Alignments for a candidate for argA in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Pseudomonas simiae WCS417

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF5312 PS417_27195 N-acetylglutamate synthase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__WCS417:GFF5312
          Length = 433

 Score =  744 bits (1920), Expect = 0.0
 Identities = 373/433 (86%), Positives = 402/433 (92%), Gaps = 1/433 (0%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           MPDYVNWLRHASPYIN+HRD TFVVMLPG+GVEHPNFGNIVHDLVLLHSLG RLVLVHGS
Sbjct: 1   MPDYVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARL ARGL P YH  LR+TDA TLECVIDAVG LRIAIEARLSMDMA+SPMQG+R
Sbjct: 61  RPQIEARLEARGLTPAYHEGLRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSR 120

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

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNS-YQAE 239
           NLACEDVA RAAIDL A+KL+L+GA+ GL+D +G+LVRELRPQQVPAHLQRLG+S YQAE
Sbjct: 181 NLACEDVATRAAIDLGADKLLLFGADMGLIDENGRLVRELRPQQVPAHLQRLGSSNYQAE 240

Query: 240 LLDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGL 299
           LLDAAA+ACR GV RSHIVSY EDGALL+ELFTR G GTLVAQEQFE +REA IEDVGGL
Sbjct: 241 LLDAAAEACRGGVGRSHIVSYAEDGALLTELFTRDGGGTLVAQEQFELVREAAIEDVGGL 300

Query: 300 IELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVN 359
           ++LI PLEEQGILVRRSREVLEREIEQFS+VEREG+IIACAALY IADS AGELACLAVN
Sbjct: 301 LDLISPLEEQGILVRRSREVLEREIEQFSVVEREGMIIACAALYQIADSNAGELACLAVN 360

Query: 360 PEYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLY 419
           PEYRHG RGD LLERIE RAR  GLKTLFVLTTRTAHWFRERGF+PSSV+RLP+ARASLY
Sbjct: 361 PEYRHGARGDVLLERIESRARAQGLKTLFVLTTRTAHWFRERGFEPSSVDRLPSARASLY 420

Query: 420 NFQRNSQVFEKSL 432
           N+QRNS++FEK+L
Sbjct: 421 NYQRNSKIFEKAL 433


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: 739
Number of extensions: 14
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: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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 GFF5312 PS417_27195 (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.2414640.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.7e-220  718.3   0.1   1.8e-220  718.2   0.1    1.0  1  FitnessBrowser__WCS417:GFF5312  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF5312  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.2   0.1  1.8e-220  1.8e-220       1     429 []       4     433 .]       4     433 .] 0.99

  Alignments for each domain:
  == domain 1  score: 718.2 bits;  conditional E-value: 1.8e-220
                       TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrGlr 79 
                                     +v+wlr+a+Pyinahrd+t+vv+l+g++ve++n+g++v+d++llhslGvrlvlvhG+rpqie rl++rg+t+ y++Glr
  FitnessBrowser__WCS417:GFF5312   4 YVNWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGNIVHDLVLLHSLGVRLVLVHGSRPQIEARLEARGLTPAYHEGLR 82 
                                     8****************************************************************************** PP

                       TIGR01890  80 vtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrlld 158
                                     +td+a+le+v++a+G+lr aiearlsm++a++pm+gsrl+v+sGn+vtarPiGv+eGvdy+htGevr++d++gi+rlld
  FitnessBrowser__WCS417:GFF5312  83 ITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSRLRVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLD 161
                                     ******************************************************************************* PP

                       TIGR01890 159 ersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverleeet.tar 236
                                     ersivllsPlg+s+tGeifnla+edvat++ai+l+adkl+l++++ G++d++G+lv+el++q+v ++++rl++   +a+
  FitnessBrowser__WCS417:GFF5312 162 ERSIVLLSPLGYSPTGEIFNLACEDVATRAAIDLGADKLLLFGADMGLIDENGRLVRELRPQQVPAHLQRLGSSNyQAE 240
                                     ***********************************************************************97544*** PP

                       TIGR01890 237 llsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPleeqGilvrrsre 315
                                     ll+aa++a+rgGv rsh+vsyaedGall+elftrdG Gtlv++e++e +rea i+dvgg+l+li+PleeqGilvrrsre
  FitnessBrowser__WCS417:GFF5312 241 LLDAAAEACRGGVGRSHIVSYAEDGALLTELFTRDGGGTLVAQEQFELVREAAIEDVGGLLDLISPLEEQGILVRRSRE 319
                                     ******************************************************************************* PP

                       TIGR01890 316 llereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttrtehW 394
                                     +lereie+fsv+e++G+ii+caaly +a++++gelaclav+Pe+r+g rG+ ll++ie+rar+ Glk+lfvlttrt+hW
  FitnessBrowser__WCS417:GFF5312 320 VLEREIEQFSVVEREGMIIACAALYQIADSNAGELACLAVNPEYRHGARGDVLLERIESRARAQGLKTLFVLTTRTAHW 398
                                     ******************************************************************************* PP

                       TIGR01890 395 frerGfaeasvdelPearrklynyqrrskilvkkl 429
                                     frerGf+++svd+lP ar++lynyqr+ski++k l
  FitnessBrowser__WCS417:GFF5312 399 FRERGFEPSSVDRLPSARASLYNYQRNSKIFEKAL 433
                                     *******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (433 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.90
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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