Align Acetylornithine deacetylase; AO; Acetylornithinase; EC 3.5.1.16; N-acetylornithinase; NAO (uncharacterized)
to candidate WP_085635729.1 MGEO_RS05565 acetylornithine deacetylase
Query= curated2:O68873 (380 letters) >NCBI__GCF_002115805.1:WP_085635729.1 Length = 388 Score = 181 bits (458), Expect = 4e-50 Identities = 133/389 (34%), Positives = 184/389 (47%), Gaps = 33/389 (8%) Query: 9 RATLTELVAMDTTSFRPNVPLIDYAQARLEAAGFSAERQKFLDDAGVEKVNLVAVKGGSG 68 R L +LV T S N+PLID+ + L G + R DD K L A G Sbjct: 8 RQILDQLVKFPTVSRDTNLPLIDWVEEYLSEHGVQSHRHVKSDDP--TKAALFAHVGPEV 65 Query: 69 SGRAALALVGHSDCVPYDAA-W-TDALRLTEKDGRLYARGACDTKGFIACALHAALNAEQ 126 G L+ GH+D VP D W TD + EKDG+L+ RG D KGF A A+ A + A+ Sbjct: 66 GGGVVLS--GHTDVVPTDGQPWSTDPFTVIEKDGKLFGRGTTDMKGFDALAIWALVEAQH 123 Query: 127 --LKAPLMVVLTADEEVGLTGAKKLVEAGLG---RARHAIVGEPTRLIPVRANKGYCLAE 181 + P+ V L+ DEE+G TGA L+EA G +A IVGEPT L V +KG Sbjct: 124 RGVSRPVQVALSYDEEIGCTGAPPLIEAMQGVVPKAETVIVGEPTMLKAVTGHKGGNTFW 183 Query: 182 VEVRGKEGHSAYPDSGASAIFRAGRFLQ---RLEHLALTVLREDLDEGFQPPFTTVNVGV 238 V + G E HS+ +G SAI + ++ R+ + + F PP+T V+VG Sbjct: 184 VHMHGFEVHSSIMHTGVSAIMYGAKLIEWANRMNAESAAAEPGPIAAQFNPPYTNVHVGQ 243 Query: 239 IQGGKAKNVIPGACRFVVEWRPIPGQPPERVSQLLETIRQELVRDEPAFEAQIRVVRTDR 298 I+GG A N+ C F + +R +PG+ E+ L E+ EA+++ VR + Sbjct: 244 IKGGTAHNITAKDCEFGLGFRVVPGETLEQWESKLREAAAEI-------EAEMKAVRPEA 296 Query: 299 GVNTRADAEVVRFLAEASG------------NAPETVSFGTEAPQMTELGAEAVVFGPGD 346 + + F E G N + VS+GTEA G VV GPGD Sbjct: 297 WIEITPVFSLPPFKPEDGGAAETLVRQLTGDNGTQYVSYGTEASHFQSAGYSVVVCGPGD 356 Query: 347 IRVAHQTGEYVPVEDLVRCEAVLARAVAH 375 I VAHQ EY+ V +A + R + H Sbjct: 357 IAVAHQPDEYITVAQFNEGQAFMERLLEH 385 Lambda K H 0.319 0.136 0.396 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: 20 Number of successful extensions: 6 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: 380 Length of database: 388 Length adjustment: 30 Effective length of query: 350 Effective length of database: 358 Effective search space: 125300 Effective search space used: 125300 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 WP_085635729.1 MGEO_RS05565 (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.948007.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-117 376.1 0.0 1e-116 375.9 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085635729.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085635729.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.9 0.0 1e-116 1e-116 2 364 .. 10 382 .. 9 383 .. 0.95 Alignments for each domain: == domain 1 score: 375.9 bits; conditional E-value: 1e-116 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 il +Lv f++vs+ +n++li++ve+yl e+gv+ ++ d+ +k l+a +Gp++ gg+vlsGhtDvvP+d NCBI__GCF_002115805.1:WP_085635729.1 10 ILDQLVKFPTVSRDTNLPLIDWVEEYLSEHGVQSHRHVKSDDPTKAALFAHVGPEV-GGGVVLSGHTDVVPTD 81 999****************************************************9.79************** PP TIGR01892 75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146 +++W++Dpf++ ekdg+L+grGt+DmkGF al++ a+ + + + +P+ ++ls+Dee+g++Ga+ liea+ NCBI__GCF_002115805.1:WP_085635729.1 82 GQPWSTDPFTVIEKDGKLFGRGTTDMKGFDALAIWALVEAQHRGVSRPVQVALSYDEEIGCTGAPPLIEAMQg 154 **********************************************************************999 PP TIGR01892 147 ..rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaaklla...rlvaladklkred 214 ++++++ivGePt l+av hkG ++ v+++G e hss ++Gvsai+ akl++ r+ a++ + ++ NCBI__GCF_002115805.1:WP_085635729.1 155 vvPKAETVIVGEPTMLKAVTGHKGGNTFWVHMHGFEVHSSIMHTGVSAIMYGAKLIEwanRMNAESAAAEPGP 227 999************************************************9999972225556666677799 PP TIGR01892 215 leeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevkv 283 F+ppy+ +++G++kGG+a ni a+ Ce+ l +R +pG ++e+ ++l+++a+e +k+ p+ +++ NCBI__GCF_002115805.1:WP_085635729.1 228 IAAQFNPPYTNVHVGQIKGGTAHNITAKDCEFGLGFRVVPGETLEQWESKLREAAAEieaeMKAVRPEAWIEI 300 9****************************************************99994444556678888888 PP TIGR01892 284 eelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355 + p +++e+ + ++ l+++l+G+ ++ vsygtea +q++G + vv+GPGdi +ahqpdeY+ + +++ NCBI__GCF_002115805.1:WP_085635729.1 301 TPVFSLPPFKPEDGGAAETLVRQLTGDnGTQYVSYGTEASHFQSAGYSVVVCGPGDIAVAHQPDEYITVAQFN 373 889999*********************89******************************************** PP TIGR01892 356 rcrallerl 364 +++a++erl NCBI__GCF_002115805.1:WP_085635729.1 374 EGQAFMERL 382 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (388 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: 00:00:00.00 # Mc/sec: 19.11 // [ok]
This GapMind analysis is from Jul 26 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