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.9346.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.61 // [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