Alignments for a candidate for argA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Shewanella oneidensis MR-1

Align amino-acid acetyltransferase (characterized)
to candidate 203326 SO4245 amino-acid acetyltransferase (NCBI ptt file)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__MR1:203326
          Length = 445

 Score =  598 bits (1542), Expect = e-175
 Identities = 288/438 (65%), Positives = 356/438 (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  ARPQIDAALAANGIEPAYHDGVRITDEDSLKVIKQVAGALQFDITARLSMSLSNTPMQGA 127

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

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

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

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           DIGGIL LIRPLE+QGILVRRSREQLE+EI++F +I+RD   I CAALYPF E+  GE A
Sbjct: 308 DIGGILNLIRPLEEQGILVRRSREQLEIEIEQFMLIERDGLVIGCAALYPFEEDNAGEFA 367

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ VHPDYR + RG +LL+ I  QA+  G S+LF LTTRSIHWF E GF   D+D LP+ 
Sbjct: 368 CLVVHPDYRDADRGSLLLKNIIGQARSRGYSRLFALTTRSIHWFLEHGFVIEDVDALPQK 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: 617
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 203326 SO4245 (amino-acid acetyltransferase (NCBI ptt file))
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.10177.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-194  632.0   0.5     3e-194  631.8   0.5    1.0  1  lcl|FitnessBrowser__MR1:203326  SO4245 amino-acid acetyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203326  SO4245 amino-acid acetyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  631.8   0.5    3e-194    3e-194       1     428 [.      12     444 ..      12     445 .] 0.99

  Alignments for each domain:
  == domain 1  score: 631.8 bits;  conditional E-value: 3e-194
                       TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrGlr 79 
                                     +v+++r++aPy+nahr+kt+vv+lgge+++++++  +++d+allhslG+++vlv+Garpqi+  la++g+++ y++G+r
  lcl|FitnessBrowser__MR1:203326  12 LVDGFRHSAPYVNAHRGKTFVVMLGGEALAQNQFRGILNDVALLHSLGIKVVLVYGARPQIDAALAANGIEPAYHDGVR 90 
                                     699**************************************************************************** PP

                       TIGR01890  80 vtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegirrlld 158
                                     +tde sl+++k++aG+l+ +i+arlsmsl+ntpm+g+++++vsGnfv+a+P+Gv++Gvd++ +G+vr+ida+g++r+ld
  lcl|FitnessBrowser__MR1:203326  91 ITDEDSLKVIKQVAGALQFDITARLSMSLSNTPMQGAQINLVSGNFVIAQPLGVDNGVDFCLSGKVRRIDAQGLKRQLD 169
                                     ******************************************************************************* PP

                       TIGR01890 159 ersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverleeet.... 233
                                     +  ivl++P++ svtGe fnl++e++at+vaiklkadk+i +++++Gild++G ++ael+++++++ +++l e+     
  lcl|FitnessBrowser__MR1:203326 170 NHCIVLMGPIAASVTGESFNLTAEEIATQVAIKLKADKMIGFSSQNGILDRNGDVIAELMPNDAQKILNKLAEQGsaci 248
                                     **********************************************************************98877799* PP

                       TIGR01890 234 .tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPleeqGilvr 311
                                      t+ +l+a ++a+r Gv+r+hlvsy  dGallqelf+r+GiGt++++e++e +r+a i d+ggil+lirPleeqGilvr
  lcl|FitnessBrowser__MR1:203326 249 gTMAFLKASIDACRNGVPRCHLVSYLDDGALLQELFSREGIGTQIVTESAERLRRASISDIGGILNLIRPLEEQGILVR 327
                                     ******************************************************************************* PP

                       TIGR01890 312 rsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvGlkrlfvlttr 390
                                     rsre+le eie+f +ie+dGl+igcaalyp+ e+++ge+acl v+P++rd++rG  llk+i+ +ar+ G +rlf+lttr
  lcl|FitnessBrowser__MR1:203326 328 RSREQLEIEIEQFMLIERDGLVIGCAALYPFEEDNAGEFACLVVHPDYRDADRGSLLLKNIIGQARSRGYSRLFALTTR 406
                                     ******************************************************************************* PP

                       TIGR01890 391 tehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                     + hWf+e+Gf+  +vd+lP+++++lynyqrrskil   
  lcl|FitnessBrowser__MR1:203326 407 SIHWFLEHGFVIEDVDALPQKKKQLYNYQRRSKILALD 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.01
//
[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