Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate PP_3571 PP_3571 putative Acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Putida:PP_3571 Length = 391 Score = 304 bits (779), Expect = 2e-87 Identities = 159/374 (42%), Positives = 225/374 (60%), Gaps = 20/374 (5%) Query: 6 ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65 +L +L+GF +V N ++ +IR YL G+ ++ PEG ++N+FAT+GP++ G + Sbjct: 14 LLARLIGFATVSRDSNLALIGFIRDYLAELGVECELFHNPEGTKANLFATVGPRDVGGVV 73 Query: 66 ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125 +SGH DVVP WT +PF L RLYGRGT DMKGF+A+VLAAVP A PLR P+ Sbjct: 74 LSGHTDVVPVDGQAWTVEPFALSERDGRLYGRGTADMKGFIASVLAAVPAFLAQPLRMPV 133 Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185 HLA SYDEE GC GV M+A L + +P +IGEPT ++ + HKGK A R V+G + Sbjct: 134 HLAFSYDEEVGCLGVRSMLAALQQRPCKPRLCLIGEPTELKPVLGHKGKLAMRCQVQGAA 193 Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKGGQAVN 243 HS+ G+NAI A L + E + P H F+PP+S++Q G +KGG+A+N Sbjct: 194 CHSAYAPYGVNAIE-YAAKLIGKLGEIGEALALPVHHDERFDPPFSTVQAGVIKGGRALN 252 Query: 244 IIPDSCEVEFEARAISGVD------------PAELLAPVRKTAEALTTLGFEVEWQELSA 291 I+PD CE +FE RA+ G + AELL +RK A + LSA Sbjct: 253 IVPDECEFDFEVRALPGFEAQAVADQLQTYAEAELLPRMRKVNTASA-----IRLAPLSA 307 Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351 YP L+ D+ A L+ L+G + V++GTE GLF +AGI ++CGPG + + HKPDE Sbjct: 308 YPGLATPEDSEAARLVALLSGSDTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDE 367 Query: 352 YILIDELMACRAMV 365 ++ +++L C AM+ Sbjct: 368 FVSVEQLRGCDAML 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: 436 Number of extensions: 14 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: 391 Length adjustment: 30 Effective length of query: 344 Effective length of database: 361 Effective search space: 124184 Effective search space used: 124184 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 PP_3571 PP_3571 (putative Acetylornithine deacetylase)
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.3363016.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-128 415.4 0.0 1.2e-128 415.2 0.0 1.0 1 FitnessBrowser__Putida:PP_3571 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Putida:PP_3571 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.2 0.0 1.2e-128 1.2e-128 2 365 .] 14 385 .. 13 385 .. 0.97 Alignments for each domain: == domain 1 score: 415.2 bits; conditional E-value: 1.2e-128 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaaWts 80 +la+L++f +vs+ sn++li +++dyl+elgv+ e +++g +k nl+a++Gp++ gg+vlsGhtDvvPvd++aWt FitnessBrowser__Putida:PP_3571 14 LLARLIGFATVSRDSNLALIGFIRDYLAELGVECELFHNPEG-TKANLFATVGPRD-VGGVVLSGHTDVVPVDGQAWTV 90 6899**************************************.************9.9********************* PP TIGR01892 81 DpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpalaivGe 156 +pf L e+dgrLYgrGtaDmkGF+a vLaavp a++L+ P+hl++s+Deevg++G++++++al +p+l ++Ge FitnessBrowser__Putida:PP_3571 91 EPFALSERDGRLYGRGTADMKGFIASVLAAVPAFLAQPLRMPVHLAFSYDEEVGCLGVRSMLAALQqrpCKPRLCLIGE 169 ***************************************************************9996666789****** PP TIGR01892 157 PtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGG 234 Pt+l++v hkGk +++ +v+G hs+++ Gv+aie aakl+++l + + l +++e F+pp++t++ G++kGG FitnessBrowser__Putida:PP_3571 170 PTELKPVLGHKGKLAMRCQVQGAACHSAYAPYGVNAIEYAAKLIGKLGEIGEALALpVHHDERFDPPFSTVQAGVIKGG 248 ******************************************************98799******************** PP TIGR01892 235 kavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvallekla 308 +a ni++++Ce+ +e+R++pG + +++ +l++ ae+ +++ + + ++ lsa+p+l+++ed+e+++l++ l+ FitnessBrowser__Putida:PP_3571 249 RALNIVPDECEFDFEVRALPGFEAQAVADQLQTYAEAellprMRKVNTASAIRLAPLSAYPGLATPEDSEAARLVALLS 327 **********************************998888766666777788888999********************* PP TIGR01892 309 Ga.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365 G+ + +v++gte gl+ ++Gi++vv+GPG++dq h+pde+v +e+l+ c+a+l rlv FitnessBrowser__Putida:PP_3571 328 GSdTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDEFVSVEQLRGCDAMLLRLV 385 *98889************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (391 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.73 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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