Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_076581961.1 BB347_RS05900 methylmalonyl-CoA mutase family protein
Query= SwissProt::P27253 (714 letters) >NCBI__GCF_001971705.1:WP_076581961.1 Length = 560 Score = 504 bits (1299), Expect = e-147 Identities = 268/514 (52%), Positives = 347/514 (67%), Gaps = 4/514 (0%) Query: 32 GIAIKPLYTEADLDNLEVTGTL--PGLPPYVRGPRATMYTAQPWTIRQYAGFSTAKESNA 89 G + LYT AD+ +++ L PG PPY RG +T Y + WT+RQYAGFST +++N Sbjct: 42 GQTVDRLYTPADISDVDYQEDLGYPGEPPYTRGVYSTGYRGRLWTMRQYAGFSTPEDTNE 101 Query: 90 FYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGVAIDTVEDMKVLFDQIPLDK 149 Y L GQ GLS+AFDL T G+DSD AG++GKAGVAID++ DM+ +FD IPLD+ Sbjct: 102 RYHYLLDQGQTGLSMAFDLPTQMGHDSDASMSAGEIGKAGVAIDSLADMETVFDGIPLDE 161 Query: 150 MSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDILKEYLCRNTYIYPPKPSMRI 209 +S SMT+N +LA YI ++QGV ++L GTIQNDILKEY+ RNTYIYPP+ SMRI Sbjct: 162 VSTSMTINAPASVLLAMYIAVGDQQGVDREQLRGTIQNDILKEYIARNTYIYPPESSMRI 221 Query: 210 IADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLADGIEYIKAAISAGLKIDDF 269 I DI +C+ P+FNTISISGYH+ EAG+ Q++AFTL DGIEY++ AI AGL +DDF Sbjct: 222 ITDIFEFCASETPKFNTISISGYHIREAGSTAAQELAFTLGDGIEYVETAIEAGLDVDDF 281 Query: 270 APRLSFFFGIGMDLFMNVAMLRAARYLWSEAV-SGFGAQDPKSLALRTHCQTSGWSLTEQ 328 AP+LSFFF ++F VA RAAR +W + + F A DPKS L+ H QT+G LT Q Sbjct: 282 APQLSFFFNGHNNIFEEVAKFRAARRMWHDIIDERFDANDPKSKQLKFHTQTAGSMLTAQ 341 Query: 329 DPYNNVIRTTIEALAATLGGTQSLHTNAFDEALGLPTDFSARIARNTQIIIQEESELCRT 388 NNV+R +ALAA LGGTQSLHTN DEAL LPT+ S R A TQ I+ ES T Sbjct: 342 QIENNVVRVAYQALAAVLGGTQSLHTNGKDEALALPTEESVRTALRTQQILAHESGAADT 401 Query: 389 VDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMAKAIEAGLPKRMIEEASAREQSLIDQ 448 +DPLAGSYY+ESLTD + ++A I++++DE GGM +AIE +R I++ S Q ID Sbjct: 402 IDPLAGSYYVESLTDDVEEEAYEILEEVDERGGMREAIEQQWVQRQIQDTSFDRQKEIDS 461 Query: 449 GKRVIVGVNKYKLDHEDETDVLEIDNVMVRNEQIASLERIRATRDDAAVTAALNALTHAA 508 R+IVGVN++++D + E DV EI + QI SLE RA RDD AV A L+AL AA Sbjct: 462 NDRIIVGVNEFEVDEDPEMDVQEITE-EDQQRQIDSLESTRADRDDDAVEAKLDALREAA 520 Query: 509 QHNENLLAAAVNAARVRATLGEISDALEVAFDRY 542 Q +NL+ ++A +V AT+GEI + L F Y Sbjct: 521 QGEDNLMPYIIDAVKVYATVGEICNVLRDEFGEY 554 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: 991 Number of extensions: 44 Number of successful extensions: 3 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: 560 Length adjustment: 38 Effective length of query: 676 Effective length of database: 522 Effective search space: 352872 Effective search space used: 352872 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 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