Alignments for a candidate for argA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Pseudomonas stutzeri RCH2

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate GFF3930 Psest_4000 amino-acid N-acetyltransferase

Query= BRENDA::P22567
         (432 letters)



>FitnessBrowser__psRCH2:GFF3930
          Length = 432

 Score =  751 bits (1940), Expect = 0.0
 Identities = 375/432 (86%), Positives = 405/432 (93%)

Query: 1   MPDYVNWLRHASPYINSHRDRTFVVMLPGEGVEHPNFGNIVHDLVLLHSLGARLVLVHGS 60
           M DYV WLR +SPYINSHRDRTFVVMLPG+G+EH NF NIVHDLVLLHSLG RLVLV GS
Sbjct: 1   MHDYVTWLRDSSPYINSHRDRTFVVMLPGDGLEHANFANIVHDLVLLHSLGVRLVLVFGS 60

Query: 61  RPQIEARLAARGLAPRYHRDLRVTDAPTLECVIDAVGSLRIAIEARLSMDMAASPMQGAR 120
           RPQIEARLAARG+ PR+HRDLRVTDAPT+ECVIDAVG LRIA+EARLSMDMAASPMQGAR
Sbjct: 61  RPQIEARLAARGIEPRFHRDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGAR 120

Query: 121 LRVAGGNLVTARPIGVVEGVDYHHTGEVRRIDRKGIGRLLDERSIVLLSPLGYSPTGEIF 180
           LRVAGGN VTARPIGV++GVD HHTGEVRRIDRKGIGRLLDER+IVLLSPLGYSPTGEIF
Sbjct: 121 LRVAGGNFVTARPIGVLDGVDLHHTGEVRRIDRKGIGRLLDERTIVLLSPLGYSPTGEIF 180

Query: 181 NLACEDVAMRAAIDLEAEKLILYGAEQGLLDASGKLVRELRPQQVPAHLQRLGNSYQAEL 240
           NLACEDVA RAAIDL+A+KL+LYGAE GLLD SGKLVRELRPQQ+PA+++RLG+ YQAEL
Sbjct: 181 NLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQIPAYVERLGSQYQAEL 240

Query: 241 LDAAAQACRAGVKRSHIVSYTEDGALLSELFTRTGNGTLVAQEQFEQLREAGIEDVGGLI 300
           LDAAAQACR GV+RSH+VSY +DGALL+ELFTR G GTLV QEQFEQLREA IEDVGGLI
Sbjct: 241 LDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVTQEQFEQLREATIEDVGGLI 300

Query: 301 ELIRPLEEQGILVRRSREVLEREIEQFSIVEREGLIIACAALYPIADSEAGELACLAVNP 360
           +LI PLEEQGILVRRSREVLERE+EQFSIVER+GLIIACAALYPIADS+AGELACLAVNP
Sbjct: 301 DLITPLEEQGILVRRSREVLEREVEQFSIVERDGLIIACAALYPIADSDAGELACLAVNP 360

Query: 361 EYRHGGRGDELLERIEERARGLGLKTLFVLTTRTAHWFRERGFQPSSVERLPAARASLYN 420
           EYRHGGRGDELLERIEERAR LGLK L VLTTRTAHWFRERGF+P SV+RLPAARASLYN
Sbjct: 361 EYRHGGRGDELLERIEERARKLGLKKLIVLTTRTAHWFRERGFEPISVDRLPAARASLYN 420

Query: 421 FQRNSQVFEKSL 432
           FQRNS++FEK L
Sbjct: 421 FQRNSKIFEKPL 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: 744
Number of extensions: 19
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 GFF3930 Psest_4000 (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.9536.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.5e-214  696.8   0.0   6.1e-214  696.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3930  Psest_4000 amino-acid N-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3930  Psest_4000 amino-acid N-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.7   0.0  6.1e-214  6.1e-214       1     429 []       4     432 .]       4     432 .] 1.00

  Alignments for each domain:
  == domain 1  score: 696.7 bits;  conditional E-value: 6.1e-214
                           TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyv 75 
                                         +v wlr+++Pyin+hrd+t+vv+l+g+++e+ n++++v+d++llhslGvrlvlv G+rpqie rla+rg++++++
  lcl|FitnessBrowser__psRCH2:GFF3930   4 YVTWLRDSSPYINSHRDRTFVVMLPGDGLEHANFANIVHDLVLLHSLGVRLVLVFGSRPQIEARLAARGIEPRFH 78 
                                         89************************************************************************* PP

                           TIGR01890  76 rGlrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkida 150
                                         r lrvtd+ ++e+v++a+G+lr a+earlsm++a++pm+g+rl+v+ GnfvtarPiGv++Gvd++htGevr+id+
  lcl|FitnessBrowser__psRCH2:GFF3930  79 RDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGARLRVAGGNFVTARPIGVLDGVDLHHTGEVRRIDR 153
                                         *************************************************************************** PP

                           TIGR01890 151 egirrlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqevesl 225
                                         +gi rllder ivllsPlg+s+tGeifnla+edvat++ai+l+adkl+l ++e+G+ld++Gklv+el++q++ + 
  lcl|FitnessBrowser__psRCH2:GFF3930 154 KGIGRLLDERTIVLLSPLGYSPTGEIFNLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQIPAY 228
                                         *************************************************************************** PP

                           TIGR01890 226 verleeettarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggileli 300
                                         verl+++++a+ll+aa++a+rgGv+rsh+vsya dGall+elftrdG Gtlv++e++e++reati+dvgg+++li
  lcl|FitnessBrowser__psRCH2:GFF3930 229 VERLGSQYQAELLDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVTQEQFEQLREATIEDVGGLIDLI 303
                                         *************************************************************************** PP

                           TIGR01890 301 rPleeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedr 375
                                          PleeqGilvrrsre+lere+e+fs++e+dGlii+caalyp+a++++gelaclav+Pe+r+ggrG++ll++ie+r
  lcl|FitnessBrowser__psRCH2:GFF3930 304 TPLEEQGILVRRSREVLEREVEQFSIVERDGLIIACAALYPIADSDAGELACLAVNPEYRHGGRGDELLERIEER 378
                                         *************************************************************************** PP

                           TIGR01890 376 arqvGlkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkkl 429
                                         ar++Glk+l vlttrt+hWfrerGf++ svd+lP+ar++lyn+qr+ski++k+l
  lcl|FitnessBrowser__psRCH2:GFF3930 379 ARKLGLKKLIVLTTRTAHWFRERGFEPISVDRLPAARASLYNFQRNSKIFEKPL 432
                                         ***************************************************987 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: 9.24
//
[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