Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_085637148.1 MGEO_RS10755 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_002115805.1:WP_085637148.1 Length = 383 Score = 252 bits (643), Expect = 1e-71 Identities = 142/382 (37%), Positives = 200/382 (52%), Gaps = 16/382 (4%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 ++ EIL L+ F ++ N +++ ++ G LE G +V+ G ++N+FAT+GP Sbjct: 4 RSTEILRDLIAFPTISADSNFEMILYMAGLLEEAGARCEVMSSACGTKANLFATLGPDRN 63 Query: 62 RGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPL 121 G ++SGH DVVP A+ WT DPF + LYGRGT DMKGF+AA LA P A Sbjct: 64 GGILLSGHSDVVPVADQAWTHDPFEMIERDGLLYGRGTCDMKGFIAAALAMAPHFAKRIA 123 Query: 122 RRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTV 181 RP+H A +YDEE GC G + L P AIIGEPT MR I HKG Sbjct: 124 ERPMHFAFTYDEEVGCLGARQLADDLSARGLVPGIAIIGEPTEMRIIDGHKGCNEYSTHF 183 Query: 182 RGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQ 240 G +GH S PD G+NA+ L + D L P F+PP++++ +G + GG Sbjct: 184 NGLAGHGSLPDHGVNAVEYAVRYLNHLLGLKDALRARAPKNSPFDPPWTTVNVGALTGGV 243 Query: 241 AVNIIPDSCEVEFEARAISGVDP-----------AELLAPVRKTAEALTTLGFEVEWQEL 289 A N+I S +V++E R + D +L P K + EV + + Sbjct: 244 AHNVIAPSAQVDWEMRPVQTGDAEFVKESLQTYCETVLLPKMKEVHPGAMITTEVIGEVV 303 Query: 290 SAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKP 349 P D ++ ELTG + V++GTEAGLFQ G D ++CGPG I +AHK Sbjct: 304 GLMPT----EDNEARRIVSELTGANSCDVVAFGTEAGLFQALGTDVVVCGPGSIEQAHKA 359 Query: 350 DEYILIDELMACRAMVEALGAR 371 DE++ +++L C M+E LGAR Sbjct: 360 DEFLALEQLSQCLTMLERLGAR 381 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: 390 Number of extensions: 15 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: 383 Length adjustment: 30 Effective length of query: 344 Effective length of database: 353 Effective search space: 121432 Effective search space used: 121432 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_085637148.1 MGEO_RS10755 (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.980624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-116 372.7 0.0 1.1e-115 372.6 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085637148.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085637148.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.6 0.0 1.1e-115 1.1e-115 1 364 [. 7 378 .. 7 379 .. 0.97 Alignments for each domain: == domain 1 score: 372.6 bits; conditional E-value: 1.1e-115 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 eil++L+af+++sa sn ++i y+++ lee+g ev+ a g +k nl+a+ Gp + +gg++lsGh+DvvPv NCBI__GCF_002115805.1:WP_085637148.1 7 EILRDLIAFPTISADSNFEMILYMAGLLEEAGARCEVMSSACG-TKANLFATLGPDR-NGGILLSGHSDVVPV 77 79****************************************9.************9.9************** PP TIGR01892 74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146 +++aWt+Dpf + e+dg LYgrGt+DmkGF+a++La +p+ a+ +P+h ++++Deevg++Ga++l++ l NCBI__GCF_002115805.1:WP_085637148.1 78 ADQAWTHDPFEMIERDGLLYGRGTCDMKGFIAAALAMAPHFAKRIAERPMHFAFTYDEEVGCLGARQLADDLS 150 **********************************************************************999 PP TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edl 215 p ai+GePt+++ + hkG + +G gh s pd+Gv+a+e a + l++l++l+d l+ ++ NCBI__GCF_002115805.1:WP_085637148.1 151 argLVPGIAIIGEPTEMRIIDGHKGCNEYSTHFNGLAGHGSLPDHGVNAVEYAVRYLNHLLGLKDALRArAPK 223 55566999***********************************************************975899 PP TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkv 283 +++F+pp++t+n+G + GG a n+ia + ++ e+Rp+ d e +++ l++ e+ +ke +pg + + NCBI__GCF_002115805.1:WP_085637148.1 224 NSPFDPPWTTVNVGALTGGVAHNVIAPSAQVDWEMRPVQTGDAEFVKESLQTYCETvllpkMKEVHPGAMITT 296 9*************************************************9999987777789999******* PP TIGR01892 284 eelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355 e+ +l + ed+e+ +++ +l+Ga + +vv++gteagl+q lG++ vv+GPG+i+qah++de++ +e+l NCBI__GCF_002115805.1:WP_085637148.1 297 EVIGEVVGLMPTEDNEARRIVSELTGAnSCDVVAFGTEAGLFQALGTDVVVCGPGSIEQAHKADEFLALEQLS 369 **************************9899******************************************* PP TIGR01892 356 rcrallerl 364 +c +lerl NCBI__GCF_002115805.1:WP_085637148.1 370 QCLTMLERL 378 ******997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (383 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.80 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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