Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate dehydratase
Query= BRENDA::P77243 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS33975 Length = 483 Score = 792 bits (2046), Expect = 0.0 Identities = 378/483 (78%), Positives = 431/483 (89%) Query: 1 MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60 MSA I+N+RP+ D + DIVDYV +Y I S +A +TA +CL+DTLGCGLEAL YPAC KL Sbjct: 1 MSAPISNVRPDPDSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKL 60 Query: 61 LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120 +GPIVPGT+VPNG +VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI Sbjct: 61 MGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120 Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180 LATADWLSR+A+A+GKAPL MK VL AMIKAHEIQGCIALENSFN+VGLDHVLLVK+AST Sbjct: 121 LATADWLSRSAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180 Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240 AVV ++L LTR+E++NAVS A+VDG +LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K Sbjct: 181 AVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240 Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300 TGEMGYPS LTA WGFYDV FKG +F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEA Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFHAQTAVEAT 300 Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360 M L+ Q+ AAG++ DI K+TIRTHEA IRIIDKKGPLNNPADRDHCIQYMVA+PL+ GR Sbjct: 301 MKLHAQLNAAGRSVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGR 360 Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420 LTAADYED++AQD RID LR K+ C EDP FT DYHDPEKR+IANA+T+EF DG+ F+EV Sbjct: 361 LTAADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEV 420 Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480 +VEYPIGH RRR+DGIP LV+KFK NLAR+FP +QQ IL+VSLD+ARLE MPVNEY+DL Sbjct: 421 IVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480 Query: 481 YVI 483 YVI Sbjct: 481 YVI 483 Lambda K H 0.321 0.136 0.406 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: 787 Number of extensions: 12 Number of successful extensions: 1 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: 483 Length of database: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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 BPHYT_RS33975 BPHYT_RS33975 (2-methylcitrate dehydratase)
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.14102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-268 876.2 0.0 3e-268 876.0 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 876.0 0.0 3e-268 3e-268 1 468 [] 13 483 .] 13 483 .] 0.99 Alignments for each domain: == domain 1 score: 876.0 bits; conditional E-value: 3e-268 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyq 70 d+vl di+dyv +y+ids++a++tar++l+dtlgcgl+al yp+ctkl+gp+v+gt+vpnga+vpgts+q lcl|FitnessBrowser__BFirm:BPHYT_RS33975 13 DSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKLMGPIVPGTIVPNGAKVPGTSFQ 82 789******************************************************************* PP TIGR02330 71 ldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikah 140 ldpv+aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr +ia gk+pl +k+vl amikah lcl|FitnessBrowser__BFirm:BPHYT_RS33975 83 LDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRSAIAAGKAPLAMKDVLIAMIKAH 152 ********************************************************************** PP TIGR02330 141 eiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrks 210 eiqg++alensfn+vgldhvllvk+astavv +ll +tr+e++na+s+afvdg+alrtyrhapntgsrks lcl|FitnessBrowser__BFirm:BPHYT_RS33975 153 EIQGCIALENSFNKVGLDHVLLVKLASTAVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKS 222 ********************************************************************** PP TIGR02330 211 waagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfpaefh 280 waagdatsr+vrlali+++gemgyps+l+a +wgf+dvlfk++ ++++r+ygsyvmenvlfkisfpaefh lcl|FitnessBrowser__BFirm:BPHYT_RS33975 223 WAAGDATSRAVRLALISKTGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFH 292 ********************************************************************** PP TIGR02330 281 aqtaveaavklheevker...ldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlv 347 aqtavea++klh +++++ +d+i++i+i+the+airiidkkgpl+npadrdhc+qy+vavpl++g+l+ lcl|FitnessBrowser__BFirm:BPHYT_RS33975 293 AQTAVEATMKLHAQLNAAgrsVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGRLT 362 ***************9987789************************************************ PP TIGR02330 348 aedyedavaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrr 417 a+dyed++a+dprid lr k+e+ved++++++y++++krsiana++++f+dgs+++ev veyp+gh+rrr lcl|FitnessBrowser__BFirm:BPHYT_RS33975 363 AADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEVIVEYPIGHKRRR 432 ********************************************************************** PP TIGR02330 418 degipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468 ++gip+lv+kfk+nla++f+ k+q il+++ldqa+lea+pvne++dl+vi lcl|FitnessBrowser__BFirm:BPHYT_RS33975 433 EDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDLYVI 483 *************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (483 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: 11.65 // [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