Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf1N1B4_4930 Acetylornithine deacetylase (EC 3.5.1.16)
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 Length = 385 Score = 240 bits (613), Expect = 4e-68 Identities = 135/373 (36%), Positives = 206/373 (55%), Gaps = 9/373 (2%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64 EIL +L+ F +V N ++ ++R L S GI ++ G ++N+FA+ GPKE G Sbjct: 7 EILKRLMAFDTVSSESNMALIEYVRDLLLSKGIESLIVQDETGKKANLFASTGPKELPGI 66 Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124 ++SGH DVVPAA WT F+ V+ R+YGRG+ DMKGF+A + A+ A L RP Sbjct: 67 LLSGHTDVVPAAGQAWTFPAFQATVQDGRIYGRGSCDMKGFIALAIDAMLDAADHSLSRP 126 Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184 L +ALS+DEE GC GV ++ L +P +IGEPT M+ + HKGK + R RG Sbjct: 127 LQIALSHDEETGCVGVRRLLDVLHLASVRPFLCLIGEPTNMQFVLGHKGKGSYRTYCRGL 186 Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243 HSS + +NAIH + +L G + ++ PYS++ +G + GG+A+N Sbjct: 187 EAHSSLAPRSVNAIHVACDFIAALRQSQQQLQAQGAQDADYDVPYSTVHVGQIVGGKALN 246 Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFE------VEWQELSAYPALSL 297 I+P+ C ++FE R + + + L +R+ AE + + +E + ++ YP L Sbjct: 247 IVPNLCTLDFEVRNLPADNLDQFLEQMRERAEVIVREAKKLSSVAAIEIETVNVYPGLDT 306 Query: 298 EPDAPLAALLEELTGREALPA-VSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355 P L+ + A VS+GTE GLF QR + ++CGPG I +AHKPDE+I I Sbjct: 307 HPSVEAVRFLKNFAAPDTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIEI 366 Query: 356 DELMACRAMVEAL 368 ++ A ++ L Sbjct: 367 SQMQAGERFLDGL 379 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: 331 Number of extensions: 11 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: 385 Length adjustment: 30 Effective length of query: 344 Effective length of database: 355 Effective search space: 122120 Effective search space used: 122120 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 Pf1N1B4_4930 (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.23622.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-111 358.0 0.0 3.2e-111 357.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 Acetylornithine deacetylase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 Acetylornithine deacetylase (EC 3.5.1.16) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.8 0.0 3.2e-111 3.2e-111 1 362 [. 7 377 .. 7 380 .. 0.94 Alignments for each domain: == domain 1 score: 357.8 bits; conditional E-value: 3.2e-111 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 eil++L+afd+vs sn++lieyv+d l ++g++ ++ g +k nl+a+ Gpke g++l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 7 EILKRLMAFDTVSSESNMALIEYVRDLLLSKGIESLIVQDETG-KKANLFASTGPKE-LPGILL 68 79*******************************9998888777.9***********9.9***** PP TIGR01892 65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvls 128 sGhtDvvP++++aWt +f+ t++dgr+YgrG++DmkGF+al+++a+ d a + L +Pl ++ls lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 69 SGHTDVVPAAGQAWTFPAFQATVQDGRIYGRGSCDMKGFIALAIDAMLDAADHSLSRPLQIALS 132 **************************************************************** PP TIGR01892 129 aDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrG 189 Dee+g+ G+++l+++l rp l ++GePt+++ v hkGk s + rG e+hss + r lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 133 HDEETGCVGVRRLLDVLHlasVRPFLCLIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLAPRS 196 ***************9988889****************************************** PP TIGR01892 190 vsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRp 252 v+ai++a +++a l + +++l+ + ++ +++py+t+++G++ GGka ni+++ C l +e+R lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 197 VNAIHVACDFIAALRQSQQQLQAqGAQDADYDVPYSTVHVGQIVGGKALNIVPNLCTLDFEVRN 260 *********************996778889********************************** PP TIGR01892 253 ipGmdpeellallekiaeevkekapg....fevkveelsatpaleleedaelvalleklaGa.. 310 +p ++++ l+++++ ae ++++a + +++e+++ +p+l++++ e+v++l++ a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 261 LPADNLDQFLEQMRERAEVIVREAKKlssvAAIEIETVNVYPGLDTHPSVEAVRFLKNFAAPdt 324 **************99999776655411115678999*********************988756 PP TIGR01892 311 aaevvsygteagll.qelGieavvlGPGdidqahqpdeYveieelkrcralle 362 + vs+gte gl+ q+l ++ vv+GPG+i+qah+pde++ei+++++++ +l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4930 325 GTAKVSFGTEGGLFkQRLDVPVVVCGPGSIEQAHKPDEFIEISQMQAGERFLD 377 7889********996789******************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (385 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: 7.40 // [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