Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate PfGW456L13_4114 2-methylcitrate dehydratase (EC 4.2.1.79)
Query= SwissProt::Q937N6 (484 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4114 Length = 494 Score = 599 bits (1544), Expect = e-176 Identities = 304/497 (61%), Positives = 371/497 (74%), Gaps = 16/497 (3%) Query: 1 MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60 MS + RPD D+VL DI DYV Y+I+S A DTARNCLIDTLGCGL AL +P CTK Sbjct: 1 MSANVDLNNRPDYDKVLQDIADYVLNYKIESKEALDTARNCLIDTLGCGLLALRFPECTK 60 Query: 61 LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120 LGPVV GT+VP GARVPGT ++LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLGG Sbjct: 61 HLGPVVEGTVVPFGARVPGTSYRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGG 120 Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180 ILA AD +S+ H+A G PLT++ VL AMI AHEIQG IALENSFN+VGLDHV+LVKVAS Sbjct: 121 ILAVADHLSQKHLANGVAPLTVRTVLEAMIMAHEIQGVIALENSFNRVGLDHVILVKVAS 180 Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240 TAV A+++G R+++L+A+S A+ DGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA +A Sbjct: 181 TAVTAKLMGANREQLLSALSHAFADGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADMA 240 Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK------------GQPFRFQRPYGTYVMENILLKISY 288 GEMG P VL+A+ WGFYDVLF + F F RPYG+YVMEN+L KIS+ Sbjct: 241 MRGEMGIPGVLSARQWGFYDVLFSHTNNDLALKPEDRRAFSFSRPYGSYVMENVLFKISF 300 Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348 PAEFHAQTA EAA+ LH + +I I I THE+ +RII K+GPL+N ADRDHC Sbjct: 301 PAEFHAQTACEAAVTLHPQVR---NRLHEIDRIVITTHESAIRIISKVGPLANAADRDHC 357 Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407 IQYM AVPL+FG L A YED A P ID LR ++ VEDP TR+Y + KRSIANA Sbjct: 358 IQYMTAVPLVFGNLVAEYYEDDFHKAHPIIDVLRDKMVIVEDPRFTREYLESDKRSIANA 417 Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467 + V DG+ + V+VEYP+GH+RRR EGIPLL +KFR NL RF ++ + I A D+ Sbjct: 418 VQVFFKDGSSTENVVVEYPIGHRRRRVEGIPLLEDKFRANLLTRFTSQRSEEIFALCKDR 477 Query: 468 ARLEAMPVNEYLDMYAI 484 +LEA PVN ++D++ I Sbjct: 478 QKLEATPVNRFVDLFVI 494 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: 662 Number of extensions: 24 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: 484 Length of database: 494 Length adjustment: 34 Effective length of query: 450 Effective length of database: 460 Effective search space: 207000 Effective search space used: 207000 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