Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate 3609471 Dshi_2855 methylmalonyl-CoA mutase, large subunit (RefSeq)
Query= SwissProt::P27253 (714 letters) >FitnessBrowser__Dino:3609471 Length = 657 Score = 396 bits (1018), Expect = e-114 Identities = 252/651 (38%), Positives = 356/651 (54%), Gaps = 23/651 (3%) Query: 71 QPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGV 130 +PW R YAG STA+ SNA YR NLA GQ GLSVAFDL T GYDSD+ G+VGK GV Sbjct: 10 RPWLFRTYAGHSTAEASNALYRGNLAKGQTGLSVAFDLPTQTGYDSDHVLSRGEVGKVGV 69 Query: 131 AIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDIL 190 + + DM+ LF IPLD+M+ SMT+N +L+ YI AEEQG KL GT+QNDI+ Sbjct: 70 PVAHLGDMRALFKDIPLDQMNTSMTINATAPWLLSLYIAVAEEQGADVTKLQGTVQNDII 129 Query: 191 KEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLA 250 KEYL R TYI PPKPS+R+I D+ A+ ++P++N +++ YH+ EAGA Q++AF LA Sbjct: 130 KEYLSRGTYICPPKPSLRMITDVAAYTREHLPKWNPMNVCSYHLQEAGATPEQELAFALA 189 Query: 251 DG---IEYIKAAISAGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEAV-SGFGA 306 ++ +K + A R+SFF G+ + +RA LW E +G Sbjct: 190 TATAVLDDLKGKVPAE-HFPAMVGRISFFVNAGIRFVTEMCKMRAFVTLWDEICRDRYGV 248 Query: 307 QDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDEALGL 363 +DPK R Q + LTEQ P NNV R IE LA TL +++ A++EALGL Sbjct: 249 EDPKFRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKNARARAVQLPAWNEALGL 308 Query: 364 PTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMA 423 P + + + Q I+ E++L D G+ ++ ++++ ARA + ID GG Sbjct: 309 PRPWDQQWSLRMQQIMALETDLLEFDDLFDGNPAVDRKVAELMEGARAELATIDGMGGAV 368 Query: 424 KAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHE----DETDVLEIDNVMVRN 479 AIE K + EA++ I+ G+ V+VGVNKY+ D + + + V Sbjct: 369 AAIE--YMKSRLVEANSDRLGRIEGGETVVVGVNKYQQGEPSPLMDADGGIMVVDPAVEA 426 Query: 480 EQIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEVAF 539 +QIA L+ RA RD+ A AL L AA N++ A++ AA+ T GE + +F Sbjct: 427 DQIARLQAWRAARDEDAAQKALADLREAALSGANVMPASIAAAKAGVTTGEWGLEIRKSF 486 Query: 540 DRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDR 599 Y P TGV A +++E DA+ A + A GR+ + L+ K G DGH Sbjct: 487 GEYRAP----TGVSANPSNRTEGLDEIRDAVSAVS----AKLGRKLKFLVGKPGLDGHSN 538 Query: 600 GAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEAL 659 GA+ IA+ D G D+ + TPEEI R A E D HVVG S L+ H LI EL+ + Sbjct: 539 GAEQIAARARDCGMDITYEGIRLTPEEIVRAAREQDAHVVGLSILSGSHIPLIEELMGRM 598 Query: 660 KKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVR-DVLNLI 709 ++ I V+ GG+IP D L+ GVA +Y P L+ + D++ L+ Sbjct: 599 READLTHIPVIVGGIIPEDDAERLRAMGVAKVYTPKDFELNRIMFDIVGLV 649 Lambda K H 0.318 0.133 0.381 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: 938 Number of extensions: 38 Number of successful extensions: 6 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: 714 Length of database: 657 Length adjustment: 39 Effective length of query: 675 Effective length of database: 618 Effective search space: 417150 Effective search space used: 417150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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