Alignments for a candidate for argA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for argA in Shewanella amazonensis SB2B

Align amino-acid acetyltransferase (characterized)
to candidate 6936133 Sama_0330 N-acetylglutamate synthase (RefSeq)

Query= CharProtDB::CH_024150
         (443 letters)



>FitnessBrowser__SB2B:6936133
          Length = 440

 Score =  593 bits (1530), Expect = e-174
 Identities = 285/438 (65%), Positives = 351/438 (80%)

Query: 5   RKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIGLLHSLGIRLVVVYG 64
           R TELV+GFRHS PY+N HRGKTFV+MLGGEA+    F +I+ND+ LLHSLGIR+V+VYG
Sbjct: 2   RTTELVDGFRHSAPYVNAHRGKTFVVMLGGEAMVQPQFRAIINDVALLHSLGIRIVLVYG 61

Query: 65  ARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQAAGTLQLDITARLSMSLNNTPLQGA 124
           ARPQIDA L  H   P YH  +R+TD  TL+++KQ AG LQ DITARLSMSL+NTP+QG 
Sbjct: 62  ARPQIDAALELHGIAPAYHNGVRITDEDTLKVIKQVAGALQFDITARLSMSLSNTPMQGT 121

Query: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGES 184
            +NVVSGNF+IAQPLGV+DGVD+C SGR+RRID + +  QLDS  IVLMGP+A SVTGES
Sbjct: 122 QLNVVSGNFVIAQPLGVEDGVDFCLSGRVRRIDVNGLKHQLDSRGIVLMGPIAASVTGES 181

Query: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYN 244
           FNLT+EE+ATQ+A+KLKA+KMIGF S  G+ + +G++++EL PN+AQ      +E G   
Sbjct: 182 FNLTAEEVATQVAVKLKADKMIGFSSQNGILDRNGEVIAELMPNDAQKIFAKMQEGGQAC 241

Query: 245 SGTVRFLRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRRATIN 304
            GT+ FL+ ++ ACR+GV RCHL+SY EDGALLQELFSRDGIGTQIV ESAE++RRA+I 
Sbjct: 242 VGTLAFLKASIDACRNGVPRCHLVSYLEDGALLQELFSRDGIGTQIVTESAERLRRASIA 301

Query: 305 DIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACAALYPFPEEKIGEMA 364
           DIGGIL LIRP+E+QGILVRRSREQLEMEI++F +I+RD   I CAALYPF E+  GE A
Sbjct: 302 DIGGILNLIRPMEEQGILVRRSREQLEMEIEQFMVIERDGLVIGCAALYPFEEDNAGEFA 361

Query: 365 CVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVLTTRSIHWFQERGFTPVDIDLLPES 424
           C+ VHPDYR + RG +LL+ I  QA+  G ++LF LTTRSIHWF E GF  V+++ LP  
Sbjct: 362 CLVVHPDYRDADRGSLLLKNIIGQARVRGYARLFALTTRSIHWFLEHGFELVEVEALPTK 421

Query: 425 KKQLYNYQRKSKVLMADL 442
           KKQLYNYQR+SK+L  DL
Sbjct: 422 KKQLYNYQRRSKILALDL 439


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: 601
Number of extensions: 10
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: 440
Length adjustment: 32
Effective length of query: 411
Effective length of database: 408
Effective search space:   167688
Effective search space used:   167688
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 6936133 Sama_0330 (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.5683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     8e-194  630.4   1.0     9e-194  630.2   1.0    1.0  1  lcl|FitnessBrowser__SB2B:6936133  Sama_0330 N-acetylglutamate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936133  Sama_0330 N-acetylglutamate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.2   1.0    9e-194    9e-194       1     428 [.       6     438 ..       6     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 630.2 bits;  conditional E-value: 9e-194
                         TIGR01890   1 fvkwlreaaPyinahrdktlvvglggelvedknlgklvadiallhslGvrlvlvhGarpqieerlakrgrtthyvrG 77 
                                       +v+++r++aPy+nahr+kt+vv+lgge++ ++++ ++++d+allhslG+r+vlv+Garpqi+  l+ +g+ + y++G
  lcl|FitnessBrowser__SB2B:6936133   6 LVDGFRHSAPYVNAHRGKTFVVMLGGEAMVQPQFRAIINDVALLHSLGIRIVLVYGARPQIDAALELHGIAPAYHNG 82 
                                       699************************************************************************** PP

                         TIGR01890  78 lrvtdeaslelvkeaaGelrlaiearlsmslantpmagsrlsvvsGnfvtarPiGvveGvdyehtGevrkidaegir 154
                                       +r+tde +l+++k++aG+l+ +i+arlsmsl+ntpm+g++l+vvsGnfv+a+P+Gv +Gvd++ +G+vr+id++g++
  lcl|FitnessBrowser__SB2B:6936133  83 VRITDEDTLKVIKQVAGALQFDITARLSMSLSNTPMQGTQLNVVSGNFVIAQPLGVEDGVDFCLSGRVRRIDVNGLK 159
                                       ***************************************************************************** PP

                         TIGR01890 155 rlldersivllsPlgfsvtGeifnlamedvatsvaiklkadklillteedGildadGklvaelsaqeveslverlee 231
                                       ++ld+r ivl++P++ svtGe fnl++e+vat+va+klkadk+i +++++Gild++G+++ael+++++++   +++e
  lcl|FitnessBrowser__SB2B:6936133 160 HQLDSRGIVLMGPIAASVTGESFNLTAEEVATQVAVKLKADKMIGFSSQNGILDRNGEVIAELMPNDAQKIFAKMQE 236
                                       ************************************************************************99998 PP

                         TIGR01890 232 et.....tarllsaavkalrgGvarshlvsyaedGallqelftrdGiGtlvskealesireatiddvggilelirPl 303
                                       +      t  +l+a ++a+r Gv+r+hlvsy edGallqelf+rdGiGt++++e++e +r+a i d+ggil+lirP+
  lcl|FitnessBrowser__SB2B:6936133 237 GGqacvgTLAFLKASIDACRNGVPRCHLVSYLEDGALLQELFSRDGIGTQIVTESAERLRRASIADIGGILNLIRPM 313
                                       877889999******************************************************************** PP

                         TIGR01890 304 eeqGilvrrsrellereieefsviekdGliigcaalypyaeeevgelaclavsPeardggrGerllkhiedrarqvG 380
                                       eeqGilvrrsre+le eie+f vie+dGl+igcaalyp+ e+++ge+acl v+P++rd++rG  llk+i+ +ar  G
  lcl|FitnessBrowser__SB2B:6936133 314 EEQGILVRRSREQLEMEIEQFMVIERDGLVIGCAALYPFEEDNAGEFACLVVHPDYRDADRGSLLLKNIIGQARVRG 390
                                       ***************************************************************************** PP

                         TIGR01890 381 lkrlfvlttrtehWfrerGfaeasvdelPearrklynyqrrskilvkk 428
                                         rlf+lttr+ hWf+e+Gf+ ++v++lP+++++lynyqrrskil   
  lcl|FitnessBrowser__SB2B:6936133 391 YARLFALTTRSIHWFLEHGFELVEVEALPTKKKQLYNYQRRSKILALD 438
                                       ********************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (440 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: 00:00:00.01
# Mc/sec: 10.36
//
[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