Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate CCNA_03746 CCNA_03746 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Caulo:CCNA_03746 Length = 391 Score = 251 bits (642), Expect = 2e-71 Identities = 151/378 (39%), Positives = 204/378 (53%), Gaps = 14/378 (3%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 +A +IL KLV F + N ++ W+ YL + +P +G +SN+ A IGP Sbjct: 11 RAIDILAKLVAFDTTSRRSNLALIEWVEQYLAELNVPTRRVPNADGTKSNLMAMIGPAVE 70 Query: 62 RGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPL 121 G ++SGH DVVP W++DP+ L RLYGRGT DMKGFLA LAA P LA L Sbjct: 71 GGVVLSGHTDVVPVDGQPWSTDPWTLTERDGRLYGRGTCDMKGFLALALAAAPDLAQANL 130 Query: 122 RRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTV 181 R+P+HLA SYDEE GC G P MI + +P ++GEPT M A+RAHKG A+ ++TV Sbjct: 131 RKPVHLAFSYDEEVGCLGAPDMIDVIAREVPRPALVVVGEPTDMVAVRAHKGIASFKVTV 190 Query: 182 RGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV-GGPFEHVFEPPYSSLQIGTVKGGQ 240 GR HSS G++A ++ V +++L F P ++L IG V GG Sbjct: 191 TGREAHSSLTHLGVSANMVAIKLMAMLVGLSEKLEREADPNSPFTPKGATLTIGQVNGGT 250 Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTL--------GFEVEWQELSAY 292 AVNI+ C F+ R +G+DP LL+ A AL G +VE + L+ Sbjct: 251 AVNILARECVFIFDLRTPAGMDPVALLSDFFAMASALDAQIKAKAPEGGVKVERRSLT-- 308 Query: 293 PALSLEPDAPLAALLEELTGREALPA--VSYGTEAGLFQRAGIDAIICGPGDIGRAHKPD 350 PA + E D A +L G PA V Y EAG FQ AG +ICGPG I +AH+P+ Sbjct: 309 PAFAPEEDGVAEAFARKLAGDNG-PARVVPYAAEAGQFQGAGFSTVICGPGSIDQAHQPN 367 Query: 351 EYILIDELMACRAMVEAL 368 EY+ I ++ A + L Sbjct: 368 EYVEISQMQRGGAFMRRL 385 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: 374 Number of extensions: 18 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: 391 Length adjustment: 30 Effective length of query: 344 Effective length of database: 361 Effective search space: 124184 Effective search space used: 124184 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 CCNA_03746 CCNA_03746 (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.18949.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-176 573.3 0.2 1.2e-176 573.1 0.2 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03746 CCNA_03746 acetylornithine deace Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03746 CCNA_03746 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 573.1 0.2 1.2e-176 1.2e-176 1 365 [] 14 386 .. 14 386 .. 0.99 Alignments for each domain: == domain 1 score: 573.1 bits; conditional E-value: 1.2e-176 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 +ilakLvafd++s+rsn++lie+ve+yl+el+v+++++p+adg +ksnl+a+iGp++ +gg+vlsGhtDvvPv lcl|FitnessBrowser__Caulo:CCNA_03746 14 DILAKLVAFDTTSRRSNLALIEWVEQYLAELNVPTRRVPNADG-TKSNLMAMIGPAV-EGGVVLSGHTDVVPV 84 79*****************************************.************9.*************** PP TIGR01892 74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146 d+++W++Dp++Lte+dgrLYgrGt+DmkGFlal+Laa+pdla+a+L+kP+hl++s+Deevg++Ga+++i+++a lcl|FitnessBrowser__Caulo:CCNA_03746 85 DGQPWSTDPWTLTERDGRLYGRGTCDMKGFLALALAAAPDLAQANLRKPVHLAFSYDEEVGCLGAPDMIDVIA 157 ************************************************************************* PP TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edl 215 +rpal++vGePt++vavRahkG+as+kvtv+Gre+hss ++ Gvsa+++a+kl+a+lv+l++kl+r +d+ lcl|FitnessBrowser__Caulo:CCNA_03746 158 revPRPALVVVGEPTDMVAVRAHKGIASFKVTVTGREAHSSLTHLGVSANMVAIKLMAMLVGLSEKLEReADP 230 9999****************************************************************989** PP TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevkve 284 +++Ftp++atl+iG+v+GG+avni+a++C+++++lR+++Gmdp++ll++++++a++ +k+kap+++vkve lcl|FitnessBrowser__Caulo:CCNA_03746 231 NSPFTPKGATLTIGQVNGGTAVNILARECVFIFDLRTPAGMDPVALLSDFFAMASAldaqIKAKAPEGGVKVE 303 ******************************************************9988889************ PP TIGR01892 285 elsatpaleleedaelvalleklaGa..aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355 ++s+tpa+++eed++++a+++klaG+ +a+vv+y++eag++q++G+++v++GPG+idqahqp+eYvei++++ lcl|FitnessBrowser__Caulo:CCNA_03746 304 RRSLTPAFAPEEDGVAEAFARKLAGDngPARVVPYAAEAGQFQGAGFSTVICGPGSIDQAHQPNEYVEISQMQ 376 **************************999******************************************** PP TIGR01892 356 rcrallerlv 365 r++a+++rlv lcl|FitnessBrowser__Caulo:CCNA_03746 377 RGGAFMRRLV 386 *******997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (391 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.02 // [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