Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_013093659.1 BC1002_RS29665 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000092885.1:WP_013093659.1 Length = 387 Score = 296 bits (757), Expect = 8e-85 Identities = 153/377 (40%), Positives = 228/377 (60%), Gaps = 10/377 (2%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 + + +L +L+GF +V N +++ +++ YL G+ ++ + ++N+FATIGP++ Sbjct: 4 LSSRALLERLIGFATVSRDSNLELIGFVQQYLADLGVQSELFHNDDRTKANLFATIGPRD 63 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 G ++SGH DVVP WT DPFRL + RLYGRGT DMKG++A+VLAA P M Sbjct: 64 RGGIVLSGHTDVVPVDGQAWTVDPFRLSEKEGRLYGRGTADMKGYIASVLAAAPAFLRMK 123 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180 L P+HLA SYDEE GC GV M+A L + +P +IGEPT ++ + HK K A R Sbjct: 124 LEVPVHLAFSYDEEVGCLGVRPMLAELEKRAHKPRMCLIGEPTELKPVLGHKSKLAMRCH 183 Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKG 238 V+G + HS+ QG+NAI A ++ + D+L P H F+PP+S++Q G + G Sbjct: 184 VKGAACHSAYAPQGVNAIQYAARLINRLEQIGDQL-AQPEHHDARFDPPFSTVQTGVING 242 Query: 239 GQAVNIIPDSCEVEFEARAISGVDPAELLAPVR--KTAEALTTL-----GFEVEWQELSA 291 G+A+NI+P CE +FE R + G DP+ ++ ++ AE L + +V Q L+A Sbjct: 243 GRALNIVPAECEFDFEVRGVPGFDPSSVVDQLQTYAAAELLPKMRTVQPDTDVRVQMLNA 302 Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351 YP L+ PD+ A LL L+G + V++GTE GLF +AGI +CGPG + + HKPDE Sbjct: 303 YPGLATSPDSDAARLLAMLSGSKEFETVAFGTEGGLFTQAGIPTAVCGPGSMDQGHKPDE 362 Query: 352 YILIDELMACRAMVEAL 368 +I +++L C AM L Sbjct: 363 FITVEQLNRCDAMFARL 379 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: 392 Number of extensions: 8 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: 387 Length adjustment: 30 Effective length of query: 344 Effective length of database: 357 Effective search space: 122808 Effective search space used: 122808 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_013093659.1 BC1002_RS29665 (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.29404.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-131 424.5 0.0 2e-131 424.3 0.0 1.0 1 lcl|NCBI__GCF_000092885.1:WP_013093659.1 BC1002_RS29665 acetylornithine d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092885.1:WP_013093659.1 BC1002_RS29665 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.3 0.0 2e-131 2e-131 2 364 .. 9 379 .. 8 380 .. 0.97 Alignments for each domain: == domain 1 score: 424.3 bits; conditional E-value: 2e-131 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDv 70 +l++L++f +vs+ sn++li +v++yl++lgv+ e + d +k nl+a+iGp++ +gg+vlsGhtDv lcl|NCBI__GCF_000092885.1:WP_013093659.1 9 LLERLIGFATVSRDSNLELIGFVQQYLADLGVQSELFHNDDR-TKANLFATIGPRD-RGGIVLSGHTDV 75 6899*******************************9988666.************9.************ PP TIGR01892 71 vPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGak 139 vPvd++aWt DpfrL ek+grLYgrGtaDmkG++a vLaa+p +kL P+hl++s+Deevg++G++ lcl|NCBI__GCF_000092885.1:WP_013093659.1 76 VPVDGQAWTVDPFRLSEKEGRLYGRGTADMKGYIASVLAAAPAFLRMKLEVPVHLAFSYDEEVGCLGVR 144 ********************************************************************* PP TIGR01892 140 klieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlva 205 +++ l ++p++ ++GePt+l++v hk k +++ +v+G hs+++ +Gv+ai+ aa+l++rl++ lcl|NCBI__GCF_000092885.1:WP_013093659.1 145 PMLAELEkraHKPRMCLIGEPTELKPVLGHKSKLAMRCHVKGAACHSAYAPQGVNAIQYAARLINRLEQ 213 **98776555899******************************************************** PP TIGR01892 206 ladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.. 271 d+l + e+++ F+pp++t++ G+++GG+a ni++a+Ce+ +e+R +pG dp+ + +l++ a++ lcl|NCBI__GCF_000092885.1:WP_013093659.1 214 IGDQLAQpEHHDARFDPPFSTVQTGVINGGRALNIVPAECEFDFEVRGVPGFDPSSVVDQLQTYAAAel 282 ******9899999*************************************************9998888 PP TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGP 336 +++ +p+++v+v++l+a+p+l++ +d+++++ll+ l+G+ + e+v++gte gl++++Gi++ v+GP lcl|NCBI__GCF_000092885.1:WP_013093659.1 283 lpkMRTVQPDTDVRVQMLNAYPGLATSPDSDAARLLAMLSGSkEFETVAFGTEGGLFTQAGIPTAVCGP 351 88888899**********************************889************************ PP TIGR01892 337 GdidqahqpdeYveieelkrcrallerl 364 G++dq h+pde++ +e+l+rc+a+ +rl lcl|NCBI__GCF_000092885.1:WP_013093659.1 352 GSMDQGHKPDEFITVEQLNRCDAMFARL 379 ************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (387 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: 11.76 // [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