Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_25400 AO356_25400 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25400 Length = 389 Score = 285 bits (730), Expect = 1e-81 Identities = 145/379 (38%), Positives = 226/379 (59%), Gaps = 10/379 (2%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 +++ +L +LV F +V N ++ ++R YL+ G+ +++ E ++N+ A+IGP Sbjct: 4 LRSRALLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAERTKANLLASIGPAL 63 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 G ++SGH DVVP WT +PF L + +GRGT DMKG+LA+VLAAVP + P Sbjct: 64 PGGVVLSGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 123 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180 LRRP+HLA SYDEE GC GV ++ LP+ QP +IGEPT ++ + HKGK A R Sbjct: 124 LRRPVHLAFSYDEEVGCLGVRSLLEVLPQRIAQPALCLIGEPTELQPVLGHKGKLAMRCH 183 Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKG 238 V+G + HS+ G+NAI A ++ + + E + P H F+P +S++Q+G V G Sbjct: 184 VKGAACHSAYAPYGVNAIEQAARLIGR-LGEIGAQLAEPSRHDPRFDPAFSTVQVGVVHG 242 Query: 239 GQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE-------VEWQELSA 291 G A+NI+P C +FE RA+ DP + ++ AE + + ++ LSA Sbjct: 243 GTALNIVPADCRFDFEVRALPDFDPLVVAEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSA 302 Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351 YP L+ PD+ A L+ L G +A V++GTE GLF +AG+ ++CGPG + + HKPDE Sbjct: 303 YPGLATSPDSAAAQLVARLCGSDAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDE 362 Query: 352 YILIDELMACRAMVEALGA 370 Y+ ++++ AC +++ L + Sbjct: 363 YVSVEQMAACDRLMDRLAS 381 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: 402 Number of extensions: 10 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: 389 Length adjustment: 30 Effective length of query: 344 Effective length of database: 359 Effective search space: 123496 Effective search space used: 123496 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 AO356_25400 AO356_25400 (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.3780.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-125 405.2 0.0 1.4e-125 405.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 AO356_25400 acetylornithine deac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 AO356_25400 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.1 0.0 1.4e-125 1.4e-125 2 364 .. 9 379 .. 8 380 .. 0.97 Alignments for each domain: == domain 1 score: 405.1 bits; conditional E-value: 1.4e-125 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 +la+Lv+f +vs+ sn++lie+v+dyl+ lgv+ e + +a+ +k nlla+iGp+ gg+vl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 9 LLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAER-TKANLLASIGPAL-PGGVVL 69 689*************************************99.************9.9***** PP TIGR01892 65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvl 127 sGhtDvvPvd++aWt +pf Lte dg+ +grGtaDmkG+la vLaavp +L++P+hl++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 70 SGHTDVVPVDGQAWTVEPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSPLRRPVHLAF 132 *************************************************************** PP TIGR01892 128 saDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpd 187 s+Deevg++G+++l+e+l+ +pal ++GePt+l++v hkGk +++ +v+G hs+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 133 SYDEEVGCLGVRSLLEVLPqriAQPALCLIGEPTELQPVLGHKGKLAMRCHVKGAACHSAYAP 195 ******************988889*************************************** PP TIGR01892 188 rGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvle 249 Gv+aie+aa+l++rl + +l + + ++ F+p ++t+++G+v+GG+a ni++a C++ +e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 196 YGVNAIEQAARLIGRLGEIGAQLAEpSRHDPRFDPAFSTVQVGVVHGGTALNIVPADCRFDFE 258 ************************98999********************************** PP TIGR01892 250 lRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvallekl 307 +R++p dp + ++l+ ae+ +++ a ++ ++ e lsa+p+l++ +d+ +++l+++l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 259 VRALPDFDPLVVAEQLQGYAEQtllpaMQAVAGDTAIRFEPLSAYPGLATSPDSAAAQLVARL 321 ****************99998877765555566677788999********************* PP TIGR01892 308 aGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364 G+ a +v++gte gl+ ++G+++vv+GPG++dq h+pdeYv +e++ +c+ l+ rl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25400 322 CGSdAFSTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRL 379 **9999*************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (389 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: 00:00:00.01 # Mc/sec: 11.71 // [ok]
This GapMind analysis is from Apr 09 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