Alignments for a candidate for argA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Acidovorax sp. GW101-3H11

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate Ac3H11_900 N-acetylglutamate synthase (EC 2.3.1.1)

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_900
          Length = 448

 Score =  389 bits (999), Expect = e-112
 Identities = 201/448 (44%), Positives = 286/448 (63%), Gaps = 27/448 (6%)

Query: 4   YVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGSRPQ 63
           +V W R  +PYI+  R++TFV+ L GE +      NI  DL L+ ++G ++VLVHG RPQ
Sbjct: 9   FVPWFRSVAPYIHKFRNQTFVIGLTGEAIAAGKLHNIAQDLALIQAMGVKIVLVHGFRPQ 68

Query: 64  IEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGARLRV 123
           +  +LAA+G A +Y   +R+TD+  L+C  +A G LR  IEA  S  +  +PM GA +RV
Sbjct: 69  VNEQLAAKGHAAKYSHGIRITDSVALDCAQEAAGQLRYEIEAAFSQGLPNTPMAGATVRV 128

Query: 124 AGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIFNLA 183
             GN +TARP+G+V+GVD+ H+G VR++D  GI + LD  ++VLLSP G+SPTGE FNL+
Sbjct: 129 ISGNFLTARPVGIVDGVDFQHSGLVRKVDVAGIRQTLDMGALVLLSPFGFSPTGEAFNLS 188

Query: 184 CEDVAMRAAIDLEAEKLILYGAEQGL-------------------LDASGKLVRELRPQQ 224
            E+VA   AI+L A+KLI     QG+                   L A+  L+ +L P Q
Sbjct: 189 MEEVATSVAIELRADKLIFLTEVQGIRMSPTEPESDDNPIDTELPLAAAQALLAQLPPAQ 248

Query: 225 VPAHLQRLGNSYQAELLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQ 284
            P              L    +AC+AGV+RSHI+ +  DG+LL E++   G GT+V  E+
Sbjct: 249 QPTD--------TGFYLQHCVKACKAGVERSHILPFAVDGSLLLEVYVHDGIGTMVIDEK 300

Query: 285 FEQLREAGIEDVGGLIELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYP 344
            E+LREA I+DVGG+++LI P E+ G LV+R R  +ER+I  ++I+E +G+I  CAALYP
Sbjct: 301 LEELREATIDDVGGILQLIEPFEKDGTLVKRDRTEIERDIATYTIIEHDGVIFGCAALYP 360

Query: 345 IADSEAGELACLAVNPEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQ 404
             +++  E+A + V+P+ +  G G++LL+RIE+RAR LGL ++FVLTTRT HWF +RGFQ
Sbjct: 361 YPEAKTAEMAAVTVSPQSQGTGDGEKLLKRIEQRARLLGLDSIFVLTTRTMHWFIKRGFQ 420

Query: 405 PSSVERLPAARASLYNFQRNSQVFEKSL 432
           P   + LP AR   YN+ R SQV  K L
Sbjct: 421 PVDPDWLPDARKRKYNWDRKSQVLVKKL 448


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: 529
Number of extensions: 20
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: 448
Length adjustment: 32
Effective length of query: 400
Effective length of database: 416
Effective search space:   166400
Effective search space used:   166400
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 Ac3H11_900 (N-acetylglutamate synthase (EC 2.3.1.1))
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.25281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   7.8e-187  607.4   0.0   8.9e-187  607.2   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900  N-acetylglutamate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900  N-acetylglutamate synthase (EC 2.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.2   0.0  8.9e-187  8.9e-187       1     429 []       9     448 .]       9     448 .] 0.95

  Alignments for each domain:
  == domain 1  score: 607.2 bits;  conditional E-value: 8.9e-187
                                       TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqiee 63 
                                                     fv w+r++aPyi+++r++t+v+gl ge++++++l ++++d+al++++Gv++vlvhG rpq++e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900   9 FVPWFRSVAPYIHKFRNQTFVIGLTGEAIAAGKLHNIAQDLALIQAMGVKIVLVHGFRPQVNE 71 
                                                     899************************************************************ PP

                                       TIGR01890  64 rlakrgrtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfv 126
                                                     +la++g  ++y +G+r+td  +l++++eaaG+lr +iea++s+ l+ntpmag+ ++v+sGnf+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900  72 QLAAKGHAAKYSHGIRITDSVALDCAQEAAGQLRYEIEAAFSQGLPNTPMAGATVRVISGNFL 134
                                                     *************************************************************** PP

                                       TIGR01890 127 tarPiGvveGvdyehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsva 189
                                                     tarP+G+v+Gvd++h+G vrk+d++gir++ld + +vllsP+gfs+tGe+fnl+me+vatsva
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900 135 TARPVGIVDGVDFQHSGLVRKVDVAGIRQTLDMGALVLLSPFGFSPTGEAFNLSMEEVATSVA 197
                                                     *************************************************************** PP

                                       TIGR01890 190 iklkadklillteedGildadGk.......lvaelsaqeveslverleeet....tarllsaa 241
                                                     i+l+adkli+lte++Gi  +  +       + +el    +++l+ +l   +    t  +l++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900 198 IELRADKLIFLTEVQGIRMSPTEpesddnpIDTELPLAAAQALLAQLPPAQqptdTGFYLQHC 260
                                                     *****************76544400001114555655556666665544437778999***** PP

                                       TIGR01890 242 vkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPle 304
                                                     vka+++Gv+rsh++++a dG+ll+e++++dGiGt+v  e+le++reatiddvggil+li+P+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900 261 VKACKAGVERSHILPFAVDGSLLLEVYVHDGIGTMVIDEKLEELREATIDDVGGILQLIEPFE 323
                                                     *************************************************************** PP

                                       TIGR01890 305 eqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGer 367
                                                     ++G+lv+r+r  +er+i+ +++ie+dG+i+gcaalypy+e++++e+a ++vsP+ +++g+Ge+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900 324 KDGTLVKRDRTEIERDIATYTIIEHDGVIFGCAALYPYPEAKTAEMAAVTVSPQSQGTGDGEK 386
                                                     *************************************************************** PP

                                       TIGR01890 368 llkhiedrarqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                                     llk+ie+rar +Gl  +fvlttrt hWf +rGf++++ d lP ar++ yn++r+s++lvkkl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_900 387 LLKRIEQRARLLGLDSIFVLTTRTMHWFIKRGFQPVDPDWLPDARKRKYNWDRKSQVLVKKL 448
                                                     ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (448 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: 9.92
//
[ok]

This GapMind analysis is from Apr 09 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