Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Phaeo:GFF769 Length = 384 Score = 261 bits (667), Expect = 2e-74 Identities = 142/382 (37%), Positives = 204/382 (53%), Gaps = 16/382 (4%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 Q IL L+ + +V N ++++++ LE G VDV+ G ++N+FAT+GP Sbjct: 4 QTTRILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGGQKANLFATLGPDTD 63 Query: 62 RGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPL 121 G ++SGH DVVP + WTSDPF + RLYGRGT DMKGF+AA LA PK A Sbjct: 64 GGIVLSGHSDVVPVTDQDWTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAEQIS 123 Query: 122 RRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTV 181 RRP+H A +YDEE GC G H++ L E +P A+IGEPT MR + HKG Sbjct: 124 RRPIHFAFTYDEEVGCIGAGHLVQALRERGLKPRLALIGEPTSMRVVEGHKGCHEYSTRF 183 Query: 182 RGRSGHSSRPDQGLNAIHGVAGVLTQAV-AEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240 +G GH S P +G+NA+ A +++ + D P + F+PP+++L IG + GG Sbjct: 184 QGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPPWTTLNIGALNGGS 243 Query: 241 AVNIIPDSCEVEFEARAISGVDP-----------AELLAPVRKTAEALTTLGFEVEWQEL 289 A N+I +V++E R + D + L P + ++ EV + Sbjct: 244 AHNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDTLLPAMQAIYPEASIETEVVGEVA 303 Query: 290 SAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKP 349 P E L+ +L G A V +GTEAGLFQ G+D ++CGPG I +AHK Sbjct: 304 GLTPTTQNE----ARELMADLLGSNAAELVPFGTEAGLFQELGMDVVVCGPGSIAQAHKA 359 Query: 350 DEYILIDELMACRAMVEALGAR 371 DEY+ +D+L C ++ L R Sbjct: 360 DEYLSLDQLSQCLTVLNRLAGR 381 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: 366 Number of extensions: 16 Number of successful extensions: 3 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: 384 Length adjustment: 30 Effective length of query: 344 Effective length of database: 354 Effective search space: 121776 Effective search space used: 121776 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 GFF769 PGA1_c07830 (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.18483.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-119 383.7 0.0 4.9e-119 383.5 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF769 PGA1_c07830 acetylornithine deac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF769 PGA1_c07830 acetylornithine deacetylase ArgE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.5 0.0 4.9e-119 4.9e-119 2 364 .. 8 378 .. 7 379 .. 0.97 Alignments for each domain: == domain 1 score: 383.5 bits; conditional E-value: 4.9e-119 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaaW 78 il++L+a ++vsa sn+++i y++++le+ g v+v+ a+g +k nl+a+ Gp + +gg+vlsGh+DvvPv ++ W lcl|FitnessBrowser__Phaeo:GFF769 8 ILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGG-QKANLFATLGPDT-DGGIVLSGHSDVVPVTDQDW 82 899***************************************.***********99.9******************* PP TIGR01892 79 tsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpala 152 tsDpf++ e dgrLYgrGt+DmkGF+a+ La +p+ a + ++P+h ++++Deevg+ Ga +l++al +p+la lcl|FitnessBrowser__Phaeo:GFF769 83 TSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAEQISRRPIHFAFTYDEEVGCIGAGHLVQALRergLKPRLA 159 ******************************************************************9988889**** PP TIGR01892 153 ivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtppyatlni 228 ++GePts++ v hkG + +G egh s+p rGv+a+e aa+ ++rl++l+ l++ +++++ F+pp++tlni lcl|FitnessBrowser__Phaeo:GFF769 160 LIGEPTSMRVVEGHKGCHEYSTRFQGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQrTPPDSRFDPPWTTLNI 236 **********************************************************986899************* PP TIGR01892 229 GtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedael 300 G ++GG+a n+ia++ ++ e+Rp+ d ++++ + + +++ p+ +++e++ +l + ++e+ lcl|FitnessBrowser__Phaeo:GFF769 237 GALNGGSAHNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDtllpaMQAIYPEASIETEVVGEVAGLTPTTQNEA 313 *********************************99998776665666688899************************ PP TIGR01892 301 valleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364 +l+++l+G+ aae v++gteagl+qelG++ vv+GPG+i qah++deY+ +++l +c +l+rl lcl|FitnessBrowser__Phaeo:GFF769 314 RELMADLLGSnAAELVPFGTEAGLFQELGMDVVVCGPGSIAQAHKADEYLSLDQLSQCLTVLNRL 378 *********99*************************************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (384 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: 8.18 // [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