Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012168732.1 AZC_RS01015 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000010525.1:WP_012168732.1 Length = 382 Score = 293 bits (751), Expect = 4e-84 Identities = 157/382 (41%), Positives = 225/382 (58%), Gaps = 8/382 (2%) Query: 1 MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60 M ++L +L+ F +V PN +++++++ +L HGIA +++ P+G ++N+FATIGP + Sbjct: 1 MSTLDLLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDGRKANLFATIGPTD 60 Query: 61 ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120 G ++SGH DVVP WT+DPFRLRV R YGRG DMKGFLAA LA + AA P Sbjct: 61 RPGIMLSGHTDVVPVEGQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARP 120 Query: 121 LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLT 180 L PLHLALS+DEE GC GV +I RL +P IIGEPT +R HKGK AAR T Sbjct: 121 LETPLHLALSHDEEVGCVGVRSLIERLSTASVRPRLCIIGEPTSLRVATGHKGKLAARAT 180 Query: 181 VRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV-GGPFEHVFEPPYSSLQIGTVKGG 239 G GHS+ + LNAIH + DR+ G + ++ PY++L G + GG Sbjct: 181 CCGVEGHSALAPKALNAIHLACDFVGLLRTHQDRIAESGARDADYDIPYTTLHAGVIAGG 240 Query: 240 QAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTT------LGFEVEWQELSAYP 293 A+NI+P+ C V+FE R I+ D +E+L + A L ++ + ++ YP Sbjct: 241 TALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARLVAERRAAFPAADIAVEVVNDYP 300 Query: 294 ALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQ-RAGIDAIICGPGDIGRAHKPDEY 352 L+ +A + A ++ L + V++GTE GLF R I +ICGPG + + HKPDE+ Sbjct: 301 GLATPKEAEVVAFVQALVDDASTFKVAFGTEGGLFDARLSIPTVICGPGSMDQGHKPDEF 360 Query: 353 ILIDELMACRAMVEALGARCTA 374 I +D+L AC M++ L R A Sbjct: 361 IALDQLEACDRMMDRLLHRLAA 382 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: 356 Number of extensions: 19 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: 382 Length adjustment: 30 Effective length of query: 344 Effective length of database: 352 Effective search space: 121088 Effective search space used: 121088 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_012168732.1 AZC_RS01015 (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.2602911.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-116 373.4 0.2 7e-116 373.2 0.2 1.0 1 NCBI__GCF_000010525.1:WP_012168732.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012168732.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.2 0.2 7e-116 7e-116 2 364 .. 6 376 .. 5 377 .. 0.95 Alignments for each domain: == domain 1 score: 373.2 bits; conditional E-value: 7e-116 TIGR01892 2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 +l +L+af++vs+ +n +li +v+++l ++g+a e + ++dg k nl+a+iGp++ + g++lsGhtDvvPv+ NCBI__GCF_000010525.1:WP_012168732.1 6 LLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDG-RKANLFATIGPTD-RPGIMLSGHTDVVPVE 76 6899**************************************.9***********9.**************** PP TIGR01892 75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146 ++aWt+DpfrL++ dgr YgrG+aDmkGFla++La + aa +L Plhl+ls Deevg+ G+++lie+l NCBI__GCF_000010525.1:WP_012168732.1 77 GQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARPLETPLHLALSHDEEVGCVGVRSLIERLSt 149 *************************************9*******************************9988 PP TIGR01892 147 ..rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edle 216 rp+l i+GePtsl+ hkGk +a+ t G eghs+ + + ++ai+la ++++ l + +d++ + + + NCBI__GCF_000010525.1:WP_012168732.1 150 asVRPRLCIIGEPTSLRVATGHKGKLAARATCCGVEGHSALAPKALNAIHLACDFVGLLRTHQDRIAEsGARD 222 889***************************************************************9978889 PP TIGR01892 217 eaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.vkek...apgfevkvee 285 ++ py+tl+ G++ GG+a ni+++ C + +e+R i+ d +e+l+ l + a+ v e+ p+ ++ ve+ NCBI__GCF_000010525.1:WP_012168732.1 223 ADYDIPYTTLHAGVIAGGTALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARlVAERraaFPAADIAVEV 295 99***************************************99988776655555244331115888999*** PP TIGR01892 286 lsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlGPGdidqahqpdeYveieelkr 356 ++ +p+l+++++ae+va+++ l + ++ v++gte gl+ +l i++v++GPG++dq h+pde++ +++l++ NCBI__GCF_000010525.1:WP_012168732.1 296 VNDYPGLATPKEAEVVAFVQALVDDaSTFKVAFGTEGGLFDaRLSIPTVICGPGSMDQGHKPDEFIALDQLEA 368 ***********************9977889**********6479***************************** PP TIGR01892 357 crallerl 364 c+ ++ rl NCBI__GCF_000010525.1:WP_012168732.1 369 CDRMMDRL 376 *****997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (382 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: 22.29 // [ok]
This GapMind analysis is from Jul 25 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