Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__azobra:AZOBR_RS31030 Length = 398 Score = 263 bits (673), Expect = 5e-75 Identities = 146/374 (39%), Positives = 209/374 (55%), Gaps = 12/374 (3%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64 E+L L+ F + N D++ +IR +L G++ ++ E ++N++ATIGP + G Sbjct: 19 ELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEERTKANLYATIGPMDRGGV 78 Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124 +SGH DVVP + W+SDPF L +L+GRGT DMKGF+AA LA P A L P Sbjct: 79 CLSGHTDVVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAANLTTP 138 Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184 +H A SYDEE GC GVP ++ +L + +P I+GEPT MR I HKGK A R V G Sbjct: 139 VHYAFSYDEELGCLGVPGLLTQLAGMAVKPRLCIVGEPTRMRVIVGHKGKVALRCRVHGH 198 Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV-GGPFEHVFEPPYSSLQIGTVKGGQAVN 243 + HSS QG+NA+ A +++ R GPF+H ++ PY+++ G ++GG A N Sbjct: 199 ACHSSLAPQGVNAVEYAAELVSFLRGMGRRFAEQGPFDHDYDIPYTTVHTGVMEGGTARN 258 Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEAL--------TTLGFEVEWQELSAYPAL 295 I+P EFE R ++ A +L +R A+ L GF W+ LS PAL Sbjct: 259 IVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVRPDAGF--SWETLSDSPAL 316 Query: 296 SLEPDAPLAALLEELTGREALPAVSYGTEAGLFQR-AGIDAIICGPGDIGRAHKPDEYIL 354 P++ L++ L + V++GTE LF A I A++CGPGDI +AHKPDEY+ Sbjct: 317 DTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVCGPGDIEQAHKPDEYVE 376 Query: 355 IDELMACRAMVEAL 368 + EL + L Sbjct: 377 LSELARAERFLHRL 390 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: 375 Number of extensions: 10 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: 398 Length adjustment: 30 Effective length of query: 344 Effective length of database: 368 Effective search space: 126592 Effective search space used: 126592 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 AZOBR_RS31030 AZOBR_RS31030 (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.30271.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-118 379.7 0.0 8.3e-118 379.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS31030 AZOBR_RS31030 acetylornithine de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.5 0.0 8.3e-118 8.3e-118 1 364 [. 19 390 .. 19 391 .. 0.96 Alignments for each domain: == domain 1 score: 379.5 bits; conditional E-value: 8.3e-118 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 e+l++L+afd++s+ sn+dli+y++d+l+elgv+ + + + ++k nl a+iGp + +gg+ lsGhtD lcl|FitnessBrowser__azobra:AZOBR_RS31030 19 ELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEE-RTKANLYATIGPMD-RGGVCLSGHTD 85 6799******************************98776655.5************9.*********** PP TIGR01892 70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138 vvPvd++ W+sDpf+Lte+dg+L+grGtaDmkGF+a++La +pd aa+L P+h ++s+Dee g++G+ lcl|FitnessBrowser__azobra:AZOBR_RS31030 86 VVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAANLTTPVHYAFSYDEELGCLGV 154 ********************************************************************* PP TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204 + l+ +la +p+l ivGePt+++ + hkGk++ + +v+G+ hss + +Gv+a+e aa+l++ l lcl|FitnessBrowser__azobra:AZOBR_RS31030 155 PGLLTQLAgmaVKPRLCIVGEPTRMRVIVGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLR 223 ****99988889********************************************************* PP TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271 ++ + + +++++ ++ py+t++ G+++GG+a ni+++ +++e+R ++ + + +l++l++ a++ lcl|FitnessBrowser__azobra:AZOBR_RS31030 224 GMGRRFAEqGPFDHDYDIPYTTVHTGVMEGGTARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTl 292 *****98879*************************************************9999998875 PP TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqe.lGieavvlG 335 +++ p+ + +e+ls pal++++++e v l+++la + v++gte +l+++ + i+avv+G lcl|FitnessBrowser__azobra:AZOBR_RS31030 293 epeMRAVRPDAGFSWETLSDSPALDTPPESEEVTLVKNLAEQnGHGKVAFGTEGALFTSiANIPAVVCG 361 566778899*******************************9977889********99983579****** PP TIGR01892 336 PGdidqahqpdeYveieelkrcrallerl 364 PGdi+qah+pdeYve++el r++ +l+rl lcl|FitnessBrowser__azobra:AZOBR_RS31030 362 PGDIEQAHKPDEYVELSELARAERFLHRL 390 *************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (398 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: 8.35 // [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