Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF997 PGA1_c10140 acetylornithine deacetylase ArgE
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Phaeo:GFF997 Length = 388 Score = 218 bits (554), Expect = 3e-61 Identities = 134/374 (35%), Positives = 191/374 (51%), Gaps = 10/374 (2%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGD-RSNIFATIGPKEARG 63 EI+ KL+ F +V N +V W+ GYL SHGI P+ ++ +FA +GP Sbjct: 9 EIMTKLISFPTVSSETNLPLVDWVEGYLASHGITAHRWVDPDQPHKAAVFAHVGPDVEGA 68 Query: 64 YIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRR 123 ++SGH DVVP W SDPF + + +GRGT DMKGF A + A+ + R Sbjct: 69 VVLSGHTDVVPIEGQPWDSDPFTVVERDGKYFGRGTCDMKGFDALAIWALVAAHHRGVAR 128 Query: 124 PLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRG 183 PL LALS+DEE GC G P MI + ++ + I+GEP+ MR + HKG + G Sbjct: 129 PLQLALSFDEEVGCTGAPPMIVAMQDVLPKGSCVIVGEPSVMRPVTGHKGGIGYSTHLVG 188 Query: 184 RSGHSSRPDQGLNAIHGVAGVLTQAVA-EADRLVGGPFE--HVFEPPYSSLQIGTVKGGQ 240 HSS G++AI A ++ A A A+ + P + +F PP+++ +G + GG Sbjct: 189 FEVHSSLMHTGVSAIMQGARLIDWANARNAENMAKTPDDVAALFTPPFTTCHVGMINGGT 248 Query: 241 AVNIIPDSCEVEFEARAISGVDPAE----LLAPVRKTAEALTTL--GFEVEWQELSAYPA 294 A NI C + R + G AE LA VR + + ++ + P Sbjct: 249 AHNITAKDCRFVMDFRVVPGESAAEWEAAYLAKVRDIEAEMQVVHPDTRIDVSKKFNVPG 308 Query: 295 LSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYIL 354 L E + L+ LTG VSYGTEAG FQ AG A+ICGPGDI +AH+P+EYI Sbjct: 309 LVPEVEGEAETLVRALTGDNGTHVVSYGTEAGQFQEAGYSAVICGPGDIAQAHQPNEYID 368 Query: 355 IDELMACRAMVEAL 368 + + A ++ L Sbjct: 369 VSQFNAGHRFMQQL 382 Lambda K H 0.319 0.137 0.410 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: 426 Number of extensions: 18 Number of successful extensions: 4 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: 374 Length of database: 388 Length adjustment: 30 Effective length of query: 344 Effective length of database: 358 Effective search space: 123152 Effective search space used: 123152 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: 50 (23.9 bits)
Align candidate GFF997 PGA1_c10140 (acetylornithine deacetylase ArgE)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))
# 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/TIGR01892.hmm # target sequence database: /tmp/gapView.25122.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01892 [M=365] Accession: TIGR01892 Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-116 375.2 0.1 2e-116 375.0 0.1 1.0 1 lcl|FitnessBrowser__Phaeo:GFF997 PGA1_c10140 acetylornithine deac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF997 PGA1_c10140 acetylornithine deacetylase ArgE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.0 0.1 2e-116 2e-116 1 365 [] 9 383 .. 9 383 .. 0.95 Alignments for each domain: == domain 1 score: 375.0 bits; conditional E-value: 2e-116 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaa 77 ei++kL++f++vs +n++l+++ve+yl+++g+++++ +d+ +k ++a +Gp + +g++vlsGhtDvvP+++++ lcl|FitnessBrowser__Phaeo:GFF997 9 EIMTKLISFPTVSSETNLPLVDWVEGYLASHGITAHRWVDPDQPHKAAVFAHVGPDV-EGAVVLSGHTDVVPIEGQP 84 79******************************************************9.9****************** PP TIGR01892 78 WtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpal 151 W sDpf++ e+dg+ +grGt+DmkGF al++ a+ + + +Pl l+ls+Deevg++Ga+ +i a+ ++ ++ lcl|FitnessBrowser__Phaeo:GFF997 85 WDSDPFTVVERDGKYFGRGTCDMKGFDALAIWALVAAHHRGVARPLQLALSFDEEVGCTGAPPMIVAMQdvlPKGSC 161 **********************************9999999***********************998887889**** PP TIGR01892 152 aivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva.ladklkr..edleeaFtppyat 225 +ivGeP +++v hkG + ++ G e hss ++Gvsai++ a+l+ + a a+++ + +d+ Ftpp++t lcl|FitnessBrowser__Phaeo:GFF997 162 VIVGEPSVMRPVTGHKGGIGYSTHLVGFEVHSSLMHTGVSAIMQGARLIDWANArNAENMAKtpDDVAALFTPPFTT 238 *************************************************988652678888756678889******* PP TIGR01892 226 lniGtvkGGkavniiaaaCelvlelRpipGmdpee....llallekiaeevkekapgfevkveelsatpaleleeda 298 ++G ++GG+a ni a+ C++v+++R +pG +e la++++i +e++ +p++ ++v ++ p+l +e ++ lcl|FitnessBrowser__Phaeo:GFF997 239 CHVGMINGGTAHNITAKDCRFVMDFRVVPGESAAEweaaYLAKVRDIEAEMQVVHPDTRIDVSKKFNVPGLVPEVEG 315 ******************************99876222256789999999999************************ PP TIGR01892 299 elvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365 e++ l++ l+G+ ++vvsygteag++qe+G +av++GPGdi qahqp+eY++++++++++ ++++l+ lcl|FitnessBrowser__Phaeo:GFF997 316 EAETLVRALTGDnGTHVVSYGTEAGQFQEAGYSAVICGPGDIAQAHQPNEYIDVSQFNAGHRFMQQLI 383 ************89***************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (388 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: 9.89 // [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