Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate H281DRAFT_00879 H281DRAFT_00879 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Burk376:H281DRAFT_00879 Length = 416 Score = 262 bits (669), Expect = 1e-74 Identities = 145/364 (39%), Positives = 210/364 (57%), Gaps = 11/364 (3%) Query: 9 KLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEAR---GYI 65 +LV +V PN ++ +R L + GI + G +N+FATI + G + Sbjct: 35 RLVSMDTVSRNPNLGLIETVRDELRALGIEGTLTHDASGKWANLFATIPAHDGETNGGVV 94 Query: 66 ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125 +SGH DVVP W SDPF+ + D+LYGRGT DMKGF+ A LA VP + L +P+ Sbjct: 95 LSGHTDVVPVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALALVPDMQRTKLAKPI 154 Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185 H ALS+DEE GC G P +IA L + +P G I+GEPT MR I AHKG A + VRG++ Sbjct: 155 HFALSFDEEVGCAGAPLLIADLMKRGVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQA 214 Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244 HSS +GLNAI A ++ AD+ GPF+ +++ P+++ Q T+ GG A+N Sbjct: 215 AHSSLTPKGLNAIEYAARLICYIRDMADQFREQGPFDELYDVPFTTAQTSTIVGGNAINT 274 Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTA-EALTTLGFE------VEWQELSAYPALSL 297 +P C+ +FE R + +DP + A + + A E L +E +++A P L Sbjct: 275 VPAECKFQFEFRNLPTLDPEPIFARIDQYARETLLPKMLREHPLAAIEITKIAAAPGLDS 334 Query: 298 EPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDE 357 A + L+ LT + V+YGTEAGLF AGI +I+CGPGDI +AHK +E++ +D+ Sbjct: 335 SEQAAITQLVRALTADQDKRKVAYGTEAGLFSLAGIPSIVCGPGDIQQAHKANEFVALDQ 394 Query: 358 LMAC 361 L+ C Sbjct: 395 LVQC 398 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: 376 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: 416 Length adjustment: 31 Effective length of query: 343 Effective length of database: 385 Effective search space: 132055 Effective search space used: 132055 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 H281DRAFT_00879 H281DRAFT_00879 (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.16654.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-115 370.2 0.0 7e-115 369.9 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00879 H281DRAFT_00879 acetylornithine Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00879 H281DRAFT_00879 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.9 0.0 7e-115 7e-115 4 364 .. 34 405 .. 32 406 .. 0.97 Alignments for each domain: == domain 1 score: 369.9 bits; conditional E-value: 7e-115 TIGR01892 4 akLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpk..egagglvlsGh 67 ++Lv++d+vs+ +n+ lie v+d l++lg++ a g + nl+a+i ++ e +gg+vlsGh lcl|FitnessBrowser__Burk376:H281DRAFT_00879 34 TRLVSMDTVSRNPNLGLIETVRDELRALGIEGTLTHDASG-KWANLFATIPAHdgETNGGVVLSGH 98 78**********************************9999.99*******988334469******* PP TIGR01892 68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeev 133 tDvvPvd+++W sDpf+ + ++LYgrGt+DmkGF+ ++La vpd++ +kL kP+h +ls+Deev lcl|FitnessBrowser__Burk376:H281DRAFT_00879 99 TDVVPVDGQQWDSDPFKPEIRGDKLYGRGTCDMKGFIGAALALVPDMQRTKLAKPIHFALSFDEEV 164 ****************************************************************** PP TIGR01892 134 glaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaiela 196 g+aGa+ li+ l+ +p+ ivGePts++++ ahkG+ + + vrG+ +hss + +G++aie a lcl|FitnessBrowser__Burk376:H281DRAFT_00879 165 GCAGAPLLIADLMkrgVKPDGCIVGEPTSMRPIVAHKGINAYQCCVRGQAAHSSLTPKGLNAIEYA 230 **********99977789************************************************ PP TIGR01892 197 akllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeel 261 a+l+ + ++ad+ ++ ++++e +++p++t + t+ GG+a n ++a+C++++e+R +p +dpe + lcl|FitnessBrowser__Burk376:H281DRAFT_00879 231 ARLICYIRDMADQFREqGPFDELYDVPFTTAQTSTIVGGNAINTVPAECKFQFEFRNLPTLDPEPI 296 **************99799*********************************************** PP TIGR01892 262 lallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygtea 321 a + + a e + +++p +++ + a p+l+ e+a + +l++ l+ + + v+ygtea lcl|FitnessBrowser__Burk376:H281DRAFT_00879 297 FARIDQYAREtllpkMLREHPLAAIEITKIAAAPGLDSSEQAAITQLVRALTADqDKRKVAYGTEA 362 ****9999988888878999*********************************98999******** PP TIGR01892 322 gllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364 gl+ +Gi+++v+GPGdi+qah+++e+v +++l++c+ +l++ lcl|FitnessBrowser__Burk376:H281DRAFT_00879 363 GLFSLAGIPSIVCGPGDIQQAHKANEFVALDQLVQCERFLHKF 405 **************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (416 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: 10.39 // [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