Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate H281DRAFT_06607 H281DRAFT_06607 2-methylcitrate dehydratase
Query= BRENDA::P74840 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_06607 Length = 483 Score = 802 bits (2071), Expect = 0.0 Identities = 386/483 (79%), Positives = 430/483 (89%) Query: 1 MSTQELNIRPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60 MS N+RPD D+ +VDIVDYV++Y+I +A +TA +CL+DTLGCGLEAL YPAC KL Sbjct: 1 MSAPISNVRPDPDKVLVDIVDYVLDYQIDGTLALETARHCLIDTLGCGLEALTYPACTKL 60 Query: 61 LGPIVPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120 LGPIVPGT+VPNGA+VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI Sbjct: 61 LGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120 Query: 121 LATADWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVAST 180 LATADWLSR A+AAGKAPL MK VL MIKAHEIQGCIALEN+FN+VGLDHVLLVK+AST Sbjct: 121 LATADWLSRTAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180 Query: 181 AVVAEMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240 AVV +M+GLTRDE++NAVS A VDGQ+LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K Sbjct: 181 AVVGQMIGLTRDELINAVSQALVDGQALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240 Query: 241 TGEMGYPSALTAKTWGFYDVSFKGETFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300 TGEMGYPS LTAKTWGFYDV FKG F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEAA Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNEFKFQRPYGSYVMENVLFKISFPAEFHAQTAVEAA 300 Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMVAVPLLFGR 360 M+L+ Q+Q G+ DI K+TIRTHEA LRIIDKKGPL+NPADRDHCIQYM+AVPL+FGR Sbjct: 301 MSLHAQLQLQGRRVEDIRKITIRTHEAALRIIDKKGPLDNPADRDHCIQYMIAVPLIFGR 360 Query: 361 LTAADYEDEVAQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEFTDGSRFGEV 420 LTAADYED VAQD RID LR K+ C EDP FT DYHDPEKR+I NA+T+EF DGS+F EV Sbjct: 361 LTAADYEDAVAQDPRIDVLRAKMACVEDPQFTKDYHDPEKRSIANALTIEFNDGSQFDEV 420 Query: 421 VVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQMPVNEYLDL 480 VVEYPIGH RRR DGIP L+EKFK NLAR+FP +QQ ILDVSLD+ARLE MPVNEY+DL Sbjct: 421 VVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480 Query: 481 YVI 483 YVI Sbjct: 481 YVI 483 Lambda K H 0.321 0.136 0.408 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: 814 Number of extensions: 17 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 H281DRAFT_06607 H281DRAFT_06607 (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.24248.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-270 881.8 0.0 5.6e-270 881.7 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06607 H281DRAFT_06607 2-methylcitrate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06607 H281DRAFT_06607 2-methylcitrate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 881.7 0.0 5.6e-270 5.6e-270 1 468 [] 13 483 .] 13 483 .] 0.99 Alignments for each domain: == domain 1 score: 881.7 bits; conditional E-value: 5.6e-270 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpg 66 d+vl+di+dyvl+y+id ++a++tar++l+dtlgcgl+al yp+ctkllgp+v+gt+vpnga+vpg lcl|FitnessBrowser__Burk376:H281DRAFT_06607 13 DKVLVDIVDYVLDYQIDGTLALETARHCLIDTLGCGLEALTYPACTKLLGPIVPGTIVPNGAKVPG 78 899*************************************************************** PP TIGR02330 67 tsyqldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkev 132 ts+qldpv+aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr++ia gk+pl +k+v lcl|FitnessBrowser__Burk376:H281DRAFT_06607 79 TSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRTAIAAGKAPLAMKDV 144 ****************************************************************** PP TIGR02330 133 leamikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrt 198 l amikaheiqg++alensfn+vgldhvllvk+astavv +++g+tr+e++na+s+a vdgqalrt lcl|FitnessBrowser__Burk376:H281DRAFT_06607 145 LIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLASTAVVGQMIGLTRDELINAVSQALVDGQALRT 210 ****************************************************************** PP TIGR02330 199 yrhapntgsrkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsy 264 yrhapntgsrkswaagdatsr+vrlali+++gemgyps+l+a +wgf+dvlfk++++k++r+ygsy lcl|FitnessBrowser__Burk376:H281DRAFT_06607 211 YRHAPNTGSRKSWAAGDATSRAVRLALISKTGEMGYPSVLTAKTWGFYDVLFKGNEFKFQRPYGSY 276 ****************************************************************** PP TIGR02330 265 vmenvlfkisfpaefhaqtaveaavklheevk...erldeierivitthesairiidkkgplanpa 327 vmenvlfkisfpaefhaqtaveaa+ lh +++ r+++i +i+i+the+a riidkkgpl+npa lcl|FitnessBrowser__Burk376:H281DRAFT_06607 277 VMENVLFKISFPAEFHAQTAVEAAMSLHAQLQlqgRRVEDIRKITIRTHEAALRIIDKKGPLDNPA 342 *****************************998333459**************************** PP TIGR02330 328 drdhclqylvavpllfgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianave 393 drdhc+qy++avpl+fg+l+a+dyedava+dprid lr k+ +ved++++++y++++krsiana++ lcl|FitnessBrowser__Burk376:H281DRAFT_06607 343 DRDHCIQYMIAVPLIFGRLTAADYEDAVAQDPRIDVLRAKMACVEDPQFTKDYHDPEKRSIANALT 408 ****************************************************************** PP TIGR02330 394 vffkdgskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpv 459 ++f+dgs+++ev+veyp+gh+rrr++gip+lv+kfk+nla++f+ k+q il+++ldqa+lea+pv lcl|FitnessBrowser__Burk376:H281DRAFT_06607 409 IEFNDGSQFDEVVVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPV 474 ****************************************************************** PP TIGR02330 460 nefldlfvi 468 ne++dl+vi lcl|FitnessBrowser__Burk376:H281DRAFT_06607 475 NEYVDLYVI 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: 00:00:00.02 # Mc/sec: 9.96 // [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