Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_367 Acetylornithine deacetylase (EC 3.5.1.16)
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 Length = 385 Score = 234 bits (598), Expect = 2e-66 Identities = 137/373 (36%), Positives = 207/373 (55%), Gaps = 11/373 (2%) Query: 6 ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65 I +L+ F +V N ++ ++R L S GI ++ G ++N+FA+ GP++ G + Sbjct: 8 IFERLLAFETVSSESNLALIEYVRELLLSKGIESLIVKDESGKKANLFASTGPRDLPGVL 67 Query: 66 ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125 +SGH DVVPAA WT F+ V R+YGRG+ DMKGF+A + A+ A L RPL Sbjct: 68 LSGHTDVVPAAGQAWTVPAFQATVRDGRVYGRGSCDMKGFIALAIDAMLDAADHSLNRPL 127 Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185 LALS+DEE GC GV ++ L +P +IGEPT M+ + HKGK + R RG Sbjct: 128 QLALSHDEEIGCVGVRRLLDVLHLAPVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLE 187 Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLV--GGPFEHVFEPPYSSLQIGTVKGGQAVN 243 HSS + +NAIH VA A+ ++ + + G + ++ PYS++ +G + GG+A+N Sbjct: 188 AHSSLAPRSVNAIH-VACDFIAALRQSQQQLQEQGAQDADYDVPYSTVHVGQIVGGKALN 246 Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALT------TLGFEVEWQELSAYPALSL 297 I+P+ C ++FE R + D L +R+ AE + + ++E + L+ YP L Sbjct: 247 IVPNLCTLDFEVRNLPDDDLDLFLEQLRERAEVIVREAKKLSSVADIEIETLNVYPGLDT 306 Query: 298 EPDAPLAALLEEL-TGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355 P L+ T VS+GTE GLF QR + ++CGPG I +AHKPDE+I I Sbjct: 307 HPSVEAVRFLKNFATPGTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIEI 366 Query: 356 DELMACRAMVEAL 368 ++ A +E L Sbjct: 367 SQMDAGERFLEGL 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: 355 Number of extensions: 12 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 Pf6N2E2_367 (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.12544.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-111 356.4 0.0 9.7e-111 356.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 Acetylornithine deacetylase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 Acetylornithine deacetylase (EC 3.5.1.16) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.3 0.0 9.7e-111 9.7e-111 2 363 .. 8 378 .. 7 380 .. 0.95 Alignments for each domain: == domain 1 score: 356.3 bits; conditional E-value: 9.7e-111 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsG 66 i+++L+af++vs sn++lieyv++ l ++g++ ++ g +k nl+a+ Gp++ g++lsG lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 8 IFERLLAFETVSSESNLALIEYVRELLLSKGIESLIVKDESG-KKANLFASTGPRD-LPGVLLSG 70 899**********************************99999.9***********9.9******* PP TIGR01892 67 htDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDe 131 htDvvP++++aWt +f+ t++dgr+YgrG++DmkGF+al+++a+ d a + L +Pl l+ls De lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 71 HTDVVPAAGQAWTVPAFQATVRDGRVYGRGSCDMKGFIALAIDAMLDAADHSLNRPLQLALSHDE 135 ***************************************************************** PP TIGR01892 132 evglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsai 193 e+g+ G+++l+++l rp l ++GePt+++ v hkGk s + rG e+hss + r v+ai lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 136 EIGCVGVRRLLDVLHlapVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLAPRSVNAI 200 ************9987889********************************************** PP TIGR01892 194 elaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmd 257 ++a +++a l + +++l++ + ++ +++py+t+++G++ GGka ni+++ C l +e+R +p d lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 201 HVACDFIAALRQSQQQLQEqGAQDADYDVPYSTVHVGQIVGGKALNIVPNLCTLDFEVRNLPDDD 265 *****************996778889*************************************** PP TIGR01892 258 peellallekiaeevkekapg....fevkveelsatpaleleedaelvallekla..Gaaaevvs 316 ++ l++l++ ae ++++a + ++++e+l+ +p+l++++ e+v++l++ a G + vs lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 266 LDLFLEQLRERAEVIVREAKKlssvADIEIETLNVYPGLDTHPSVEAVRFLKNFAtpGTGTAKVS 330 ********999998776654411115678999********************98744779999** PP TIGR01892 317 ygteagll.qelGieavvlGPGdidqahqpdeYveieelkrcraller 363 +gte gl+ q+l ++ vv+GPG+i+qah+pde++ei+++ +++ +le lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 331 FGTEGGLFkQRLDVPVVVCGPGSIEQAHKPDEFIEISQMDAGERFLEG 378 ******996789*******************************99975 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: 7.71 // [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