Aligments for a candidate for argA in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Aligments for a candidate for argA in Pseudomonas fluorescens GW456-L13

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate PfGW456L13_913 N-acetylglutamate synthase (EC 2.3.1.1)

Query= BRENDA::P22567
         (432 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913
           N-acetylglutamate synthase (EC 2.3.1.1)
          Length = 432

 Score =  750 bits (1936), Expect = 0.0
 Identities = 373/432 (86%), Positives = 404/432 (93%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           MP+YVNWLRHASPYIN+HRD TFVVMLPG+GVEHPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MPEYVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARLAARGL P YH  +R+TDA TLECVIDAVG LRIAIEARLSMDMA+SPMQG+R
Sbjct: 61  RPQIEARLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSR 120

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

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL A+KL+L+GA+ GL+D  G+LVRELRPQQVPAHLQRLG++YQAEL
Sbjct: 181 NLACEDVATRAAIDLGADKLLLFGADLGLIDEHGRLVRELRPQQVPAHLQRLGSNYQAEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAA+ACR GV RSHIVSY EDGALL+ELFTR G GTLVAQEQFE +REA IEDVGGL+
Sbjct: 241 LDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQEQFEVVREAAIEDVGGLL 300

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

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           EYRHGGRGDELLERIE RAR  GLKTLFVLTTRTAHWFRERGF PSSV+RLP+ARASLYN
Sbjct: 361 EYRHGGRGDELLERIETRARAQGLKTLFVLTTRTAHWFRERGFVPSSVDRLPSARASLYN 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: 736
Number of extensions: 14
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 PfGW456L13_913 (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.29805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   2.5e-224  730.9   0.2   2.8e-224  730.7   0.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  N-acetylglutamate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  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 !  730.7   0.2  2.8e-224  2.8e-224       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 730.7 bits;  conditional E-value: 2.8e-224
                                              TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhG 56 
                                                            +v+wlr+a+Pyinahrd+t+vv+l+g++ve++n+g++v+d++llhslGvrlvlvhG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913   4 YVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHG 59 
                                                            8******************************************************* PP

                                              TIGR01890  57 arpqieerlakrgrtthyvrGlrvtdeaslelvkeaaGelrlaiearlsmslantp 112
                                                            +rpqie rla+rg+t+hy++G+r+td+a+le+v++a+G+lr aiearlsm++a++p
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913  60 SRPQIEARLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSP 115
                                                            ******************************************************** PP

                                              TIGR01890 113 magsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrlldersivllsPl 168
                                                            m+gsrl+v+sGn+vtarPiGv+eGvdy+htGevr++d++gi+rlldersivllsPl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 116 MQGSRLRVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPL 171
                                                            ******************************************************** PP

                                              TIGR01890 169 gfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeves 224
                                                            g+s+tGeifnla+edvat++ai+l+adkl+l++++ G++d++G+lv+el++q+v +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 172 GYSPTGEIFNLACEDVATRAAIDLGADKLLLFGADLGLIDEHGRLVRELRPQQVPA 227
                                                            ******************************************************** PP

                                              TIGR01890 225 lverleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvske 280
                                                            +++rl+++++a+ll+aa++a+rgGvarsh+vsyaedGall+elftrdG Gtlv++e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 228 HLQRLGSNYQAELLDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQE 283
                                                            ******************************************************** PP

                                              TIGR01890 281 alesireatiddvggilelirPleeqGilvrrsrellereieefsviekdGliigc 336
                                                            ++e++rea i+dvgg+l+li+PleeqGilvrrsre+lereie+fsv+e++G+ii+c
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 284 QFEVVREAAIEDVGGLLDLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIAC 339
                                                            ******************************************************** PP

                                              TIGR01890 337 aalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrte 392
                                                            aaly +a++++gelaclav+Pe+r+ggrG++ll++ie+rar+ Glk+lfvlttrt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 340 AALYQIADSDAGELACLAVNPEYRHGGRGDELLERIETRARAQGLKTLFVLTTRTA 395
                                                            ******************************************************** PP

                                              TIGR01890 393 hWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                                            hWfrerGf+++svd+lP ar++lynyqr+ski++k l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 396 HWFRERGFVPSSVDRLPSARASLYNYQRNSKIFEKAL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.70
//
[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:

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, 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

GapMind for Amino acid biosynthesis