Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_085638538.1 MGEO_RS13260 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_002115805.1:WP_085638538.1 Length = 386 Score = 248 bits (633), Expect = 2e-70 Identities = 145/380 (38%), Positives = 204/380 (53%), Gaps = 14/380 (3%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 + A ++L +LV F +V N ++V+++ YL+SH I + PEGD++ ++A IGP+ Sbjct: 3 LTARQLLERLVAFPTVSDQSNLELVNFVETYLQSHEITPTKVMNPEGDKAALYANIGPET 62 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 A G ++SGH DVVP W SDPF L RLYGRGT DMKG A LAAVP P Sbjct: 63 AGGVVLSGHTDVVPVKRQDWRSDPFTLTERDGRLYGRGTCDMKGSDALALAAVPLALRKP 122 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIAR-LPELCRQPLGAIIGEPTGMRAIRAHKGKAAARL 179 L+RPL +ALSYDEE G G P MI L +P I+GEP+ M+ + HKG ++ Sbjct: 123 LKRPLQIALSYDEETGMTGAPPMIDHMLSHGLPRPGAVIVGEPSMMKVVTGHKGGFGYQV 182 Query: 180 TVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADR----LVGGPFEHVFEPPYSSLQIGT 235 VRG HSS +G++A+ +AG L +R G F PPY+++ +GT Sbjct: 183 HVRGHEVHSSMMHEGVSAVM-MAGELVSWANRMNRQCAQATPGALAGDFVPPYTTIHVGT 241 Query: 236 VKGGQAVNIIPDSCEVEFEARAISGVDPAEL-------LAPVRKTAEALTTLGFEVEWQE 288 + GG A NI C E + R + G D +E +A +++ +A+ Q+ Sbjct: 242 ISGGTAHNITARDCRFEIDFRVVPGEDHSEWQQKFLGEVAALQRQMQAIHPDARITADQD 301 Query: 289 LSAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHK 348 L+ E L LTG A VSY TE GLFQ G+ +ICGPGDI +AH+ Sbjct: 302 FGV-AGLAPETQGEAEKLARRLTGDNATHVVSYATEGGLFQERGLSTVICGPGDIAQAHQ 360 Query: 349 PDEYILIDELMACRAMVEAL 368 PDE++ +D+ +E L Sbjct: 361 PDEFMSLDQFQKGEIFMERL 380 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: 361 Number of extensions: 16 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_085638538.1 MGEO_RS13260 (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.941965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-119 385.6 0.1 1.3e-119 385.4 0.1 1.0 1 NCBI__GCF_002115805.1:WP_085638538.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085638538.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 385.4 0.1 1.3e-119 1.3e-119 2 365 .] 8 381 .. 7 381 .. 0.94 Alignments for each domain: == domain 1 score: 385.4 bits; conditional E-value: 1.3e-119 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 +l++Lvaf++vs +sn++l+++ve yl++++++ ++ +++g +k l a iGp++ agg+vlsGhtDvvPv NCBI__GCF_002115805.1:WP_085638538.1 8 LLERLVAFPTVSDQSNLELVNFVETYLQSHEITPTKVMNPEG-DKAALYANIGPET-AGGVVLSGHTDVVPVK 78 6899**************************************.***********99.**************** PP TIGR01892 75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146 + W sDpf+Lte+dgrLYgrGt+DmkG al+Laavp ++Lk+Pl ++ls+Dee+g++Ga+ +i+ ++ NCBI__GCF_002115805.1:WP_085638538.1 79 RQDWRSDPFTLTERDGRLYGRGTCDMKGSDALALAAVPLALRKPLKRPLQIALSYDEETGMTGAPPMIDHMLs 151 *************************************999999**************************9999 PP TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr...e 213 +rp +ivGeP ++ v hkG +v+vrG+e hss ++Gvsa+++a++l++ + +++ + + + NCBI__GCF_002115805.1:WP_085638538.1 152 hglPRPGAVIVGEPSMMKVVTGHKGGFGYQVHVRGHEVHSSMMHEGVSAVMMAGELVSWANRMNRQCAQatpG 224 9999*****************************************************9998888887773235 PP TIGR01892 214 dleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevk 282 l F ppy+t+++Gt+ GG+a ni a+ C++++++R +pG d +e ++++ ++ +++ +p+ + NCBI__GCF_002115805.1:WP_085638538.1 225 ALAGDFVPPYTTIHVGTISGGTAHNITARDCRFEIDFRVVPGEDHSEWQQKFLGEVAAlqrqMQAIHPDARIT 297 67789***************************************99887776544444122267777888888 PP TIGR01892 283 veelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieel 354 ++ +l++e ++e+++l+++l+G+ a++vvsy+te gl+qe G+++v++GPGdi qahqpde++ ++++ NCBI__GCF_002115805.1:WP_085638538.1 298 ADQDFGVAGLAPETQGEAEKLARRLTGDnATHVVSYATEGGLFQERGLSTVICGPGDIAQAHQPDEFMSLDQF 370 88889999********************99******************************************* PP TIGR01892 355 krcrallerlv 365 ++++ ++erlv NCBI__GCF_002115805.1:WP_085638538.1 371 QKGEIFMERLV 381 ********997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 23.01 // [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