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_029151571.1 METMI_RS0108775 (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.31933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-166  541.0   0.0   1.2e-166  540.8   0.0    1.0  1  lcl|NCBI__GCF_000384075.1:WP_029151571.1  METMI_RS0108775 amino-acid N-ace


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_029151571.1  METMI_RS0108775 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.8   0.0  1.2e-166  1.2e-166       1     428 [.       7     435 ..       7     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 540.8 bits;  conditional E-value: 1.2e-166
                                 TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrg 69 
                                               fv+w+r+++Pyi+ahr+kt+v+ +gge+v +  +++ v+d all+slG+rlvlvhG rpqi++rl  + 
  lcl|NCBI__GCF_000384075.1:WP_029151571.1   7 FVNWFRSSSPYIHAHRNKTFVISFGGEAVLAADFEHHVHDFALLNSLGIRLVLVHGIRPQIDQRLH-NS 74 
                                               8***************************************************************97.56 PP

                                 TIGR01890  70 rtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvd 138
                                                 +++++ lr+td+ +l+ vkeaaG +r +iea ls  lan+pmag++++v+sGnfvta+P+Gv++G+d
  lcl|NCBI__GCF_000384075.1:WP_029151571.1  75 APPRFHNHLRITDDLALQAVKEAAGLVRVEIEALLSLGLANSPMAGAKIKVASGNFVTAKPLGVIDGID 143
                                               79******************************************************************* PP

                                 TIGR01890 139 yehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGil 207
                                               y+htGevr+id+e+i+++ld+ ++vl+sP+g+s++Geifnl++e+vat vai+lka+kl+llte+    
  lcl|NCBI__GCF_000384075.1:WP_029151571.1 144 YCHTGEVRRIDSEAIHQQLDQDNVVLISPIGYSPSGEIFNLSAEQVATAVAIALKAEKLVLLTEQSCCH 212
                                               ********************************************************************* PP

                                 TIGR01890 208 dadGklvaelsaqeveslverle..eettarllsaavkalrgGvarshlvsyaedGallqelftrdGiG 274
                                                 +Gk ++++++ e+ + +++    +et ++ l+aa++a+++G+ar+hl++  ++Gall+elftrdGiG
  lcl|NCBI__GCF_000384075.1:WP_029151571.1 213 PDSGKPIQQMTTAEISAFLDKHPnlHETMSQPLKAAIHACNSGIARVHLIDRTQNGALLLELFTRDGIG 281
                                               *****************998865124667899************************************* PP

                                 TIGR01890 275 tlvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypya 343
                                               tl+s + +e +r a ++d+ggileli+Ple+qG+l +rsre +e ei+++ +ie+dGliigc al++  
  lcl|NCBI__GCF_000384075.1:WP_029151571.1 282 TLISSNPFEDLRPASLHDIGGILELIKPLEQQGVLAKRSREKIEMEIADYFIIERDGLIIGCIALHADL 350
                                               ********************************************************************* PP

                                 TIGR01890 344 eeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPear 412
                                               + + g +aclav+P++r + r +rll     +a+q+ lk++fvl+t+t hWf erGf ++++ +lPe  
  lcl|NCBI__GCF_000384075.1:WP_029151571.1 351 QRHFGVIACLAVHPDYRRSARANRLLDYASRKAKQLNLKKIFVLSTQTVHWFIERGFLSSDITNLPEPL 419
                                               ********************************************************************* PP

                                 TIGR01890 413 rklynyqrrskilvkk 428
                                               + lyn qr+skil k 
  lcl|NCBI__GCF_000384075.1:WP_029151571.1 420 KALYNPQRNSKILCKD 435
                                               *************985 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: 10.69
//
[ok]

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