Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_1185 Acetylornithine deacetylase (EC 3.5.1.16)
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 Length = 413 Score = 283 bits (723), Expect = 8e-81 Identities = 153/376 (40%), Positives = 210/376 (55%), Gaps = 10/376 (2%) Query: 5 EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64 EI L+GF SV N D++ W+ GYL G+ +LP G ++N+FA++GP G Sbjct: 28 EIARTLIGFPSVSDRSNLDLIEWVSGYLHGFGVQAQILPDASGRKANLFASLGPPRPGGI 87 Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124 I+SGH DVVP A W DPF ++ DRLYGRG++DMKGF+A VLA VP+L A R+ Sbjct: 88 ILSGHTDVVPVAGQAWAQDPFSAYLDQDRLYGRGSSDMKGFIAVVLAMVPELMASA-RQS 146 Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184 HLALSYDEE G G H+ + + +P G I+GEPT M + HKG+ V G+ Sbjct: 147 FHLALSYDEEVGAMGAKHLAPFITQAQLEPAGCIVGEPTSMALVIGHKGRHEINCCVHGK 206 Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244 HSS P++G+NAI A V Q A RL GP + F+ PY+++Q+ V GG A N+ Sbjct: 207 VAHSSLPNEGVNAIDYAARVQMQLQHVARRLSQGPLDSGFDVPYTTVQVCRVNGGVAGNV 266 Query: 245 IPDSCEVEFEARAISGVDPAELLAPVRKTAEAL-------TTLGFEVEWQELSAYPALSL 297 IP C +FE R + G D +LL ++ A+ +E+ P L Sbjct: 267 IPGQCSFDFEIRYLPGCDAEQLLVQIKDDAKQAMHSETDDRAWAASIEFSHTLHTPGLDE 326 Query: 298 EPDAPLAALLEELTG-REALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356 + + A + E + V+Y TEAGLFQ AGI I+CGPG I +AHK +EY+ + Sbjct: 327 KGNQAFAQWVREASSMAHGRQRVAYSTEAGLFQAAGIPTIVCGPGSIKQAHKVNEYVDLA 386 Query: 357 ELMACRAMVEALGARC 372 +L AC + L ARC Sbjct: 387 QLKACEQFLRRL-ARC 401 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: 426 Number of extensions: 16 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: 413 Length adjustment: 31 Effective length of query: 343 Effective length of database: 382 Effective search space: 131026 Effective search space used: 131026 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 Pf6N2E2_1185 (Acetylornithine deacetylase (EC 3.5.1.16))
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.929.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-116 374.7 0.0 2.7e-116 374.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 Acetylornithine deacetylase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 Acetylornithine deacetylase (EC 3.5.1.16) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 374.5 0.0 2.7e-116 2.7e-116 1 364 [. 28 398 .. 28 399 .. 0.94 Alignments for each domain: == domain 1 score: 374.5 bits; conditional E-value: 2.7e-116 TIGR01892 1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvl 64 ei + L++f+svs rsn+dlie+v +yl+ gv+++ lp a g k nl+a+ Gp + gg++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 28 EIARTLIGFPSVSDRSNLDLIEWVSGYLHGFGVQAQILPDASG-RKANLFASLGPPR-PGGIIL 89 68899**************************************.9***********9.9***** PP TIGR01892 65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvls 128 sGhtDvvPv+++aW++Dpf ++rLYgrG++DmkGF+a+vLa vp+l a ++ hl+ls lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 90 SGHTDVVPVAGQAWAQDPFSAYLDQDRLYGRGSSDMKGFIAVVLAMVPELMAS-ARQSFHLALS 152 **************************************************875.699******* PP TIGR01892 129 aDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrG 189 +Deevg +Gak+l+ ++ pa ivGePts+ v hkG + v+G+ +hss p++G lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 153 YDEEVGAMGAKHLAPFITqaqLEPAGCIVGEPTSMALVIGHKGRHEINCCVHGKVAHSSLPNEG 216 ************98777666699***************************************** PP TIGR01892 190 vsaielaakllarlvaladklkredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpi 253 v+ai aa++ +l + a +l +++l+++F++py+t+++ +v+GG a n+i+++C + +e+R + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 217 VNAIDYAARVQMQLQHVARRLSQGPLDSGFDVPYTTVQVCRVNGGVAGNVIPGQCSFDFEIRYL 280 **************************************************************** PP TIGR01892 254 pGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.. 310 pG d e+ll ++++ a++ +a + ++ ++ tp+l+ + ++ ++ +++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 281 PGCDAEQLLVQIKDDAKQamhseTDDRAWAASIEFSHTLHTPGLDEKGNQAFAQWVREASSMah 344 *********99998766633333445556667778888899******************99855 PP TIGR01892 311 aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364 + v+y+teagl+q +Gi+++v+GPG+i+qah+ +eYv++ +lk+c+++l+rl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 345 GRQRVAYSTEAGLFQAAGIPTIVCGPGSIKQAHKVNEYVDLAQLKACEQFLRRL 398 6789***********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (413 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.60 // [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