Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate N515DRAFT_0031 N515DRAFT_0031 2-methylcitrate dehydratase (EC 4.2.1.79)
Query= BRENDA::P74840 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0031 Length = 483 Score = 581 bits (1498), Expect = e-170 Identities = 295/486 (60%), Positives = 363/486 (74%), Gaps = 6/486 (1%) Query: 1 MSTQELNI--RPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACK 58 MST +L RPD D +VDI DYV++Y I S AYDTA Y LLD+L + A+++P C Sbjct: 1 MSTHDLRSARRPDPDPPMVDIADYVVDYRIDSAEAYDTARYMLLDSLASAMLAMKFPECV 60 Query: 59 KLLGPIVPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLG 118 K LGP+VPG V+P GARVPGT +LDP QAAF IG IRWLDFNDTWLAAEWGHPSDNLG Sbjct: 61 KHLGPLVPGAVLPGGARVPGTSHELDPAQAAFAIGTQIRWLDFNDTWLAAEWGHPSDNLG 120 Query: 119 GILATADWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVA 178 ILA AD+L R AV G +++ VL IKAHEIQGC AL N+FNRVG DHV+LV++A Sbjct: 121 AILALADYLGRKAVREGGRASSLRDVLGWAIKAHEIQGCYALRNSFNRVGQDHVILVRLA 180 Query: 179 STAVVAEMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALM 238 STAV MLG +++I+ AVS +W+D +LR+YRHAPNTG RKSWAAGDA RAV A+ Sbjct: 181 STAVATAMLGGGKEQIVTAVSHSWIDNGALRSYRHAPNTGPRKSWAAGDACRRAVIHAIN 240 Query: 239 A-KTGEMGYPSALTAKTWGFYDVSFKGETFRFQRPYGSYVMENVLFKISFPAEFHSQTAV 297 A G +GYPSAL+A TWG+YDV+F+G+ F F+RP+GSYVMENVLFK+S+PAEFH+QTAV Sbjct: 241 AVDRGVVGYPSALSAATWGYYDVAFEGKAFEFERPFGSYVMENVLFKLSYPAEFHAQTAV 300 Query: 298 EAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMVAVPLL 357 E AM L+ Q+ AG+ A+I++V I T EA RIIDK GPL N ADRDHCIQYMVAVPLL Sbjct: 301 ECAMRLHGQV--AGR-IAEIDQVVIETQEAGARIIDKTGPLANYADRDHCIQYMVAVPLL 357 Query: 358 FGRLTAADYEDEVAQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEFTDGSRF 417 FGRLTA DY DEVA D RIDALRE++ E+P FT DY DP++R IGN++ V F DGS Sbjct: 358 FGRLTADDYGDEVAADPRIDALRERMAVSENPRFTRDYFDPDRRYIGNSVQVFFKDGSHT 417 Query: 418 GEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQMPVNEY 477 +V ++YPIGH RRRA+GIP L+ KF+ + P + + IL + D A L+ MPV E+ Sbjct: 418 DKVSIDYPIGHRRRRAEGIPVLLGKFEAAIRGHLPAHRVKAILQATSDPAGLDSMPVQEF 477 Query: 478 LDLYVI 483 L+L+ + Sbjct: 478 LELFTL 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: 710 Number of extensions: 25 Number of successful extensions: 3 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)
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