Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO353_28235 AO353_28235 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28235 Length = 385 Score = 241 bits (616), Expect = 2e-68 Identities = 139/374 (37%), Positives = 211/374 (56%), Gaps = 11/374 (2%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64 +IL +L+ F +V N ++ ++R L S GI ++ G ++N+FA+ GPKE G Sbjct: 7 DILKRLMAFDTVSSESNMALIEYVRDLLLSKGIESLIVKDETGKKANLFASTGPKELPGI 66 Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124 ++SGH DVVPAA WT F+ V+ R+YGRG+ DMKGF+A + A+ A L RP Sbjct: 67 LLSGHTDVVPAAGQAWTVPAFQATVQEGRIYGRGSCDMKGFIALAIDAMLDAADHSLSRP 126 Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184 L LALS+DEE GC GV ++ L +P +IGEPT M+ + HKGK + R RG Sbjct: 127 LQLALSHDEETGCVGVRRLLDVLHLAPVRPFLCLIGEPTNMQFVLGHKGKGSYRTYCRGL 186 Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV--GGPFEHVFEPPYSSLQIGTVKGGQAV 242 HSS + +NAIH VA A+ ++ + + G + ++ PYS++ +G + GG+A+ Sbjct: 187 EAHSSLAPRSVNAIH-VACDFIAALRQSQQQLQEQGAQDTDYDVPYSTVHVGQIVGGKAL 245 Query: 243 NIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALT------TLGFEVEWQELSAYPALS 296 NI+P+ C ++FE R + D + L ++ AE + + ++E + L+ YP L Sbjct: 246 NIVPNLCTLDFEVRNLPADDLDQFLTQMQARAEVIVREAKKLSSVADIEIETLNVYPGLD 305 Query: 297 LEPDAPLAALLEELTGREALPA-VSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYIL 354 P L+ + A VS+GTE GLF QR + ++CGPG I +AHKPDE+I Sbjct: 306 THPSVEAVRFLKNFAAPDTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIE 365 Query: 355 IDELMACRAMVEAL 368 I ++ A +E L Sbjct: 366 ISQMEAGERFLEGL 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: 341 Number of extensions: 13 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 AO353_28235 AO353_28235 (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.30174.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-111 358.8 0.0 1.8e-111 358.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 AO353_28235 acetylornithine deac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 AO353_28235 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.7 0.0 1.8e-111 1.8e-111 1 363 [. 7 378 .. 7 380 .. 0.95 Alignments for each domain: == domain 1 score: 358.7 bits; conditional E-value: 1.8e-111 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvls 65 +il++L+afd+vs sn++lieyv+d l ++g++ ++ g +k nl+a+ Gpke g++ls lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 7 DILKRLMAFDTVSSESNMALIEYVRDLLLSKGIESLIVKDETG-KKANLFASTGPKE-LPGILLS 69 79*********************************99999888.9***********9.9****** PP TIGR01892 66 GhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaD 130 GhtDvvP++++aWt +f+ t+++gr+YgrG++DmkGF+al+++a+ d a + L +Pl l+ls D lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 70 GHTDVVPAAGQAWTVPAFQATVQEGRIYGRGSCDMKGFIALAIDAMLDAADHSLSRPLQLALSHD 134 ***************************************************************** PP TIGR01892 131 eevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsa 192 ee+g+ G+++l+++l rp l ++GePt+++ v hkGk s + rG e+hss + r v+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 135 EETGCVGVRRLLDVLHlapVRPFLCLIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLAPRSVNA 199 *************9987889********************************************* PP TIGR01892 193 ielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGm 256 i++a +++a l + +++l++ + ++ +++py+t+++G++ GGka ni+++ C l +e+R +p lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 200 IHVACDFIAALRQSQQQLQEqGAQDTDYDVPYSTVHVGQIVGGKALNIVPNLCTLDFEVRNLPAD 264 ******************996788999************************************** PP TIGR01892 257 dpeellallekiaeevkekapg....fevkveelsatpaleleedaelvalleklaGa..aaevv 315 d+++ l+++++ ae ++++a + ++++e+l+ +p+l++++ e+v++l++ a + v lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 265 DLDQFLTQMQARAEVIVREAKKlssvADIEIETLNVYPGLDTHPSVEAVRFLKNFAAPdtGTAKV 329 **********99998776654411115678999*********************9887567889* PP TIGR01892 316 sygteagll.qelGieavvlGPGdidqahqpdeYveieelkrcraller 363 s+gte gl+ q+l ++ vv+GPG+i+qah+pde++ei+++++++ +le lcl|FitnessBrowser__pseudo3_N2E3:AO353_28235 330 SFGTEGGLFkQRLDVPVVVCGPGSIEQAHKPDEFIEISQMEAGERFLEG 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: 12.38 // [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