Align Acetylornithine deacetylase; AO; Acetylornithinase; N-acetylornithinase; NAO; EC 3.5.1.16 (characterized)
to candidate BWI76_RS00840 BWI76_RS00840 acetylornithine deacetylase
Query= SwissProt::P23908 (383 letters) >FitnessBrowser__Koxy:BWI76_RS00840 Length = 383 Score = 741 bits (1913), Expect = 0.0 Identities = 353/383 (92%), Positives = 370/383 (96%) Query: 1 MKNKLPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRN 60 MKNKLPPFIEIYRALIATPSISATEEALDQSN LI LLA WF+D+GFNVEVQPVP TRN Sbjct: 1 MKNKLPPFIEIYRALIATPSISATEEALDQSNESLINLLAGWFRDIGFNVEVQPVPDTRN 60 Query: 61 KFNMLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFI 120 KFN+LAS G GAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHD KLYGLGTADMKGFFAFI Sbjct: 61 KFNLLASSGHGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDNKLYGLGTADMKGFFAFI 120 Query: 121 LDALRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHK 180 LDALRDVDVT+LKKPLYILATADEETSMAGARYFAETT LRPDCAIIGEPTSLQP+RAHK Sbjct: 121 LDALRDVDVTQLKKPLYILATADEETSMAGARYFAETTQLRPDCAIIGEPTSLQPIRAHK 180 Query: 181 GHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLN 240 GH+SNA+RIQGQSGHSSDPARGVNAIELMHDAIG I+QLRD+LKERYHY AFTVP+PTLN Sbjct: 181 GHMSNAVRIQGQSGHSSDPARGVNAIELMHDAIGRIMQLRDDLKERYHYAAFTVPWPTLN 240 Query: 241 LGHIHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHP 300 LG IHGGDASNRICACCELHMDIRPLPGMTLN+LNGLLN+ALAPVSERWPGRLTV ELHP Sbjct: 241 LGAIHGGDASNRICACCELHMDIRPLPGMTLNDLNGLLNEALAPVSERWPGRLTVSELHP 300 Query: 301 PIPGYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360 PIPGYECPP+H+LVEVVEKLLGA+T+VVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY Sbjct: 301 PIPGYECPPDHKLVEVVEKLLGAQTDVVNYCTEAPFIQTLCPTLVLGPGSINQAHQPDEY 360 Query: 361 LETRFIKPTRELITQVIHHFCWH 383 LETRFIKPTRELITQV+HHFCWH Sbjct: 361 LETRFIKPTRELITQVVHHFCWH 383 Lambda K H 0.320 0.139 0.430 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: 649 Number of extensions: 10 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: 383 Length of database: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate BWI76_RS00840 BWI76_RS00840 (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.6450.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-171 555.4 0.0 3.2e-171 555.3 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS00840 BWI76_RS00840 acetylornithine de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS00840 BWI76_RS00840 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.3 0.0 3.2e-171 3.2e-171 1 365 [] 10 377 .. 10 377 .. 1.00 Alignments for each domain: == domain 1 score: 555.3 bits; conditional E-value: 3.2e-171 TIGR01892 1 eilakLvafdsvsar......snvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvls 65 ei+++L+a++s+sa+ sn li+++++++++ g++vev+pv+d+++k+nlla+ G +gaggl+l+ lcl|FitnessBrowser__Koxy:BWI76_RS00840 10 EIYRALIATPSISATeealdqSNESLINLLAGWFRDIGFNVEVQPVPDTRNKFNLLASSG--HGAGGLLLA 78 79**********************************************************..99******* PP TIGR01892 66 GhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevgla 136 GhtD+vP+d+++Wt+Dpf+Lte+d++LYg+GtaDmkGF+a++L+a++d+++++LkkPl+++++aDee+++a lcl|FitnessBrowser__Koxy:BWI76_RS00840 79 GHTDTVPFDDGRWTRDPFTLTEHDNKLYGLGTADMKGFFAFILDALRDVDVTQLKKPLYILATADEETSMA 149 *********************************************************************** PP TIGR01892 137 GakkliealarrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvala 207 Ga++++e++ rp++ai+GePtsl+++RahkG++s++v+++G++ghss+p+rGv+aiel++++++r+++l+ lcl|FitnessBrowser__Koxy:BWI76_RS00840 150 GARYFAETTQLRPDCAIIGEPTSLQPIRAHKGHMSNAVRIQGQSGHSSDPARGVNAIELMHDAIGRIMQLR 220 *********************************************************************** PP TIGR01892 208 dklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevkekapg 278 d lk+++++ aFt+p++tln+G ++GG+a+n+i+a+Cel++++Rp+pGm++++l++ll++++++v+e++pg lcl|FitnessBrowser__Koxy:BWI76_RS00840 221 DDLKERYHYAAFTVPWPTLNLGAIHGGDASNRICACCELHMDIRPLPGMTLNDLNGLLNEALAPVSERWPG 291 *********************************************************************** PP TIGR01892 279 fevkveelsatpaleleedaelvalleklaGaaaevvsygteagllqelGieavvlGPGdidqahqpdeYv 349 + ++ e+++++p++e+++d++lv+++ekl+Ga+++vv+y+tea+++q+l ++++vlGPG+i+qahqpdeY+ lcl|FitnessBrowser__Koxy:BWI76_RS00840 292 RLTVSELHPPIPGYECPPDHKLVEVVEKLLGAQTDVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYL 361 *************************************************.********************* PP TIGR01892 350 eieelkrcrallerlv 365 e++++k++r+l++++v lcl|FitnessBrowser__Koxy:BWI76_RS00840 362 ETRFIKPTRELITQVV 377 *************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (383 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.05 // [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