Align 2-methylcitrate dehydratase; 2-MC dehydratase; Aconitate hydratase; ACN; Aconitase; EC 4.2.1.79; EC 4.2.1.3 (characterized)
to candidate PP_2338 PP_2338 2-methylcitrate dehydratase
Query= SwissProt::Q937N6 (484 letters) >lcl|FitnessBrowser__Putida:PP_2338 PP_2338 2-methylcitrate dehydratase Length = 494 Score = 576 bits (1485), Expect = e-169 Identities = 294/497 (59%), Positives = 362/497 (72%), Gaps = 16/497 (3%) Query: 1 MSTDTPSAQRPDPDQVLVDIVDYVTRYEIKSGLAYDTARNCLIDTLGCGLEALSYPACTK 60 MS + RPD D+VL + DY Y + S A DTARNCL+DTLGCGL AL +P CTK Sbjct: 1 MSANVDLNDRPDYDRVLQTLADYALGYRVDSREALDTARNCLMDTLGCGLLALRFPECTK 60 Query: 61 LLGPVVPGTIVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGG 120 LLGP V GT+VPNGARVPGT ++LDPV+AA++IG +RWLD+NDTWLAAEW HPSDNLGG Sbjct: 61 LLGPQVEGTLVPNGARVPGTSYRLDPVKAAWDIGCTVRWLDYNDTWLAAEWAHPSDNLGG 120 Query: 121 ILATADWISRNHIAAGRKPLTMKAVLAAMIKAHEIQGCIALENSFNQVGLDHVVLVKVAS 180 ILA AD +S+ +AAG KPL M+ VL AM+ AHEIQG +ALEN+FN+VGLDHV+LVKVAS Sbjct: 121 ILAVADHLSQKRVAAGEKPLLMRDVLEAMVMAHEIQGVLALENAFNRVGLDHVILVKVAS 180 Query: 181 TAVVAQMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNAGSRKSWAHGDATSRAVRLALIA 240 TAV A+++G R+++L+A+S A+VDGQ+LRTYRHAPNAGSRKSWA GDA+SR VRLA IA Sbjct: 181 TAVCARLMGANREQMLSALSHAFVDGQALRTYRHAPNAGSRKSWAAGDASSRGVRLADIA 240 Query: 241 RTGEMGYPSVLTAKTWGFYDVLFK-----------GQ-PFRFQRPYGTYVMENILLKISY 288 GEMG P VLTA WGFYDV F GQ R + G+YVMEN+L K+S+ Sbjct: 241 LRGEMGVPGVLTASQWGFYDVSFSHTNKDLALKPAGQYELRLPQALGSYVMENVLFKVSF 300 Query: 289 PAEFHAQTAVEAAMQLHGALALAGRSAADIAAITIRTHEACLRIIDKLGPLSNPADRDHC 348 PAEFHAQTA EAA+ LH L ++ I I T E+ +RII K GPL+N ADRDHC Sbjct: 301 PAEFHAQTACEAAVTLH---PLVRNRLHEVDRIVITTQESAIRIISKSGPLANAADRDHC 357 Query: 349 IQYMVAVPLLFGRLTAADYEDRIAAD-PRIDALRGRITCVEDPALTRDYHDPAKRSIANA 407 +QYMVAVPL+FG L A YED A+ P ID LR ++ VEDP +R+Y +P KRSIANA Sbjct: 358 LQYMVAVPLIFGHLVAEHYEDAFHANHPSIDRLREKMEVVEDPRFSREYLEPGKRSIANA 417 Query: 408 LTVTLADGTVLDEVLVEYPLGHKRRRAEGIPLLVEKFRTNLARRFPPKQQQAILAASLDQ 467 L V DG+ ++V+VEYP+GH+RRR EGIPLL KFR NLA RF ++ Q + DQ Sbjct: 418 LQVFFKDGSSTEQVVVEYPIGHRRRRGEGIPLLEAKFRANLATRFARQRCQQVFELCKDQ 477 Query: 468 ARLEAMPVNEYLDMYAI 484 +LE V+ ++D++ I Sbjct: 478 QKLEGTAVHRFVDLFVI 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: 643 Number of extensions: 20 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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