Alignments for a candidate for argA in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Shewanella sp. ANA-3

Align amino-acid acetyltransferase (characterized)
to candidate 7026634 Shewana3_3767 N-acetylglutamate synthase (RefSeq)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__ANA3:7026634
          Length = 445

 Score =  596 bits (1537), Expect = e-175
 Identities = 286/438 (65%), Positives = 357/438 (81%)

Query: 5   RKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYG 64
           R TELV+GFRHS PY+N HRGKTFV+MLGGEA+    F  I+ND+ LLHSLGI++V+VYG
Sbjct: 8   RTTELVDGFRHSAPYVNAHRGKTFVVMLGGEALAQNQFRGILNDVALLHSLGIKVVLVYG 67

Query: 65  ARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGA 124
           ARPQIDA LAA+  EP YH+ +R+TD  +L+++KQ AG LQ DITARLSMSL+NTP+QGA
Sbjct: 68  ARPQIDAALAANGIEPAYHEGVRITDEDSLKVIKQVAGALQFDITARLSMSLSNTPMQGA 127

Query: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGES 184
            IN+VSGNF+IAQPLGVD+GVD+C SG++RRID   + RQLD+  IVLMGP+A SVTGES
Sbjct: 128 QINLVSGNFVIAQPLGVDNGVDFCLSGKVRRIDTQGLKRQLDNHCIVLMGPIAASVTGES 187

Query: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYN 244
           FNLT+EEIATQ+AIKLKA+KMIGF S  G+ + +GD+++EL PN+AQ  +    E+G   
Sbjct: 188 FNLTAEEIATQVAIKLKADKMIGFSSQNGILDRNGDVIAELMPNDAQNILTKLAEQGSAC 247

Query: 245 SGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATIN 304
            GT+ FL+ ++ ACR+GV RCHL+SY +DGALLQELFSR+GIGTQIV ESAE++RRA+I+
Sbjct: 248 VGTMAFLKASIDACRNGVPRCHLVSYLDDGALLQELFSREGIGTQIVTESAERLRRASIS 307

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           DIGG+L LIRPLE+QGILVRRSREQLE+EI++F +I+RD   I CAALYPF E+  GE A
Sbjct: 308 DIGGVLNLIRPLEEQGILVRRSREQLEIEIEQFMLIERDGLVIGCAALYPFEEDNAGEFA 367

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ VHPDYR + RG +LL+ I  QA+  G S+LF LTTRSIHWF E GF   D++ LP+ 
Sbjct: 368 CLVVHPDYRDADRGSLLLKNIIGQARSRGYSRLFALTTRSIHWFLEHGFVIEDVEALPQK 427

Query: 425 KKQLYNYQRKSKVLMADL 442
           KKQLYNYQR+SK+L  DL
Sbjct: 428 KKQLYNYQRRSKILALDL 445


Lambda     K      H
   0.319    0.136    0.384 

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: 611
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: 443
Length of database: 445
Length adjustment: 32
Effective length of query: 411
Effective length of database: 413
Effective search space:   169743
Effective search space used:   169743
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 7026634 Shewana3_3767 (N-acetylglutamate synthase (RefSeq))
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.29369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-193  629.5   0.6   1.7e-193  629.3   0.6    1.0  1  lcl|FitnessBrowser__ANA3:7026634  Shewana3_3767 N-acetylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026634  Shewana3_3767 N-acetylglutamate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.3   0.6  1.7e-193  1.7e-193       1     428 [.      12     444 ..      12     445 .] 0.99

  Alignments for each domain:
  == domain 1  score: 629.3 bits;  conditional E-value: 1.7e-193
                         TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrG 77 
                                       +v+++r++aPy+nahr+kt+vv+lgge+++++++  +++d+allhslG+++vlv+Garpqi+  la++g+++ y++G
  lcl|FitnessBrowser__ANA3:7026634  12 LVDGFRHSAPYVNAHRGKTFVVMLGGEALAQNQFRGILNDVALLHSLGIKVVLVYGARPQIDAALAANGIEPAYHEG 88 
                                       699************************************************************************** PP

                         TIGR01890  78 lrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegir 154
                                       +r+tde sl+++k++aG+l+ +i+arlsmsl+ntpm+g+++++vsGnfv+a+P+Gv++Gvd++ +G+vr+id++g++
  lcl|FitnessBrowser__ANA3:7026634  89 VRITDEDSLKVIKQVAGALQFDITARLSMSLSNTPMQGAQINLVSGNFVIAQPLGVDNGVDFCLSGKVRRIDTQGLK 165
                                       ***************************************************************************** PP

                         TIGR01890 155 rlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverlee 231
                                       r+ld+  ivl++P++ svtGe fnl++e++at+vaiklkadk+i +++++Gild++G ++ael+++++++ + +l e
  lcl|FitnessBrowser__ANA3:7026634 166 RQLDNHCIVLMGPIAASVTGESFNLTAEEIATQVAIKLKADKMIGFSSQNGILDRNGDVIAELMPNDAQNILTKLAE 242
                                       ***********************************************************************999988 PP

                         TIGR01890 232 et.....tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPl 303
                                       +      t+ +l+a ++a+r Gv+r+hlvsy  dGallqelf+r+GiGt++++e++e +r+a i d+gg+l+lirPl
  lcl|FitnessBrowser__ANA3:7026634 243 QGsacvgTMAFLKASIDACRNGVPRCHLVSYLDDGALLQELFSREGIGTQIVTESAERLRRASISDIGGVLNLIRPL 319
                                       77789************************************************************************ PP

                         TIGR01890 304 eeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvG 380
                                       eeqGilvrrsre+le eie+f +ie+dGl+igcaalyp+ e+++ge+acl v+P++rd++rG  llk+i+ +ar+ G
  lcl|FitnessBrowser__ANA3:7026634 320 EEQGILVRRSREQLEIEIEQFMLIERDGLVIGCAALYPFEEDNAGEFACLVVHPDYRDADRGSLLLKNIIGQARSRG 396
                                       ***************************************************************************** PP

                         TIGR01890 381 lkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                        +rlf+lttr+ hWf+e+Gf+  +v++lP+++++lynyqrrskil   
  lcl|FitnessBrowser__ANA3:7026634 397 YSRLFALTTRSIHWFLEHGFVIEDVEALPQKKKQLYNYQRRSKILALD 444
                                       ********************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (445 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: 8.52
//
[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