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)
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