Alignments for a candidate for argA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_018232567.1 THITHI_RS0108035 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_000378965.1:WP_018232567.1
          Length = 442

 Score =  474 bits (1221), Expect = e-138
 Identities = 239/430 (55%), Positives = 306/430 (71%), Gaps = 2/430 (0%)

Query: 5   VNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQI 64
           +NW R+A+PYIN+HR RTFV+   GE V+   F  ++HD+ +L SLG RLVLVHG+RPQI
Sbjct: 12  INWFRNAAPYINAHRGRTFVIAFGGEAVQDTGFARLIHDIAMLQSLGVRLVLVHGARPQI 71

Query: 65  EARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRVA 124
           E RL ARG A  Y   LR+TDA  L+ V +A G LR+ IEA+LSM +A +PM GAR+RVA
Sbjct: 72  EQRLRARGQAFHYAAGLRITDADALQEVKEAAGCLRVEIEAQLSMGLANTPMSGARIRVA 131

Query: 125 GGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLAC 184
            GN V A+P+GV +GVDY HTGEVRRID +GI R L+   +VLLSPLGYSPTGE+FNL+ 
Sbjct: 132 SGNHVMAKPLGVRDGVDYQHTGEVRRIDAEGIRRHLENGEVVLLSPLGYSPTGEVFNLSA 191

Query: 185 EDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGN--SYQAELLD 242
           EDVA   AI L+A+KLI    E  L D   + + ++  +Q    L R     S  A  L 
Sbjct: 192 EDVATATAISLKADKLIFLTEEPRLRDGRRRPISQMTAEQARTWLNRRRGPASETARHLT 251

Query: 243 AAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLIEL 302
           +A  ACR  V+R H+V    DGALL EL+TR G GTL+  E +E+LR A I+DVGG++EL
Sbjct: 252 SAIHACRHAVERVHLVERAVDGALLLELYTRDGVGTLITGETYERLRRATIDDVGGILEL 311

Query: 303 IRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPEY 362
           I+PLE +G+LVRRSRE LE EI++FS++ER+G+++ C A YP  +   GELACLA++P+Y
Sbjct: 312 IQPLEAEGVLVRRSREQLELEIDRFSVIERDGVVLGCTAFYPFPEESVGELACLAIHPQY 371

Query: 363 RHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNFQ 422
           R   RGD LL+ +E  AR LG+  LFVLTTRTAHWFRERGF+P  ++ LP  R  LYN+Q
Sbjct: 372 RTASRGDRLLDFVEAEARTLGIARLFVLTTRTAHWFRERGFEPGDIKALPLRRRELYNYQ 431

Query: 423 RNSQVFEKSL 432
           RNS+VF K L
Sbjct: 432 RNSKVFIKGL 441


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: 591
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: 442
Length adjustment: 32
Effective length of query: 400
Effective length of database: 410
Effective search space:   164000
Effective search space used:   164000
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_018232567.1 THITHI_RS0108035 (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.18207.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-189  615.6   0.3   2.7e-189  615.4   0.3    1.0  1  lcl|NCBI__GCF_000378965.1:WP_018232567.1  THITHI_RS0108035 amino-acid N-ac


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000378965.1:WP_018232567.1  THITHI_RS0108035 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.4   0.3  2.7e-189  2.7e-189       2     428 ..      12     440 ..      11     441 .. 0.99

  Alignments for each domain:
  == domain 1  score: 615.4 bits;  conditional E-value: 2.7e-189
                                 TIGR01890   2 vkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgr 70 
                                               ++w+r+aaPyinahr++t+v+++gge+v+d  +++l++dia+l+slGvrlvlvhGarpqie+rl +rg+
  lcl|NCBI__GCF_000378965.1:WP_018232567.1  12 INWFRNAAPYINAHRGRTFVIAFGGEAVQDTGFARLIHDIAMLQSLGVRLVLVHGARPQIEQRLRARGQ 80 
                                               79******************************************************************* PP

                                 TIGR01890  71 tthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdy 139
                                                 hy  Glr+td+ +l+ vkeaaG lr +iea+lsm lantpm+g+r++v+sGn v+a+P+Gv +Gvdy
  lcl|NCBI__GCF_000378965.1:WP_018232567.1  81 AFHYAAGLRITDADALQEVKEAAGCLRVEIEAQLSMGLANTPMSGARIRVASGNHVMAKPLGVRDGVDY 149
                                               ********************************************************************* PP

                                 TIGR01890 140 ehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGild 208
                                               +htGevr+idaegirr+l+++++vllsPlg+s+tGe+fnl++edvat +ai+lkadkli+ltee+ + d
  lcl|NCBI__GCF_000378965.1:WP_018232567.1 150 QHTGEVRRIDAEGIRRHLENGEVVLLSPLGYSPTGEVFNLSAEDVATATAISLKADKLIFLTEEPRLRD 218
                                               ********************************************************************* PP

                                 TIGR01890 209 adGklvaelsaqeveslverleeet..tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGt 275
                                                  + + +++a+++++ ++r ++    tar l++a++a+r  v+r+hlv+ a dGall+el+trdG+Gt
  lcl|NCBI__GCF_000378965.1:WP_018232567.1 219 GRRRPISQMTAEQARTWLNRRRGPAseTARHLTSAIHACRHAVERVHLVERAVDGALLLELYTRDGVGT 287
                                               *******************999876669***************************************** PP

                                 TIGR01890 276 lvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyae 344
                                               l++ e++e +r+atiddvggileli+Ple++G+lvrrsre+le ei++fsvie+dG+++gc+a+yp++e
  lcl|NCBI__GCF_000378965.1:WP_018232567.1 288 LITGETYERLRRATIDDVGGILELIQPLEAEGVLVRRSREQLELEIDRFSVIERDGVVLGCTAFYPFPE 356
                                               ********************************************************************* PP

                                 TIGR01890 345 eevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearr 413
                                               e+vgelacla++P++r + rG+rll  +e+ ar++G+ rlfvlttrt+hWfrerGf++ ++++lP  rr
  lcl|NCBI__GCF_000378965.1:WP_018232567.1 357 ESVGELACLAIHPQYRTASRGDRLLDFVEAEARTLGIARLFVLTTRTAHWFRERGFEPGDIKALPLRRR 425
                                               ********************************************************************* PP

                                 TIGR01890 414 klynyqrrskilvkk 428
                                               +lynyqr+sk+++k 
  lcl|NCBI__GCF_000378965.1:WP_018232567.1 426 ELYNYQRNSKVFIKG 440
                                               ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (442 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: 12.14
//
[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