Alignments for a candidate for argA in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Thioalkalivibrio denitrificans ALJD

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_077280366.1 B1C78_RS17130 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>NCBI__GCF_002000365.1:WP_077280366.1
          Length = 445

 Score =  480 bits (1235), Expect = e-140
 Identities = 245/430 (56%), Positives = 305/430 (70%), Gaps = 2/430 (0%)

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

Query: 65  EARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRVA 124
           E RL ARGLA RY   LRVTDA  L  V +A G LR+ IEA LSM +A +PM GAR+RVA
Sbjct: 72  EQRLRARGLAFRYEAGLRVTDADALAAVKEAGGCLRVEIEALLSMGLANTPMSGARIRVA 131

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

Query: 185 EDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHL--QRLGNSYQAELLD 242
           EDVA   AI L+A+KLI      G  D   + V +L  +Q    L  +R  +   A+ L 
Sbjct: 192 EDVATATAIALKADKLIFLTETPGPRDGRRRRVSQLSVEQAQVWLGGRRKLDPETAQHLK 251

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

Query: 303 IRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNPEY 362
           I+PLE +GILVRRSRE LE EI++FS++ER+G+++ CAA YP      GELACLA++PEY
Sbjct: 312 IQPLEAEGILVRRSREQLELEIDRFSVIERDGIVLGCAAFYPFPAESVGELACLAIHPEY 371

Query: 363 RHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYNFQ 422
           R  GRGD LLE +E  A  LG+  LFVLTTRTAHWFRERGF+P  +  LP  +  LYN+Q
Sbjct: 372 RTAGRGDRLLEFVEAEAAALGIARLFVLTTRTAHWFRERGFEPGDIRNLPLRKRELYNYQ 431

Query: 423 RNSQVFEKSL 432
           RNS++F K L
Sbjct: 432 RNSKIFIKEL 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: 587
Number of extensions: 23
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: 445
Length adjustment: 32
Effective length of query: 400
Effective length of database: 413
Effective search space:   165200
Effective search space used:   165200
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_077280366.1 B1C78_RS17130 (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.2845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-187  607.1   0.2     1e-186  607.0   0.2    1.0  1  lcl|NCBI__GCF_002000365.1:WP_077280366.1  B1C78_RS17130 amino-acid N-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077280366.1  B1C78_RS17130 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.0   0.2    1e-186    1e-186       2     429 .]      12     441 ..      11     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 607.0 bits;  conditional E-value: 1e-186
                                 TIGR01890   2 vkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgr 70 
                                               ++w+r+aaPyinahr++t+v+++gge+v+d  +++l++d+a+l+slGvrlvlvhGarpqie+rl +rg+
  lcl|NCBI__GCF_002000365.1:WP_077280366.1  12 INWFRNAAPYINAHRGRTFVIAFGGEAVQDAGFAQLIHDLAMLQSLGVRLVLVHGARPQIEQRLRARGL 80 
                                               79******************************************************************* PP

                                 TIGR01890  71 tthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdy 139
                                                 +y  Glrvtd+ +l  vkea G lr +iea lsm lantpm+g+r++v+sGn v+a+P+Gv +Gvdy
  lcl|NCBI__GCF_002000365.1:WP_077280366.1  81 AFRYEAGLRVTDADALAAVKEAGGCLRVEIEALLSMGLANTPMSGARIRVASGNHVIAKPLGVRDGVDY 149
                                               ********************************************************************* PP

                                 TIGR01890 140 ehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGild 208
                                               +htGevr+idaegirr l++++ vllsPlg+s+tGe+fnl++edvat +ai+lkadkli+lte++G  d
  lcl|NCBI__GCF_002000365.1:WP_077280366.1 150 QHTGEVRRIDAEGIRRRLESGETVLLSPLGYSPTGEVFNLSAEDVATATAIALKADKLIFLTETPGPRD 218
                                               ********************************************************************* PP

                                 TIGR01890 209 adGklvaelsaqeveslverleeet..tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGt 275
                                                  + v +ls ++++  +   ++    ta+ l++av+a+r Gvar+hlv+ + dGall+el+trdG+Gt
  lcl|NCBI__GCF_002000365.1:WP_077280366.1 219 GRRRRVSQLSVEQAQVWLGGRRKLDpeTAQHLKSAVHACRQGVARVHLVERNVDGALLLELYTRDGVGT 287
                                               **********999998874333221337***************************************** PP

                                 TIGR01890 276 lvskealesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigcaalypyae 344
                                               l++ e++e +r+a iddvggileli+Ple++Gilvrrsre+le ei++fsvie+dG+++gcaa+yp++ 
  lcl|NCBI__GCF_002000365.1:WP_077280366.1 288 LITGETYERMRRASIDDVGGILELIQPLEAEGILVRRSREQLELEIDRFSVIERDGIVLGCAAFYPFPA 356
                                               ********************************************************************* PP

                                 TIGR01890 345 eevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearr 413
                                               e+vgelacla++Pe+r +grG+rll+ +e+ a ++G+ rlfvlttrt+hWfrerGf++ ++ +lP  +r
  lcl|NCBI__GCF_002000365.1:WP_077280366.1 357 ESVGELACLAIHPEYRTAGRGDRLLEFVEAEAAALGIARLFVLTTRTAHWFRERGFEPGDIRNLPLRKR 425
                                               ********************************************************************* PP

                                 TIGR01890 414 klynyqrrskilvkkl 429
                                               +lynyqr+ski++k+l
  lcl|NCBI__GCF_002000365.1:WP_077280366.1 426 ELYNYQRNSKIFIKEL 441
                                               *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (445 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: 00:00:00.02
# Mc/sec: 7.91
//
[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