Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate CA265_RS25460 CA265_RS25460 methylmalonyl-CoA mutase
Query= SwissProt::O86028 (712 letters) >FitnessBrowser__Pedo557:CA265_RS25460 Length = 515 Score = 488 bits (1256), Expect = e-142 Identities = 253/515 (49%), Positives = 349/515 (67%), Gaps = 7/515 (1%) Query: 28 TPEGIDVKPLYTSDDMSGIGHLNSLPGFEPFVRGPRATMYAGRPWTVRQYAGFSTAEASN 87 T GI++K LYT + LPG PF RG + MY GR WT+RQYAGFSTAE SN Sbjct: 8 TTSGIEIKALYTKAKP-----MEELPGEFPFTRGIQKDMYRGRLWTMRQYAGFSTAEESN 62 Query: 88 AFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVEDMKILFDGIPLD 147 Y LA G G+SVAFDL T GYDSDH G+VGK GVAIDS++D++ILFDGI L Sbjct: 63 KRYHYLLAQGTTGLSVAFDLPTQIGYDSDHEMADGEVGKVGVAIDSLKDIEILFDGIQLK 122 Query: 148 RISVSMTMNGAVIPILASFIVAGEEQGVSRDKLSGTIQNDILKEFMVRNTYIYPPEPSMR 207 I+ SMT+N +LA +I ++QG ++SGTIQNDILKE+ R TYIYPP+ SMR Sbjct: 123 DITTSMTINATASILLAMYIALAKKQGADLKQISGTIQNDILKEYAARGTYIYPPKQSMR 182 Query: 208 IVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAALAKGLNVDD 267 ++ DI E+ +KE+PK+N+ISISGYH++EAG+T VQELAFTLA+G+ Y++AAL KGL+++ Sbjct: 183 LITDIFEFCSKEVPKWNTISISGYHIREAGSTAVQELAFTLANGKTYLKAALDKGLDINV 242 Query: 268 FAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMQEFKPEKASSLMLRTHCQTSGVSLQEQ 327 FA RLSFFF NFF E AK RAAR +W +I ++ + MLR H QT G +L Q Sbjct: 243 FAKRLSFFFNCHNNFFEEIAKFRAARRMWAKITKDLGATDEKAQMLRFHTQTGGSTLTAQ 302 Query: 328 DPYNNIVRTAFEAMSAVLGGTQSLHTNSFDEAMALPTDFSARIARNTQLILQHETGVTKV 387 P NN++R + +AM+AVLGGTQSLHTN +DEA++LPT+ +A+IA TQ I+ E+GVT Sbjct: 303 QPLNNVIRVSNQAMAAVLGGTQSLHTNGYDEALSLPTESAAKIALRTQQIIAFESGVTDT 362 Query: 388 VDPLAGSYYVESLTNELAEKAWGLIEEVEALGGMTKAVNAGLPKRLIEEAATRRQAAVDR 447 VDPLAGS++VE+LT+E+ AW I+ ++A+GG A+ + + I A+ + Q ++ Sbjct: 363 VDPLAGSFFVENLTDEVETAAWAYIDRIDAMGGSVNAIESDYMQNEIAGASYQYQKEIES 422 Query: 448 AEEVIVGVNKYRLENEQPIDILQIDNAAVRTAQVKRIEETRRRRDSQKMKQALDALADVA 507 E + VGVNK+ E E ++ ID+ ++R Q +++E + RD+ +++AL +L + A Sbjct: 423 GERISVGVNKFTQEEEGLTEVFNIDD-SIRKLQSEKLEILKTTRDNDAVEKALQSLHEAA 481 Query: 508 RSGKGNLLAAAVEAARARATVGEITDAMREAFGDY 542 + G+ NL+ ++A AT+GEI D R FG Y Sbjct: 482 K-GETNLMPLIIDAVEKYATLGEIADVFRGTFGVY 515 Lambda K H 0.318 0.134 0.379 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: 810 Number of extensions: 29 Number of successful extensions: 2 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: 712 Length of database: 515 Length adjustment: 37 Effective length of query: 675 Effective length of database: 478 Effective search space: 322650 Effective search space used: 322650 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: 53 (25.0 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