Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_011649391.1 RL_RS36080 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000009265.1:WP_011649391.1 Length = 373 Score = 610 bits (1573), Expect = e-179 Identities = 302/372 (81%), Positives = 325/372 (87%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 MQA EIL +LVGF SVVG PN ++V+WIR YL+SHG V LPGPEGDRSN+FATIGPK Sbjct: 1 MQAIEILERLVGFPSVVGTPNREIVAWIRHYLQSHGAVVTELPGPEGDRSNLFATIGPKG 60 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 GYI+SGHMDVVPAAE GWTSDPFRLR EADRLYGRG TDMKGFLAAVLAAVP LA P Sbjct: 61 EPGYILSGHMDVVPAAEGGWTSDPFRLRAEADRLYGRGATDMKGFLAAVLAAVPVLAETP 120 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180 LRRP+HLA SYDEEAGCRGVPHMIARLPELC PLGAIIGEP+GMRAIRAHKGKAAARLT Sbjct: 121 LRRPVHLAFSYDEEAGCRGVPHMIARLPELCATPLGAIIGEPSGMRAIRAHKGKAAARLT 180 Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQ 240 V+GRSGHSSRPDQGLNAIH + VL A AEA+RL GPFEHVFEPPYSSLQ+GT+KGGQ Sbjct: 181 VKGRSGHSSRPDQGLNAIHAITDVLACARAEAERLTRGPFEHVFEPPYSSLQVGTLKGGQ 240 Query: 241 AVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQELSAYPALSLEPD 300 AVNIIPD+CE EFEARAISGVDP LLAP+R AE L+ LGF+VEW+ELSAYPALSL D Sbjct: 241 AVNIIPDTCEAEFEARAISGVDPITLLAPLRAAAEGLSQLGFQVEWRELSAYPALSLAAD 300 Query: 301 APLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMA 360 APLA LL ELTG E L AVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE+IL EL+A Sbjct: 301 APLATLLRELTGLEPLAAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEFILAGELLA 360 Query: 361 CRAMVEALGARC 372 C+AM+EALG RC Sbjct: 361 CQAMIEALGRRC 372 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: 529 Number of extensions: 13 Number of successful extensions: 1 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: 373 Length adjustment: 30 Effective length of query: 344 Effective length of database: 343 Effective search space: 117992 Effective search space used: 117992 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 WP_011649391.1 RL_RS36080 (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.5073.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-154 499.7 0.0 2.8e-154 499.5 0.0 1.0 1 lcl|NCBI__GCF_000009265.1:WP_011649391.1 RL_RS36080 acetylornithine deace Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011649391.1 RL_RS36080 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 499.5 0.0 2.8e-154 2.8e-154 1 364 [. 5 368 .. 5 369 .. 0.99 Alignments for each domain: == domain 1 score: 499.5 bits; conditional E-value: 2.8e-154 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 eil++Lv+f+sv++++n +++ ++++yl+++g v lp ++g ++snl+a+iGpk g+ g++lsGh+D lcl|NCBI__GCF_000009265.1:WP_011649391.1 5 EILERLVGFPSVVGTPNREIVAWIRHYLQSHGAVVTELPGPEG-DRSNLFATIGPK-GEPGYILSGHMD 71 79*****************************************.**********97.59********** PP TIGR01892 70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138 vvP++e++WtsDpfrL+ +++rLYgrG++DmkGFla+vLaavp la ++L++P+hl++s+Dee+g++G+ lcl|NCBI__GCF_000009265.1:WP_011649391.1 72 VVPAAEGGWTSDPFRLRAEADRLYGRGATDMKGFLAAVLAAVPVLAETPLRRPVHLAFSYDEEAGCRGV 140 ********************************************************************* PP TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204 +++i++l+ p ai+GeP +++a+RahkGka+a++tv+Gr+ghssrpd+G++ai+ ++++la + lcl|NCBI__GCF_000009265.1:WP_011649391.1 141 PHMIARLPelcATPLGAIIGEPSGMRAIRAHKGKAAARLTVKGRSGHSSRPDQGLNAIHAITDVLACAR 209 *******999899******************************************************** PP TIGR01892 205 aladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaeevk 273 a+a++l+r+++e++F+ppy++l++Gt+kGG+avnii+++Ce ++e+R+i+G+dp lla+l+++ae + lcl|NCBI__GCF_000009265.1:WP_011649391.1 210 AEAERLTRGPFEHVFEPPYSSLQVGTLKGGQAVNIIPDTCEAEFEARAISGVDPITLLAPLRAAAEGL- 277 ******************************************************************66. PP TIGR01892 274 ekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidq 341 +++gf+v+++elsa+pal+l +da+l+ ll++l+G ++ +vsygteagl+q++Gi+a+++GPGdi++ lcl|NCBI__GCF_000009265.1:WP_011649391.1 278 -SQLGFQVEWRELSAYPALSLAADAPLATLLRELTGLePLAAVSYGTEAGLFQRAGIDAIICGPGDIGR 345 .89*********************************9899***************************** PP TIGR01892 342 ahqpdeYveieelkrcrallerl 364 ah+pde++ el +c+a++e+l lcl|NCBI__GCF_000009265.1:WP_011649391.1 346 AHKPDEFILAGELLACQAMIEAL 368 ********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (373 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: 9.59 // [ok]
This GapMind analysis is from Apr 10 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