Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate RR42_RS14485 RR42_RS14485 2-methylcitrate dehydratase
Query= SwissProt::Q937N6 (484 letters) >FitnessBrowser__Cup4G11:RR42_RS14485 Length = 483 Score = 847 bits (2187), Expect = 0.0 Identities = 410/475 (86%), Positives = 442/475 (93%) Query: 10 RPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTKLLGPVVPGT 69 RP+PD V+ DIVDYVTRY++KS LAYDTARNCLIDTLGCGLEALSYPACTKLLGP+VPGT Sbjct: 9 RPEPDPVMADIVDYVTRYQVKSALAYDTARNCLIDTLGCGLEALSYPACTKLLGPIVPGT 68 Query: 70 IVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWIS 129 +VPNGA+VPGTQFQLDP+QAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADW+S Sbjct: 69 VVPNGAKVPGTQFQLDPIQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLS 128 Query: 130 RNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVASTAVVAQMLG 189 RN++AAGRKPLTMK VL MIKAHEIQGCIALEN+FN+VGLDHVVLVKVASTAVVAQMLG Sbjct: 129 RNNVAAGRKPLTMKDVLTGMIKAHEIQGCIALENAFNKVGLDHVVLVKVASTAVVAQMLG 188 Query: 190 LTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIARTGEMGYPS 249 L DEILNAVSLAWVDGQ+LRTYRHAPN GSRKSWA GDATSRAVRLALIARTGEMGYPS Sbjct: 189 LAVDEILNAVSLAWVDGQALRTYRHAPNTGSRKSWAAGDATSRAVRLALIARTGEMGYPS 248 Query: 250 VLTAKTWGFYDVLFKGQPFRFQRPYGTYVMENILLKISYPAEFHAQTAVEAAMQLHGALA 309 VL+AK WGFYDVLFKGQPFRFQRPYGTYVMEN+L KI++PAEFHAQTAVEAAM LHG L Sbjct: 249 VLSAKGWGFYDVLFKGQPFRFQRPYGTYVMENVLFKIAFPAEFHAQTAVEAAMTLHGQLC 308 Query: 310 LAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHCIQYMVAVPLLFGRLTAADYED 369 AG++AA I +TIRTHEAC+RIIDK GPL+NPADRDHCIQYMVAVPLLFGRL+A DYED Sbjct: 309 AAGKTAAQIRQVTIRTHEACIRIIDKKGPLANPADRDHCIQYMVAVPLLFGRLSAEDYED 368 Query: 370 RIAADPRIDALRGRITCVEDPALTRDYHDPAKRSIANALTVTLADGTVLDEVLVEYPLGH 429 +IAADPRIDALR +I CVEDP T DYHDP KRSIANALTVTL DGTVL EV+V+YPLGH Sbjct: 369 KIAADPRIDALRDKIVCVEDPRFTADYHDPDKRSIANALTVTLDDGTVLPEVVVDYPLGH 428 Query: 430 KRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQARLEAMPVNEYLDMYAI 484 KRRR EGIPLLVEKF+TNLARRFP +QQQAILA SLDQARLEAMPVNEY+D+Y I Sbjct: 429 KRRRDEGIPLLVEKFKTNLARRFPARQQQAILAVSLDQARLEAMPVNEYVDLYVI 483 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: 816 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: 484 Length of database: 483 Length adjustment: 34 Effective length of query: 450 Effective length of database: 449 Effective search space: 202050 Effective search space used: 202050 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 RR42_RS14485 RR42_RS14485 (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.2075.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-267 871.0 0.0 1.1e-266 870.8 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS14485 RR42_RS14485 2-methylcitrate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS14485 RR42_RS14485 2-methylcitrate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 870.8 0.0 1.1e-266 1.1e-266 1 468 [] 13 483 .] 13 483 .] 0.99 Alignments for each domain: == domain 1 score: 870.8 bits; conditional E-value: 1.1e-266 TIGR02330 1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsy 69 d v+ di+dyv y+++s++aydtar++l+dtlgcgl+al yp+ctkllgp+v+gt+vpnga+vpgt++ lcl|FitnessBrowser__Cup4G11:RR42_RS14485 13 DPVMADIVDYVTRYQVKSALAYDTARNCLIDTLGCGLEALSYPACTKLLGPIVPGTVVPNGAKVPGTQF 81 66899**************************************************************** PP TIGR02330 70 qldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamik 138 qldp++aafniga++rwld+ndtwlaaewghpsdnlggila+ad+lsr+++a g++pl++k+vl+ mik lcl|FitnessBrowser__Cup4G11:RR42_RS14485 82 QLDPIQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADWLSRNNVAAGRKPLTMKDVLTGMIK 150 ********************************************************************* PP TIGR02330 139 aheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgs 207 aheiqg++alen+fn+vgldhv+lvkvastavva++lg+ +eilna+s+a+vdgqalrtyrhapntgs lcl|FitnessBrowser__Cup4G11:RR42_RS14485 151 AHEIQGCIALENAFNKVGLDHVVLVKVASTAVVAQMLGLAVDEILNAVSLAWVDGQALRTYRHAPNTGS 219 ********************************************************************* PP TIGR02330 208 rkswaagdatsrgvrlalialkgemgypsalsapvwgfedvlfkkeklklareygsyvmenvlfkisfp 276 rkswaagdatsr+vrlalia++gemgyps+lsa wgf+dvlfk++ ++++r+yg+yvmenvlfki+fp lcl|FitnessBrowser__Cup4G11:RR42_RS14485 220 RKSWAAGDATSRAVRLALIARTGEMGYPSVLSAKGWGFYDVLFKGQPFRFQRPYGTYVMENVLFKIAFP 288 ********************************************************************* PP TIGR02330 277 aefhaqtaveaavklheevker...ldeierivitthesairiidkkgplanpadrdhclqylvavpll 342 aefhaqtaveaa++lh ++ ++ +++i +++i+the++iriidkkgplanpadrdhc+qy+vavpll lcl|FitnessBrowser__Cup4G11:RR42_RS14485 289 AEFHAQTAVEAAMTLHGQLCAAgktAAQIRQVTIRTHEACIRIIDKKGPLANPADRDHCIQYMVAVPLL 357 ******************988766799****************************************** PP TIGR02330 343 fgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveypl 411 fg+l aedyed++aadprid+lr+k+++ved+r++++y+++dkrsiana++v+ +dg++ ev+v+ypl lcl|FitnessBrowser__Cup4G11:RR42_RS14485 358 FGRLSAEDYEDKIAADPRIDALRDKIVCVEDPRFTADYHDPDKRSIANALTVTLDDGTVLPEVVVDYPL 426 ********************************************************************* PP TIGR02330 412 ghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468 gh+rrrdegip+lv+kfk+nla++f++++q+ il ++ldqa+lea+pvne++dl+vi lcl|FitnessBrowser__Cup4G11:RR42_RS14485 427 GHKRRRDEGIPLLVEKFKTNLARRFPARQQQAILAVSLDQARLEAMPVNEYVDLYVI 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.47 // [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