Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate H281DRAFT_06479 H281DRAFT_06479 arginine succinyltransferase
Query= reanno::Marino:GFF3098 (339 letters) >FitnessBrowser__Burk376:H281DRAFT_06479 Length = 352 Score = 219 bits (557), Expect = 1e-61 Identities = 140/344 (40%), Positives = 191/344 (55%), Gaps = 10/344 (2%) Query: 1 MWLVRPAEPDDLDQILAIAGTQCARLSSTLPKQGDALAYKIEQSLASFAGRISAEDDPPR 60 M VRP DLD + +A T L S LP AL ++ S SF + + Sbjct: 1 MLFVRPGRLADLDALEHMARTAQPVLHS-LPHDRRALEARVALSEDSFRAEVDFPGEE-F 58 Query: 61 FLFVLEDTETGDIAGTAGIDAHAGNGQPFYSYRRDALIHASHELGVSRRVEVLYPSHSLT 120 +LFVLED+E+G + GTA I A AG PFY++R DALIHAS EL V+R++ L SH LT Sbjct: 59 YLFVLEDSESGKLMGTASIVAAAGYSDPFYAFRNDALIHASRELHVNRKIHALTMSHELT 118 Query: 121 DVSLLCSFSIRPELQGTDAFELLSRARILFIADHREWFTQRMAVEIQGVQLEDGSVPFWD 180 S L + I P L+G A L+SRAR+++IA +R+ FT + + GV E+G PFW+ Sbjct: 119 GKSRLAGYYIDPSLRGDAAAHLMSRARMMYIAANRKRFTPEVFSLLLGVTDENGVSPFWE 178 Query: 181 SLGRHFFDMDFETADQYSGQLSKTFIAELMPPNPIYVTLLSEAAQKAMGQPHQITVPNFE 240 ++GR FF +F + SG S+TFIAE+MP PIYV LL EAAQ+ +G+P + +E Sbjct: 179 AVGRKFFGRNFADIEIESGGRSRTFIAEVMPTYPIYVPLLPEAAQRVLGEPDSKALLAYE 238 Query: 241 LLQREGFQPGNYLDIFDAGPVLEARTDSLKTLVTSHPKELH----GTNEDTGETCLIA-A 295 + EGF+ ++DIFDAGPVL A+ D + + + H G N G T LIA Sbjct: 239 IHLEEGFETDRFIDIFDAGPVLTAQVDRSACVTLNETRVAHEAAAGAN---GSTYLIAHN 295 Query: 296 GEGEQFRCTLTPVAESLDDKLKVPVSTWNTLNRTAGDRVRIAPL 339 G QFRC L + + ++ + L GD VR PL Sbjct: 296 GADGQFRCVLGELPTARNEGAPLAQPARAALGVQDGDTVRCVPL 339 Lambda K H 0.319 0.135 0.403 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: 344 Number of extensions: 16 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: 339 Length of database: 352 Length adjustment: 29 Effective length of query: 310 Effective length of database: 323 Effective search space: 100130 Effective search space used: 100130 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate H281DRAFT_06479 H281DRAFT_06479 (arginine succinyltransferase)
to HMM TIGR03245 (aruF: arginine/ornithine succinyltransferase, alpha subunit (EC 2.3.1.109))
# 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.carbon/TIGR03245.hmm # target sequence database: /tmp/gapView.19149.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03245 [M=336] Accession: TIGR03245 Description: arg_AOST_alph: arginine/ornithine succinyltransferase, alpha subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-155 502.4 0.0 4.8e-155 502.2 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06479 H281DRAFT_06479 arginine succiny Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06479 H281DRAFT_06479 arginine succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.2 0.0 4.8e-155 4.8e-155 1 336 [] 3 339 .. 3 339 .. 0.98 Alignments for each domain: == domain 1 score: 502.2 bits; conditional E-value: 4.8e-155 TIGR03245 1 vvrParladldaierlaresaigvtslPadrekleekiaqsessfaaevsfsgeesylfvledset 66 +vrP+rladlda+e++ar+++++++slP+dr +le+++a+se+sf+aev+f+gee+ylfvledse+ lcl|FitnessBrowser__Burk376:H281DRAFT_06479 3 FVRPGRLADLDALEHMARTAQPVLHSLPHDRRALEARVALSEDSFRAEVDFPGEEFYLFVLEDSES 68 69**************************************************************** PP TIGR03245 67 gkllGtasivasaGyaePfysyrndtlvhasrelkvnnkihvlslsheltGksllasfyvdpelre 132 gkl+Gtasiva+aGy++Pfy++rnd+l+hasrel+vn+kih+l++sheltGks+la++y+dp+lr+ lcl|FitnessBrowser__Burk376:H281DRAFT_06479 69 GKLMGTASIVAAAGYSDPFYAFRNDALIHASRELHVNRKIHALTMSHELTGKSRLAGYYIDPSLRG 134 ****************************************************************** PP TIGR03245 133 aeaaellsrarllfiaaererfasrviaellGvsdeaGesPfWdaiGrkffdldfaaverasglks 198 ++aa+l+srar+++iaa+r+rf+++v+++llGv+de+G sPfW+a+Grkff+++fa++e++sg +s lcl|FitnessBrowser__Burk376:H281DRAFT_06479 135 DAAAHLMSRARMMYIAANRKRFTPEVFSLLLGVTDENGVSPFWEAVGRKFFGRNFADIEIESGGRS 200 ****************************************************************** PP TIGR03245 199 ktfiaelmPsyPiyvpllpdeaqealgqvheraelafdlllreGfeadryidifdgGpvleaeldr 264 +tfiae+mP+yPiyvpllp++aq++lg+++++a la++++l+eGfe+dr+idifd+Gpvl+a++dr lcl|FitnessBrowser__Burk376:H281DRAFT_06479 201 RTFIAEVMPTYPIYVPLLPEAAQRVLGEPDSKALLAYEIHLEEGFETDRFIDIFDAGPVLTAQVDR 266 ****************************************************************** PP TIGR03245 265 lktvkksrekpvkieeaatggstylvs.nglledfravladlavvdGkalrlkadaaealgvseGd 329 ++v+ ++++ ++++a +gstyl++ ng +fr+vl +l ++ + l + a++algv +Gd lcl|FitnessBrowser__Burk376:H281DRAFT_06479 267 SACVTLNETRVAHEAAAGANGSTYLIAhNGADGQFRCVLGELPTARNEGAPLAQPARAALGVQDGD 332 *******99999999999999****984677779********9999999999************** PP TIGR03245 330 avrlval 336 +vr+v+l lcl|FitnessBrowser__Burk376:H281DRAFT_06479 333 TVRCVPL 339 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (352 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: 6.90 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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