Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_043879258.1 AZC_RS11665 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000010525.1:WP_043879258.1 Length = 386 Score = 266 bits (679), Expect = 9e-76 Identities = 140/382 (36%), Positives = 216/382 (56%), Gaps = 9/382 (2%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 Q + L +L+ F + N ++ + +L + GI + + E ++++ T+GP++ Sbjct: 5 QTLDWLARLISFDTTSRNSNLPLIEAVEEFLTAEGIFFERVENTEEKKASLITTLGPRDV 64 Query: 62 RGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPL 121 G ++SGH D VP WTSDPF + +LYGRGT DMKGFLA L V ++ A PL Sbjct: 65 PGIVLSGHTDTVPVDGQEWTSDPFTVTERDGKLYGRGTCDMKGFLAVCLGMVAEMKAQPL 124 Query: 122 RRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTV 181 ++P+H A+SYDEE GC GV +I + +P I+GEPT M+ + HKGK + + Sbjct: 125 KKPIHFAISYDEEVGCVGVRPLIEHMVANGYKPEACIVGEPTSMQVVVGHKGKKSYATVI 184 Query: 182 RGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVG-GPFEHVFEPPYSSLQIGTVKGGQ 240 G GHSSR + +NA+ ++ + +DRL G + +++ P+S+ +GT GG Sbjct: 185 TGAGGHSSRAPELVNAVEAGGRLVAKVADLSDRLAAEGRRDDLYDIPHSTAHVGTFHGGT 244 Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE-------VEWQELSAYP 293 A+NI+P+ +++E RA+ D L + A G + +E++ SA+P Sbjct: 245 ALNIVPELATIDWEVRALPEDDVEALTGEIIAYATDTLEPGMKAKAPHTGIEFKLKSAFP 304 Query: 294 ALSLEPDAPLAALLEELTGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEY 352 LS PDAP+A L + GR V+YGTEAGLF + AGI ++CGPG I +AH+PDEY Sbjct: 305 GLSTSPDAPVAVLAKHFAGRNDHAKVAYGTEAGLFVEMAGIPTVVCGPGSIVQAHQPDEY 364 Query: 353 ILIDELMACRAMVEALGARCTA 374 + ++L AC A + + A C A Sbjct: 365 LEKNQLDACEAFIRRVIAYCAA 386 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: 374 Number of extensions: 13 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: 386 Length adjustment: 30 Effective length of query: 344 Effective length of database: 356 Effective search space: 122464 Effective search space used: 122464 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 WP_043879258.1 AZC_RS11665 (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.20780.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-118 379.9 0.1 7.1e-118 379.7 0.1 1.0 1 lcl|NCBI__GCF_000010525.1:WP_043879258.1 AZC_RS11665 acetylornithine deac Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_043879258.1 AZC_RS11665 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.7 0.1 7.1e-118 7.1e-118 3 365 .] 10 381 .. 8 381 .. 0.97 Alignments for each domain: == domain 1 score: 379.7 bits; conditional E-value: 7.1e-118 TIGR01892 3 lakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 la+L++fd++s+ sn++lie ve++l + g+ e+++++++ +k l+ + Gp++ g+vlsGhtD+v lcl|NCBI__GCF_000010525.1:WP_043879258.1 10 LARLISFDTTSRNSNLPLIEAVEEFLTAEGIFFERVENTEE-KKASLITTLGPRD-VPGIVLSGHTDTV 76 899**************************************.9***********9.9************ PP TIGR01892 72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakk 140 Pvd+++WtsDpf++te+dg+LYgrGt+DmkGFla+ L v +++a++LkkP+h ++s+Deevg+ G++ lcl|NCBI__GCF_000010525.1:WP_043879258.1 77 PVDGQEWTSDPFTVTERDGKLYGRGTCDMKGFLAVCLGMVAEMKAQPLKKPIHFAISYDEEVGCVGVRP 145 ********************************************************************* PP TIGR01892 141 lieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlval 206 lie + +p+ ivGePts++ v hkGk s + ++G ghssr+ + v+a+e ++l+a++ +l lcl|NCBI__GCF_000010525.1:WP_043879258.1 146 LIEHMVangYKPEACIVGEPTSMQVVVGHKGKKSYATVITGAGGHSSRAPELVNAVEAGGRLVAKVADL 214 ***9988999*********************************************************** PP TIGR01892 207 adklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee... 271 +d+l + ++ ++ p++t ++Gt +GG+a ni+++ + e+R++p d e+l++++ + a + lcl|NCBI__GCF_000010525.1:WP_043879258.1 215 SDRLAAeGRRDDLYDIPHSTAHVGTFHGGTALNIVPELATIDWEVRALPEDDVEALTGEIIAYATDtle 283 ****98688999***********************************************9988887788 PP TIGR01892 272 ..vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqe.lGieavvlGP 336 +k+kap ++++ +++sa p+l++ +da+++ l+++ aG+ v+ygteagl+ e +Gi++vv+GP lcl|NCBI__GCF_000010525.1:WP_043879258.1 284 pgMKAKAPHTGIEFKLKSAFPGLSTSPDAPVAVLAKHFAGRnDHAKVAYGTEAGLFVEmAGIPTVVCGP 352 899**************************************78889********986538********* PP TIGR01892 337 GdidqahqpdeYveieelkrcrallerlv 365 G+i qahqpdeY+e ++l +c+a+++r++ lcl|NCBI__GCF_000010525.1:WP_043879258.1 353 GSIVQAHQPDEYLEKNQLDACEAFIRRVI 381 **************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (386 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: 00:00:00.01 # Mc/sec: 11.36 // [ok]
This GapMind analysis is from Apr 10 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