Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AZOBR_RS30425 AZOBR_RS30425 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__azobra:AZOBR_RS30425 Length = 385 Score = 292 bits (747), Expect = 1e-83 Identities = 159/376 (42%), Positives = 228/376 (60%), Gaps = 10/376 (2%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64 +IL +LV F +V N D++ W + LE+ G ++P +G ++N+FA++GP + G Sbjct: 9 DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDGRKANLFASVGPADRPGV 68 Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124 ++SGH DVVP WTSDPFRL A LYGRGT DMKGF+AA +A + + L +P Sbjct: 69 LLSGHTDVVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQP 128 Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184 LHLALSYDEE GC GV +I + L +P I+GEPT M+ + AHKGK A R+ RG Sbjct: 129 LHLALSYDEEVGCLGVRRLIDMMAALPVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGV 188 Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243 HSS QG+NAIH +LT +R+ G + ++ P++++ G ++GG A+N Sbjct: 189 ECHSSLAPQGMNAIHMACDMLTGLRRLQERVQTEGSRDADYDVPWTTIHAGVIQGGSALN 248 Query: 244 IIPDSCEVEFEARAISGVDPAE-LLAPVRKTAEALTTL------GFEVEWQELSAYPALS 296 I+P+ C ++ E R + DP E LL VR A A+ T VE ELS+YP+L Sbjct: 249 IVPNHCRLDMEIRHLP-QDPVEPLLDAVRAEAAAIETRARSAFPAAAVEIAELSSYPSLD 307 Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355 + D+ + + ++ LTG +L +S+GTE GLF QR + ++CGPG IG AHKPDE+I Sbjct: 308 TDGDSEVVSFVKALTGGNSLGKISFGTEGGLFQQRLSLPTVVCGPGSIGEAHKPDEFIAE 367 Query: 356 DELMACRAMVEALGAR 371 ++L AC M++ L R Sbjct: 368 EQLAACDRMLDLLLTR 383 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: 367 Number of extensions: 15 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 AZOBR_RS30425 AZOBR_RS30425 (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.22408.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-122 394.6 0.0 2.5e-122 394.4 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS30425 AZOBR_RS30425 acetylornithine de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS30425 AZOBR_RS30425 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.4 0.0 2.5e-122 2.5e-122 1 362 [. 9 378 .. 9 381 .. 0.96 Alignments for each domain: == domain 1 score: 394.4 bits; conditional E-value: 2.5e-122 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 +il++Lvaf++vs+ sn+dli +++++le++g +++ +p dg k nl+a++Gp++ + g++lsGhtD lcl|FitnessBrowser__azobra:AZOBR_RS30425 9 DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDG-RKANLFASVGPAD-RPGVLLSGHTD 75 79*****************************************.9***********9.*********** PP TIGR01892 70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138 vvPvd++aWtsDpfrLt ++g LYgrGtaDmkGF+a+++a ++ L +Plhl+ls+Deevg++G+ lcl|FitnessBrowser__azobra:AZOBR_RS30425 76 VVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQPLHLALSYDEEVGCLGV 144 ********************************************************************* PP TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204 ++li+++a rp+ ivGePt ++ v ahkGk + ++ rG e hss + +G++ai++a ++l+ l lcl|FitnessBrowser__azobra:AZOBR_RS30425 145 RRLIDMMAalpVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGVECHSSLAPQGMNAIHMACDMLTGLR 213 *****9998889********************************************************* PP TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271 +l+++++ + + +++p++t++ G+++GG+a ni+++ C+l +e+R +p + e ll +++ a++ lcl|FitnessBrowser__azobra:AZOBR_RS30425 214 RLQERVQTeGSRDADYDVPWTTIHAGVIQGGSALNIVPNHCRLDMEIRHLPQDPVEPLLDAVRAEAAAi 282 ******985788999************************************999999*****9999983 PP TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlG 335 ++ p+ v++ els +p+l+++ d+e+v +++ l+G ++ +s+gte gl+q +l +++vv+G lcl|FitnessBrowser__azobra:AZOBR_RS30425 283 etrARSAFPAAAVEIAELSSYPSLDTDGDSEVVSFVKALTGGnSLGKISFGTEGGLFQqRLSLPTVVCG 351 33344557999*****************************87699***********963699******* PP TIGR01892 336 PGdidqahqpdeYveieelkrcralle 362 PG+i++ah+pde++ e+l +c+ +l lcl|FitnessBrowser__azobra:AZOBR_RS30425 352 PGSIGEAHKPDEFIAEEQLAACDRMLD 378 ***********************9986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.26 // [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