GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argA in Pseudomonas fluorescens FW300-N2C3

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate AO356_13085 AO356_13085 N-acetylglutamate synthase

Query= BRENDA::P22567
         (432 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 AO356_13085
           N-acetylglutamate synthase
          Length = 432

 Score =  751 bits (1940), Expect = 0.0
 Identities = 372/432 (86%), Positives = 403/432 (93%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           MP+YVNWLRHASPYIN+HRD TF+VMLPG+GVEHPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MPEYVNWLRHASPYINAHRDCTFIVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIE RLAARGL P YH  +R+TDA TLECVIDAVG LRIAIEARLSMDMA+SPMQG+R
Sbjct: 61  RPQIETRLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSR 120

Query: 121 LRVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIF 180
           LRVA GNLVTARPIGV+EGVDYHHTGEVRR+DRKGI RLLDERSIVLLSPLGYSPTGEIF
Sbjct: 121 LRVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGYSPTGEIF 180

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL A+KL+L+GAEQGL+   G+LVRELRPQQVP H+QRLG+ YQAEL
Sbjct: 181 NLACEDVATRAAIDLAADKLLLFGAEQGLIGEDGRLVRELRPQQVPGHMQRLGSDYQAEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAAQACR GV RSHIVSY EDGALL+ELFTR G+GTLVAQEQFE +REA IEDVGGL+
Sbjct: 241 LDAAAQACRGGVARSHIVSYAEDGALLAELFTRDGSGTLVAQEQFEVVREAAIEDVGGLL 300

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           +LI PLEEQGILVRRSREVLEREIEQFS+VEREG+IIACAALY IADS+AGELACLAVNP
Sbjct: 301 DLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIACAALYQIADSDAGELACLAVNP 360

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           EYRHGGRGDELLERIE RAR  GLKTLFVLTTRTAHWFRERGF+PSSV+RLPAARASLYN
Sbjct: 361 EYRHGGRGDELLERIETRARAQGLKTLFVLTTRTAHWFRERGFEPSSVDRLPAARASLYN 420

Query: 421 FQRNSQVFEKSL 432
           +QRNS++FEK+L
Sbjct: 421 YQRNSKIFEKAL 432


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: 724
Number of extensions: 15
Number of successful extensions: 1
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: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
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 AO356_13085 AO356_13085 (N-acetylglutamate synthase)
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.12046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.4e-224  729.8   0.2   6.1e-224  729.6   0.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085  AO356_13085 N-acetylglutamate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085  AO356_13085 N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.6   0.2  6.1e-224  6.1e-224       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 729.6 bits;  conditional E-value: 6.1e-224
                                       TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqiee 63 
                                                     +v+wlr+a+Pyinahrd+t++v+l+g++ve++n+g++v+d++llhslGvrlvlvhG+rpqie 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085   4 YVNWLRHASPYINAHRDCTFIVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGSRPQIET 66 
                                                     8************************************************************** PP

                                       TIGR01890  64 rlakrgrtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfv 126
                                                     rla+rg+t+hy++G+r+td+a+le+v++a+G+lr aiearlsm++a++pm+gsrl+v+sGn+v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085  67 RLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSRLRVASGNLV 129
                                                     *************************************************************** PP

                                       TIGR01890 127 tarPiGvveGvdyehtGevrkidaegirrlldersivllsPlgfsvtGeifnlamedvatsva 189
                                                     tarPiGv+eGvdy+htGevr++d++gi+rlldersivllsPlg+s+tGeifnla+edvat++a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 130 TARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGYSPTGEIFNLACEDVATRAA 192
                                                     *************************************************************** PP

                                       TIGR01890 190 iklkadklillteedGildadGklvaelsaqeveslverleeettarllsaavkalrgGvars 252
                                                     i+l adkl+l+++e+G++ +dG+lv+el++q+v  +++rl+++++a+ll+aa++a+rgGvars
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 193 IDLAADKLLLFGAEQGLIGEDGRLVRELRPQQVPGHMQRLGSDYQAELLDAAAQACRGGVARS 255
                                                     *************************************************************** PP

                                       TIGR01890 253 hlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPleeqGilvrrsre 315
                                                     h+vsyaedGall elftrdG Gtlv++e++e++rea i+dvgg+l+li+PleeqGilvrrsre
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 256 HIVSYAEDGALLAELFTRDGSGTLVAQEQFEVVREAAIEDVGGLLDLISPLEEQGILVRRSRE 318
                                                     *************************************************************** PP

                                       TIGR01890 316 llereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarq 378
                                                     +lereie+fsv+e++G+ii+caaly +a++++gelaclav+Pe+r+ggrG++ll++ie+rar+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 319 VLEREIEQFSVVEREGMIIACAALYQIADSDAGELACLAVNPEYRHGGRGDELLERIETRARA 381
                                                     *************************************************************** PP

                                       TIGR01890 379 vGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                                      Glk+lfvlttrt+hWfrerGf+++svd+lP+ar++lynyqr+ski++k l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13085 382 QGLKTLFVLTTRTAHWFRERGFEPSSVDRLPAARASLYNYQRNSKIFEKAL 432
                                                     ***********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (432 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.41
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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