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.17443.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.95 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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