Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate WP_090438381.1 BLS63_RS00685 2-methylcitrate dehydratase
Query= SwissProt::Q937N6 (484 letters) >NCBI__GCF_900100495.1:WP_090438381.1 Length = 494 Score = 583 bits (1504), Expect = e-171 Identities = 299/497 (60%), Positives = 370/497 (74%), Gaps = 16/497 (3%) Query: 1 MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60 MS + RPD DQVL DI DYV Y ++S A DTARNCL+D+LGCGL AL +P CTK Sbjct: 1 MSANVDLNTRPDYDQVLQDIADYVLGYRVESAEALDTARNCLLDSLGCGLLALRFPECTK 60 Query: 61 LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120 LGP+V GT+VP+GARVPGT F+LDPV+AA++IG +RWLD+NDTWLAAEWGHPSDNLGG Sbjct: 61 HLGPLVEGTVVPHGARVPGTSFRLDPVKAAWDIGCCVRWLDYNDTWLAAEWGHPSDNLGG 120 Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180 ILA AD +S+ ++ G PL M+AVL AMI AHEIQG ALENSFN+VGLDHV+LVKVAS Sbjct: 121 ILAVADHLSQRRVSQGDAPLRMRAVLEAMIMAHEIQGVFALENSFNRVGLDHVMLVKVAS 180 Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240 TAV A+++G +R+++L+A+S A+VDGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA Sbjct: 181 TAVCAKLMGASREQLLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240 Query: 241 RTGEMGYPSVLTAKTWGFYDVLF------------KGQPFRFQRPYGTYVMENILLKISY 288 GEMG P VL+A WGFYDV F + + F F + +G+YVMEN+L KIS+ Sbjct: 241 MRGEMGIPGVLSAPQWGFYDVSFSHSNQDLALKPAEQRQFSFAQGFGSYVMENVLFKISF 300 Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348 PAEFHAQTA EAA+ LH + +IA I I T E+ +RII K+GPL+NPADRDHC Sbjct: 301 PAEFHAQTACEAAVILHPQVK---DRLHEIARIVISTQESAIRIISKVGPLANPADRDHC 357 Query: 349 IQYMVAVPLLFGRLTAADYEDRI-AADPRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407 +QYM AVPL FG+L A YED AA P ID LR ++ VED +R+Y + KRSIANA Sbjct: 358 LQYMTAVPLAFGKLVAEHYEDEFHAAQPIIDELRRKMEVVEDARYSREYLEADKRSIANA 417 Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467 + V ADG+ ++V VEYP+GH+RRRA+GIPLL EKF+ +LA RF ++ I DQ Sbjct: 418 VQVFFADGSATEKVEVEYPIGHRRRRAKGIPLLEEKFKASLATRFTGQRSVRIFDLCKDQ 477 Query: 468 ARLEAMPVNEYLDMYAI 484 ARLEA PV ++D++ I Sbjct: 478 ARLEATPVQRFMDLFVI 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: 635 Number of extensions: 23 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 24 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