Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS25460 CA265_RS25460 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__Pedo557:CA265_RS25460 Length = 515 Score = 641 bits (1654), Expect = 0.0 Identities = 328/523 (62%), Positives = 406/523 (77%), Gaps = 10/523 (1%) Query: 35 KEKFMTDDGFEIKRIYTPADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAG 94 ++K T G EIK +YT A ME+L PGE+PFTRG+ MYRGR+WTMRQYAG Sbjct: 3 EKKHTTTSGIEIKALYTKA------KPMEEL--PGEFPFTRGIQKDMYRGRLWTMRQYAG 54 Query: 95 YATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRI 154 ++TAEESNKRY YLL+QG TGLSVAFDLPTQ+GYDSDH +A+GEVGKVGVAIDSL D+ I Sbjct: 55 FSTAEESNKRYHYLLAQGTTGLSVAFDLPTQIGYDSDHEMADGEVGKVGVAIDSLKDIEI 114 Query: 155 LFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYI 214 LFDGI L ++TSMTIN+TA+ LLAMYI +A++QG +++ GT+QNDILKEY ARGTYI Sbjct: 115 LFDGIQLKDITTSMTINATASILLAMYIALAKKQGADLKQISGTIQNDILKEYAARGTYI 174 Query: 215 FPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVI 274 +PP+ SMRL TDI +C++ VPKWN ISISGYHIREAG+ AVQE+AFTLA+G Y+KA + Sbjct: 175 YPPKQSMRLITDIFEFCSKEVPKWNTISISGYHIREAGSTAVQELAFTLANGKTYLKAAL 234 Query: 275 ERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQ 334 ++G+D++ FA RLSFFF HNNF EEIAKFRAARR+WA I K+ A + ++ MLRFHTQ Sbjct: 235 DKGLDINVFAKRLSFFFNCHNNFFEEIAKFRAARRMWAKITKD-LGATDEKAQMLRFHTQ 293 Query: 335 TAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQII 394 T GSTLTAQQP NN++RV+ QA+AAVLGGTQSLHTN YDEALSLPTE + +IALRTQQII Sbjct: 294 TGGSTLTAQQPLNNVIRVSNQAMAAVLGGTQSLHTNGYDEALSLPTESAAKIALRTQQII 353 Query: 395 AYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAA 454 A+ESGV DTVDPL G++++E LTD + A YI++I MGG + AIE Y+Q EIA A+ Sbjct: 354 AFESGVTDTVDPLAGSFFVENLTDEVETAAWAYIDRIDAMGGSVNAIESDYMQNEIAGAS 413 Query: 455 YKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEA 514 Y+YQKEIE G+RI VGVN F +E E+ +D SIR+ Q E+L+ L++ RDN V++A Sbjct: 414 YQYQKEIESGERISVGVNKFTQEEEGLTEVFNIDDSIRKLQSEKLEILKTTRDNDAVEKA 473 Query: 515 LDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEY 557 L L AA K + NLMP II+A ATL E+ DV R +G Y Sbjct: 474 LQSLHEAA-KGETNLMPLIIDAVEKYATLGEIADVFRGTFGVY 515 Lambda K H 0.318 0.134 0.388 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: 798 Number of extensions: 33 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: 563 Length of database: 515 Length adjustment: 35 Effective length of query: 528 Effective length of database: 480 Effective search space: 253440 Effective search space used: 253440 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: 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:
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