Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16)
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 Length = 394 Score = 285 bits (730), Expect = 1e-81 Identities = 147/379 (38%), Positives = 225/379 (59%), Gaps = 10/379 (2%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 +++ +L +LV F +V N ++ ++R YL+ G+ +++ E ++N+ A+IGP Sbjct: 9 LRSRALLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAERTKANLLASIGPAV 68 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 G ++SGH DVVP WT DPF L + +GRGT DMKG+LA+VLAAVP + P Sbjct: 69 PGGVVLSGHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 128 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180 LRRP+HLA SYDEE GC GV ++ L QP +IGEPT +R + HKGK A R Sbjct: 129 LRRPVHLAFSYDEEVGCLGVHSLLEVLVRRIAQPALCLIGEPTQLRPVLGHKGKLAMRCH 188 Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKG 238 VRG + HS+ G+NAI A ++ + + E + P H F+P S++Q+G V G Sbjct: 189 VRGAACHSAYAPYGVNAIEQAARLIGR-LGEIGAQLAEPSRHDPRFDPACSTVQVGVVHG 247 Query: 239 GQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE-------VEWQELSA 291 G A+NI+P C +FE RA+ DP ++ ++ AE + + ++ LSA Sbjct: 248 GTALNIVPADCRFDFEVRALPDFDPLVVVEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSA 307 Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351 YP L+ PD+ A L+ +L G +A V++GTE GLF +AG+ ++CGPG + + HKPDE Sbjct: 308 YPGLATSPDSAAARLIAQLCGSDAFGTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDE 367 Query: 352 YILIDELMACRAMVEALGA 370 Y+ ++++ AC +++ L + Sbjct: 368 YVSVEQMAACDRLMDRLAS 386 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: 413 Number of extensions: 11 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: 394 Length adjustment: 30 Effective length of query: 344 Effective length of database: 364 Effective search space: 125216 Effective search space used: 125216 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 Pf6N2E2_1339 (Acetylornithine deacetylase (EC 3.5.1.16))
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.30009.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-125 404.8 0.0 1.9e-125 404.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 Acetylornithine deacetylase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.6 0.0 1.9e-125 1.9e-125 2 364 .. 14 384 .. 13 385 .. 0.96 Alignments for each domain: == domain 1 score: 404.6 bits; conditional E-value: 1.9e-125 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvls 65 +la+Lv+f +vs+ sn++lie+v+dyl+ lgv+ e + +a+ +k nlla+iGp++ gg+vls lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 14 LLAELVSFATVSRDSNLALIEFVRDYLQGLGVNSELIYNAER-TKANLLASIGPAV-PGGVVLS 75 689*************************************99.************9.9****** PP TIGR01892 66 GhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsa 129 GhtDvvPvd++aWt Dpf Lte dg+ +grGtaDmkG+la vLaavp +L++P+hl++s+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 76 GHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSPLRRPVHLAFSY 139 **************************************************************** PP TIGR01892 130 DeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGv 190 Deevg++G+++l+e+l +pal ++GePt+l++v hkGk +++ +vrG hs+++ Gv lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 140 DEEVGCLGVHSLLEVLVrriAQPALCLIGEPTQLRPVLGHKGKLAMRCHVRGAACHSAYAPYGV 203 ***************9977789****************************************** PP TIGR01892 191 saielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpi 253 +aie+aa+l++rl + +l + + ++ F+p +t+++G+v+GG+a ni++a C++ +e+R++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 204 NAIEQAARLIGRLGEIGAQLAEpSRHDPRFDPACSTVQVGVVHGGTALNIVPADCRFDFEVRAL 267 *********************98999************************************** PP TIGR01892 254 pGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.a 311 p dp + ++l+ ae+ +++ a ++ ++ e lsa+p+l++ +d+ +++l+++l G+ a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 268 PDFDPLVVVEQLQGYAEQtllpaMQAVAGDTAIRFEPLSAYPGLATSPDSAAARLIAQLCGSdA 331 ********999999998877765555566677788999***********************989 PP TIGR01892 312 aevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364 +v++gte gl+ ++G+++vv+GPG++dq h+pdeYv +e++ +c+ l+ rl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 332 FGTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRLMDRL 384 9*************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (394 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