Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_038216092.1 Q392_RS27135 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000745855.1:WP_038216092.1 Length = 401 Score = 211 bits (538), Expect = 2e-59 Identities = 132/391 (33%), Positives = 192/391 (49%), Gaps = 29/391 (7%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 +A E LV +V N +++ + R +L GI + + ++N+FAT+G + Sbjct: 9 RALEFAQTLVQMNTVSANSNLELIDFARDHLAGLGIRSRLTWNADRTKANLFATLGAGKP 68 Query: 62 RGYIISGHMDVVPAAETGWTSDPFRLRVE------------ADRLYGRGTTDMKGFLAAV 109 G I+SGH D V W+ DP V+ + RLYGRG DMKGF+A Sbjct: 69 AGVILSGHTDTVSWDGQDWSVDPLSAIVQDWPITEGDDFRGSARLYGRGAADMKGFIAVA 128 Query: 110 LAAVPKLAAMPLRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIR 169 LA + +HLALSY+EE GC GV +IA L E +PL I+GEPT M Sbjct: 129 LANAERFVESDAPFSVHLALSYEEEIGCFGVRELIADLKEADIRPLACIVGEPTLMVPAI 188 Query: 170 AHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGV------LTQAVAEADRLVGGPFEHV 223 AHKG R VRG+ HSS Q +NA+ A V + + A+R G Sbjct: 189 AHKGVYRWRCCVRGKEAHSSLTPQSVNAVEMAARVVGKLRDMAELYERAERRYTG----- 243 Query: 224 FEPPYSSLQIGTVKGGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE 283 F+ PYS+ +G GG A N++P E +E R + VD + V A +L + Sbjct: 244 FDVPYSTASVGQFHGGIADNVVPRDAEFRYEFRNLPMVDALAMQREVEAYARSLEPAMKK 303 Query: 284 V------EWQELSAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAII 337 V ++ + PA + + L + L G V++GTEAGLF+ AGI ++ Sbjct: 304 VAPEAGFRFETICEIPAFQGDEKDAVTRLAQRLAGEPRTTLVAFGTEAGLFKGAGIPTVV 363 Query: 338 CGPGDIGRAHKPDEYILIDELMACRAMVEAL 368 CGPG I +AH+PDEY+ +++L C ++ L Sbjct: 364 CGPGSIAQAHQPDEYVTLEQLARCEVFMQGL 394 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: 370 Number of extensions: 15 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: 401 Length adjustment: 30 Effective length of query: 344 Effective length of database: 371 Effective search space: 127624 Effective search space used: 127624 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_038216092.1 Q392_RS27135 (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.30241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-104 334.2 0.0 5.8e-104 334.0 0.0 1.1 1 lcl|NCBI__GCF_000745855.1:WP_038216092.1 Q392_RS27135 acetylornithine dea Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038216092.1 Q392_RS27135 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 334.0 0.0 5.8e-104 5.8e-104 4 363 .. 15 393 .. 12 395 .. 0.94 Alignments for each domain: == domain 1 score: 334.0 bits; conditional E-value: 5.8e-104 TIGR01892 4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvP 72 + Lv +++vsa sn++li++++d+l+ lg+ + +ad +k nl+a+ G+ + +g++lsGhtD+v lcl|NCBI__GCF_000745855.1:WP_038216092.1 15 QTLVQMNTVSANSNLELIDFARDHLAGLGIRSRLTWNADR-TKANLFATLGAGK-PAGVILSGHTDTVS 81 689****************************999999988.**********877.89************ PP TIGR01892 73 vdeaaWtsDp.......frLtekdg.....rLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsa 129 d++ W+ Dp + +te d+ rLYgrG+aDmkGF+a++La + + +hl+ls+ lcl|NCBI__GCF_000745855.1:WP_038216092.1 82 WDGQDWSVDPlsaivqdWPITEGDDfrgsaRLYGRGAADMKGFIAVALANAERFVESDAPFSVHLALSY 150 *********9333333345777776666669********************99999999999******* PP TIGR01892 130 DeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaiel 195 +ee+g+ G+++li+ l rp ivGePt +v+ ahkG + vrG+e+hss + + v+a+e+ lcl|NCBI__GCF_000745855.1:WP_038216092.1 151 EEEIGCFGVRELIADLKeadIRPLACIVGEPTLMVPAIAHKGVYRWRCCVRGKEAHSSLTPQSVNAVEM 219 **************9988889************************************************ PP TIGR01892 196 aakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeella 263 aa+++++l ++a+ +r e + +F++py+t +G+ +GG a n++++ e+ e+R +p +d +++ lcl|NCBI__GCF_000745855.1:WP_038216092.1 220 AARVVGKLRDMAELYERaERRYTGFDVPYSTASVGQFHGGIADNVVPRDAEFRYEFRNLPMVDALAMQR 288 ****************978899*********************************************** PP TIGR01892 264 llekiaee....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqel 327 ++e+ a + +k+ ap+ + + e+ +pa++ +e + +l+++laG+ ++ v++gteagl++++ lcl|NCBI__GCF_000745855.1:WP_038216092.1 289 EVEAYARSlepaMKKVAPEAGFRFETICEIPAFQGDEKDAVTRLAQRLAGEpRTTLVAFGTEAGLFKGA 357 **999887677788999**********************************89999************* PP TIGR01892 328 GieavvlGPGdidqahqpdeYveieelkrcraller 363 Gi++vv+GPG+i qahqpdeYv +e+l rc+ +++ lcl|NCBI__GCF_000745855.1:WP_038216092.1 358 GIPTVVCGPGSIAQAHQPDEYVTLEQLARCEVFMQG 393 ********************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (401 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.32 // [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