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.30770.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: 6.99
//
[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:

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:

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