Alignments for a candidate for argA in Thiothrix lacustris DSM 21227

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Thiothrix lacustris DSM 21227

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_028489948.1 Q394_RS0114840 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000621325.1:WP_028489948.1
          Length = 424

 Score =  366 bits (940), Expect = e-106
 Identities = 195/429 (45%), Positives = 276/429 (64%), Gaps = 13/429 (3%)

Query: 5   VNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQI 64
           VN LR ASPYI  HR++TFV+  PGE VE P F  ++ D+  + +LG+R+V+VHG+R QI
Sbjct: 8   VNLLREASPYIQQHRNKTFVIAFPGEVVEQPTFSRLIQDIATVSALGSRIVIVHGTRAQI 67

Query: 65  EARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRVA 124
             RLAA G     H ++RVT    +  V +AVG LRI IE+ LS  +    ++ A + V+
Sbjct: 68  NQRLAAAGRVAHIHHNIRVTHPDDIPLVEEAVGYLRIKIESLLSHALNQPGLENASIGVS 127

Query: 125 GGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLAC 184
            GN +TA+P+G+++GVDY HTG++RRI  + I + LD  +IVL+SP+GYSP+GE +N+  
Sbjct: 128 SGNYITAQPLGIIDGVDYGHTGKIRRIAHRFIQQQLDSHNIVLMSPIGYSPSGETYNIDY 187

Query: 185 EDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAELLDAA 244
           E VA+  A  L A+K+I       + D   +L  E+   Q+ A      ++  +  L   
Sbjct: 188 EHVALSTAKALNADKIIF------ISDNDAQLPHEITAGQIDA------DANASPFLKKI 235

Query: 245 AQACRAG-VKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIELI 303
           A+    G  +R H+++   DGALL E++TR G G+L+A + FEQ+R A +ED+ G+++LI
Sbjct: 236 ARILLDGDSERVHLLNAATDGALLLEVYTRDGVGSLIAAQHFEQMRAATVEDISGILDLI 295

Query: 304 RPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPEYR 363
           RPLE +G L++RSRE LE EI  F +  R+  IIAC ALY   + +  ELACLAV+ +YR
Sbjct: 296 RPLESKGTLIKRSREQLELEISNFHVTVRDQKIIACVALYHTDNPDIAELACLAVHTDYR 355

Query: 364 HGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNFQR 423
            G RGD+LL  I + A+  G   L VLTT+T  WFRERGF   SV+ LP  + SLYN+QR
Sbjct: 356 SGNRGDKLLRHIAQLAKTQGTARLLVLTTQTTDWFRERGFIKGSVDELPPNKKSLYNYQR 415

Query: 424 NSQVFEKSL 432
           NSQV  K+L
Sbjct: 416 NSQVLFKTL 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: 496
Number of extensions: 21
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: 424
Length adjustment: 32
Effective length of query: 400
Effective length of database: 392
Effective search space:   156800
Effective search space used:   156800
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_028489948.1 Q394_RS0114840 (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.12834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-146  472.8   0.5     7e-146  472.4   0.5    1.1  1  lcl|NCBI__GCF_000621325.1:WP_028489948.1  Q394_RS0114840 amino-acid N-acet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028489948.1  Q394_RS0114840 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.4   0.5    7e-146    7e-146       2     429 .]       8     424 .]       7     424 .] 0.97

  Alignments for each domain:
  == domain 1  score: 472.4 bits;  conditional E-value: 7e-146
                                 TIGR01890   2 vkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgr 70 
                                               v+ lrea+Pyi++hr+kt+v++++ge+ve++++++l++dia +++lG r+v+vhG+r qi++rla+ gr
  lcl|NCBI__GCF_000621325.1:WP_028489948.1   8 VNLLREASPYIQQHRNKTFVIAFPGEVVEQPTFSRLIQDIATVSALGSRIVIVHGTRAQINQRLAAAGR 76 
                                               899****************************************************************** PP

                                 TIGR01890  71 tthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdy 139
                                                +h ++ +rvt    + lv+ea+G lr +ie+ ls++l++   + + + v sGn++ta+P+G+++Gvdy
  lcl|NCBI__GCF_000621325.1:WP_028489948.1  77 VAHIHHNIRVTHPDDIPLVEEAVGYLRIKIESLLSHALNQPGLENASIGVSSGNYITAQPLGIIDGVDY 145
                                               ********************************************************************* PP

                                 TIGR01890 140 ehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGild 208
                                                htG++r+i  + i+++ld+ +ivl+sP+g+s++Ge++n++ e+va s+a +l+adk+i++      +d
  lcl|NCBI__GCF_000621325.1:WP_028489948.1 146 GHTGKIRRIAHRFIQQQLDSHNIVLMSPIGYSPSGETYNIDYEHVALSTAKALNADKIIFI------SD 208
                                               ***********************************************************96......67 PP

                                 TIGR01890 209 adGklvaelsaqeveslverleeettarllsaavkal.rgGvarshlvsyaedGallqelftrdGiGtl 276
                                               +d +l +e++a ++++ ++       + +l+++++ l  g  +r+hl++ a+dGall+e++trdG+G l
  lcl|NCBI__GCF_000621325.1:WP_028489948.1 209 NDAQLPHEITAGQIDADAN------ASPFLKKIARILlDGDSERVHLLNAATDGALLLEVYTRDGVGSL 271
                                               8899999999888876543......357899988875267789************************** PP

                                 TIGR01890 277 vskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyaee 345
                                               ++ +++e++r at++d++gil+lirPle +G+l++rsre+le ei++f v  +d  ii+c aly   + 
  lcl|NCBI__GCF_000621325.1:WP_028489948.1 272 IAAQHFEQMRAATVEDISGILDLIRPLESKGTLIKRSREQLELEISNFHVTVRDQKIIACVALYHTDNP 340
                                               ********************************************************************* PP

                                 TIGR01890 346 evgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrk 414
                                               +++elaclav+ ++r g+rG++ll+hi + a++ G  rl+vltt+t++WfrerGf + svdelP ++++
  lcl|NCBI__GCF_000621325.1:WP_028489948.1 341 DIAELACLAVHTDYRSGNRGDKLLRHIAQLAKTQGTARLLVLTTQTTDWFRERGFIKGSVDELPPNKKS 409
                                               ********************************************************************* PP

                                 TIGR01890 415 lynyqrrskilvkkl 429
                                               lynyqr+s++l k l
  lcl|NCBI__GCF_000621325.1:WP_028489948.1 410 LYNYQRNSQVLFKTL 424
                                               ***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (424 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.61
//
[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