Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate Pf1N1B4_3823 2-methylcitrate dehydratase (EC 4.2.1.79)
Query= SwissProt::Q937N6 (484 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 Length = 494 Score = 594 bits (1532), Expect = e-174 Identities = 303/497 (60%), Positives = 368/497 (74%), Gaps = 16/497 (3%) Query: 1 MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60 MS + RPD D VL DI DYV ++I+S A DTARNCL+DTLGCGL AL +P CTK Sbjct: 1 MSANVDLNIRPDYDTVLQDIADYVLNFKIESPEALDTARNCLMDTLGCGLLALRFPECTK 60 Query: 61 LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120 LGP+V GT+VP GARVPGT ++LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLG Sbjct: 61 HLGPIVEGTVVPFGARVPGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGA 120 Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180 ILA AD +S+ +A G PLT++ VL AMI AHEIQG IALENSFN+VG+DHV+LVKVAS Sbjct: 121 ILAVADHLSQKRLANGDAPLTIRVVLEAMIMAHEIQGVIALENSFNRVGIDHVILVKVAS 180 Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240 TAV A+++G R+++L+A+S A+ DGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA Sbjct: 181 TAVAAKLMGANREQLLSALSHAFADGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240 Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288 GEMG P VLTAK WGFYDVLF + F F RP+G+YVMEN+L KIS+ Sbjct: 241 MRGEMGIPGVLTAKQWGFYDVLFSHTNNDLALKPEDKRAFSFSRPFGSYVMENVLFKISF 300 Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348 PAEFHAQTA EAA+ LH L +I I I THE+ +RII K+GPL+N ADRDHC Sbjct: 301 PAEFHAQTACEAAVTLH---PLVRNRLHEIDRIVITTHESAIRIISKVGPLANAADRDHC 357 Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407 IQYM+AVPL+FG L A YED A P ID LR ++ VEDP TR+Y +P KRSIANA Sbjct: 358 IQYMIAVPLVFGNLVAEQYEDDFHAVHPIIDVLRDKMVIVEDPRFTREYLEPDKRSIANA 417 Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467 + V DG+ V+VEYP+GH+RRRAEGI LL +KF+ NLA RF ++ I A DQ Sbjct: 418 VQVFFKDGSSTKNVVVEYPIGHRRRRAEGIALLEDKFKANLATRFTAQRSAEIFALCKDQ 477 Query: 468 ARLEAMPVNEYLDMYAI 484 ARLE VN ++D++ I Sbjct: 478 ARLEETAVNRFVDLFVI 494 Lambda K H 0.322 0.136 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: 653 Number of extensions: 21 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: 484 Length of database: 494 Length adjustment: 34 Effective length of query: 450 Effective length of database: 460 Effective search space: 207000 Effective search space used: 207000 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 (21.9 bits) S2: 52 (24.6 bits)
Align candidate Pf1N1B4_3823 (2-methylcitrate dehydratase (EC 4.2.1.79))
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))
# 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.carbon/TIGR02330.hmm # target sequence database: /tmp/gapView.16012.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02330 [M=468] Accession: TIGR02330 Description: prpD: 2-methylcitrate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-269 877.8 0.1 9.6e-269 877.6 0.1 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 2-methylcitrate dehydratase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 2-methylcitrate dehydratase (EC 4.2.1.79) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 877.6 0.1 9.6e-269 9.6e-269 1 468 [] 14 494 .] 14 494 .] 1.00 Alignments for each domain: == domain 1 score: 877.6 bits; conditional E-value: 9.6e-269 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarv 64 d+vl+diadyvl+++i+s+ea+dtar++l+dtlgcgllal++pectk+lgp+vegt+vp garv lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 14 DTVLQDIADYVLNFKIESPEALDTARNCLMDTLGCGLLALRFPECTKHLGPIVEGTVVPFGARV 77 789************************************************************* PP TIGR02330 65 pgtsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplk 128 pgtsy+ldpvkaa++ig++vrwldyndtwlaaewghpsdnlg+ilavad+ls+kr+a+g++pl+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 78 PGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGAILAVADHLSQKRLANGDAPLT 141 **************************************************************** PP TIGR02330 129 vkevleamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvd 192 ++ vleami+aheiqgv+alensfnrvg+dhv+lvkvastav+akl+ga+re++l+alshaf d lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 142 IRVVLEAMIMAHEIQGVIALENSFNRVGIDHVILVKVASTAVAAKLMGANREQLLSALSHAFAD 205 **************************************************************** PP TIGR02330 193 gqalrtyrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkke... 253 gqalrtyrhapn+gsrkswaagda+srgvrla+ia++gemg+p++l+a +wgf+dvlf+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 206 GQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIAMRGEMGIPGVLTAKQWGFYDVLFSHTnnd 269 **************************************************************** PP TIGR02330 254 .........klklareygsyvmenvlfkisfpaefhaqtaveaavklheevkerldeierivit 308 ++++r++gsyvmenvlfkisfpaefhaqta+eaav+lh+ v++rl+ei+rivit lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 270 lalkpedkrAFSFSRPFGSYVMENVLFKISFPAEFHAQTACEAAVTLHPLVRNRLHEIDRIVIT 333 ********99****************************************************** PP TIGR02330 309 thesairiidkkgplanpadrdhclqylvavpllfgdlvaedyeda.vaadpridelreklevv 371 thesairii+k+gplan adrdhc+qy++avpl+fg+lvae+yed +a +p id lr+k+++v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 334 THESAIRIISKVGPLANAADRDHCIQYMIAVPLVFGNLVAEQYEDDfHAVHPIIDVLRDKMVIV 397 ********************************************9989**************** PP TIGR02330 372 edkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklvdkfkanlatk 435 ed+r++reyle+dkrsianav+vffkdgs+t++v+veyp+ghrrrr+egi +l dkfkanlat+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 398 EDPRFTREYLEPDKRSIANAVQVFFKDGSSTKNVVVEYPIGHRRRRAEGIALLEDKFKANLATR 461 **************************************************************** PP TIGR02330 436 fsskkqerilelcldqakleatpvnefldlfvi 468 f++++ ++i+ lc dqa+le+t+vn+f+dlfvi lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3823 462 FTAQRSAEIFALCKDQARLEETAVNRFVDLFVI 494 *******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (494 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.48 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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