Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate GFF1971 HP15_1928 2-methylcitrate dehydratase PrpD
Query= BRENDA::P77243 (483 letters) >FitnessBrowser__Marino:GFF1971 Length = 494 Score = 577 bits (1488), Expect = e-169 Identities = 291/497 (58%), Positives = 368/497 (74%), Gaps = 17/497 (3%) Query: 1 MSAQIN-NIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKK 59 MSA + N RP++D + I DYV+ YEI+S+ A++TA YCL+DTLGC L AL +P C K Sbjct: 1 MSATFDLNERPDYDEVLQKIADYVLTYEITSEEAWNTARYCLMDTLGCALLALRFPECTK 60 Query: 60 LLGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 119 LGPIV GT+VP+G RVPGT ++LDPV+AA++IG +RWLD+NDTWLAAEWGHPSDNLG Sbjct: 61 HLGPIVEGTMVPHGARVPGTPYRLDPVKAAWDIGCNVRWLDYNDTWLAAEWGHPSDNLGA 120 Query: 120 ILATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAS 179 ILA AD LS+ VA GK PLTM+ VL AMI AHEIQG +ALENSFNRVGLDHV+LVKVAS Sbjct: 121 ILAVADHLSQKRVAEGKEPLTMRTVLEAMIMAHEIQGVLALENSFNRVGLDHVVLVKVAS 180 Query: 180 TAVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMA 239 TAV + ++G RE++L+A+S AWVDGQSLRTYRHAPN G+RKSWAAGDATSRAVRLA +A Sbjct: 181 TAVASRLMGADREQLLSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRAVRLADIA 240 Query: 240 KTGEMGYPSALTAPVWGFYDVSFK------------GESFRFQRPYGSYVMENVLFKISF 287 GEMG P LTAP WGFYDV F F + +GSYVMEN+LFKISF Sbjct: 241 MRGEMGVPGVLTAPQWGFYDVLFSKTNKDQKLKPEDKRQFSLPQEFGSYVMENILFKISF 300 Query: 288 PAEFHSQTAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHC 347 PAEFH+QTA EAA+ LY +++ +I K+ I THE+ IRII K G L N ADRDHC Sbjct: 301 PAEFHAQTAAEAAVILYPEVK---DRLNEINKIVITTHESAIRIISKVGKLANAADRDHC 357 Query: 348 IQYMVAIPLLFGRLTAADYEDNVAQ-DKRIDALREKINCFEDPAFTADYHDPEKRAIANA 406 +QYM A+PL FG LTA YED+ + + ID LR+K+ ED +T +Y +PEKR+IANA Sbjct: 358 LQYMAAVPLAFGSLTAEHYEDSFHRANPIIDELRDKMEVVEDERYTREYLEPEKRSIANA 417 Query: 407 ITLEFTDGTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDR 466 I + F DG+ +++ VEYPIGH RRR++G+P L +KF NL + P+++ +L++ D Sbjct: 418 IQVFFNDGSNTDKIAVEYPIGHRRRRKEGMPLLEEKFLSNLKTRLPSKRCDTVLKMCQDP 477 Query: 467 ARLEQMPVNEYLDLYVI 483 +LE PV+E+++L +I Sbjct: 478 EKLENTPVHEFMNLLLI 494 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: 674 Number of extensions: 21 Number of successful extensions: 4 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: 494 Length adjustment: 34 Effective length of query: 449 Effective length of database: 460 Effective search space: 206540 Effective search space used: 206540 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