Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate HSERO_RS16100 HSERO_RS16100 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__HerbieS:HSERO_RS16100 Length = 400 Score = 266 bits (680), Expect = 7e-76 Identities = 146/371 (39%), Positives = 207/371 (55%), Gaps = 12/371 (3%) Query: 2 QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61 Q +IL L+GF +V N ++ W+R +LE HG + E ++N+FAT+G Sbjct: 15 QTLDILTTLIGFNTVSRESNLGLIEWVRDHLERHGAVTRLTYDAERRKANLFATLGDAGP 74 Query: 62 R--GYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAM 119 G + SGH DVVP W +DPF V +L+GRG DMKGF+A +A +P + Sbjct: 75 GRFGTVFSGHTDVVPVTGQKWDTDPFVAHVADGKLFGRGACDMKGFIAICMARLPAIDLA 134 Query: 120 PLRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARL 179 L PLH + SYDEE GC GV ++A L + +P G IIGEPT M+ + AHKGK + R Sbjct: 135 RLHTPLHFSFSYDEEVGCLGVRELLADLQQNDIRPTGVIIGEPTMMQPVIAHKGKRSYRC 194 Query: 180 TVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV--GGPFEHVFEPPYSSLQIGTVK 237 +V G + HSS P G+N+I A ++ + E V G + F+ PYSS+ Sbjct: 195 SVHGHAAHSSCPHLGINSI-DFAAMMQLKIREIALRVRHSGVQDDDFDVPYSSIATTLTS 253 Query: 238 GGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAE-------ALTTLGFEVEWQELS 290 GG A NIIPD E FE R + G+DPAE+ V+ AE + + +E++ L+ Sbjct: 254 GGNAPNIIPDKAEFVFEHRFLPGIDPAEVFEEVKAYAEQEILPQMRIDGVQGRIEFETLT 313 Query: 291 AYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPD 350 +YP + D PL + G E V +GTE GLF +AG+ A+ICGPGDI AHKP+ Sbjct: 314 SYPGMCTPADDPLVTSALRILGSERARKVGFGTEGGLFGQAGMPAVICGPGDIAHAHKPN 373 Query: 351 EYILIDELMAC 361 E++ +++L C Sbjct: 374 EFVTLEQLARC 384 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: 380 Number of extensions: 15 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: 400 Length adjustment: 30 Effective length of query: 344 Effective length of database: 370 Effective search space: 127280 Effective search space used: 127280 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 HSERO_RS16100 HSERO_RS16100 (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.32516.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-112 360.6 0.0 5.4e-112 360.4 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS16100 HSERO_RS16100 acetylornithine de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS16100 HSERO_RS16100 acetylornithine deacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 360.4 0.0 5.4e-112 5.4e-112 1 362 [. 18 389 .. 18 392 .. 0.96 Alignments for each domain: == domain 1 score: 360.4 bits; conditional E-value: 5.4e-112 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpk.egagglvlsGh 67 +il+ L++f++vs+ sn+ lie+v+d+le +g ++ a+ k nl+a+ G + g+ g v+sGh lcl|FitnessBrowser__HerbieS:HSERO_RS16100 18 DILTTLIGFNTVSRESNLGLIEWVRDHLERHGAVTRLTYDAER-RKANLFATLGDAgPGRFGTVFSGH 84 79******************************77766666665.9*********9989********** PP TIGR01892 68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevgl 135 tDvvPv +++W +Dpf + dg+L+grG++DmkGF+a+ +a +p ++ a+L+ Plh +s+Deevg+ lcl|FitnessBrowser__HerbieS:HSERO_RS16100 85 TDVVPVTGQKWDTDPFVAHVADGKLFGRGACDMKGFIAICMARLPAIDLARLHTPLHFSFSYDEEVGC 152 ******************************************************************** PP TIGR01892 136 aGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakll 200 +G+++l++ l rp+ +i+GePt +++v ahkGk s + v+G+ +hss p+ G++ i aa + lcl|FitnessBrowser__HerbieS:HSERO_RS16100 153 LGVRELLADLQqndIRPTGVIIGEPTMMQPVIAHKGKRSYRCSVHGHAAHSSCPHLGINSIDFAAMMQ 220 ******999887889**************************************************999 PP TIGR01892 201 arlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallek 267 ++ + a ++++ + +++ F++py+++ GG+a nii+++ e+v+e R +pG+dp+e+ +++++ lcl|FitnessBrowser__HerbieS:HSERO_RS16100 221 LKIREIALRVRHsGVQDDDFDVPYSSIATTLTSGGNAPNIIPDKAEFVFEHRFLPGIDPAEVFEEVKA 288 9*********99788999************************************************** PP TIGR01892 268 iaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGi 329 ae+ ++ + ++ ++ e+l+ +p++ +++d +lv + +++G+ +a+ v +gte gl+ ++G+ lcl|FitnessBrowser__HerbieS:HSERO_RS16100 289 YAEQeilpqMRIDGVQGRIEFETLTSYPGMCTPADDPLVTSALRILGSeRARKVGFGTEGGLFGQAGM 356 99888877777788899999***************************989****************** PP TIGR01892 330 eavvlGPGdidqahqpdeYveieelkrcralle 362 +av++GPGdi +ah+p+e+v +e+l rc+ + lcl|FitnessBrowser__HerbieS:HSERO_RS16100 357 PAVICGPGDIAHAHKPNEFVTLEQLARCERFFD 389 *****************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (400 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: 9.81 // [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