Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011781416.1 MVAN_RS21370 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000015305.1:WP_011781416.1 Length = 529 Score = 555 bits (1431), Expect = e-162 Identities = 281/526 (53%), Positives = 378/526 (71%), Gaps = 9/526 (1%) Query: 40 TDDGFEIKRIYTPADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAE 99 T G ++ +Y P D D PGEYPFTRG +A+ YRG+ WT RQY+G+ TAE Sbjct: 11 TPSGIPLEPVYGPGDRAADPPP------PGEYPFTRGNFASGYRGKTWTFRQYSGFGTAE 64 Query: 100 ESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGI 159 ESN+RY+YLL QG TGLSVA DLPTQ GYDSD EVG+VGVA+D+L D ILFDGI Sbjct: 65 ESNRRYRYLLEQGGTGLSVALDLPTQCGYDSDDAEYGEEVGRVGVAVDTLADAEILFDGI 124 Query: 160 PLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQP 219 PLDK+STS TIN TAA LLA Y+ AE++GV +EKL GT+QNDILKEY +RGT+I+PP+P Sbjct: 125 PLDKISTSFTINGTAAILLAFYVAAAEKKGVPREKLTGTIQNDILKEYASRGTWIWPPEP 184 Query: 220 SMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERG-M 278 S+RL D I +CA VPK+N IS++G H R+AGANAVQE+AFTLADG+ Y V+ERG M Sbjct: 185 SLRLIADTIEFCAAEVPKFNAISVAGAHFRDAGANAVQEMAFTLADGVTYCDTVVERGRM 244 Query: 279 DVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGS 338 +DKFAP++SFFF H +F EEIAK+RA RR WA I++E + A ++ M RF G+ Sbjct: 245 TIDKFAPQISFFFYTHGDFFEEIAKYRAGRRRWATIVRERYGATTDKASMFRFGCVAGGA 304 Query: 339 TLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYES 398 +L A Q +NN+VRVA +A+AAVLGG QS+ T ++DE +LP+E+S +ALRTQQI+AYE+ Sbjct: 305 SLYAPQAQNNLVRVAYEAMAAVLGGVQSMFTAAWDEPFALPSEESATLALRTQQILAYET 364 Query: 399 GVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQ 458 GV DPLGG+Y++E LTD E+ ++ + ++ GGM+R IE GY+Q IA+ A+K Sbjct: 365 GVTKVADPLGGSYFVEALTDATEEKIIEIMADLEAHGGMVRCIEDGYLQGLIADEAFKIH 424 Query: 459 KEIEEGKRIIVGVNAFVTDE-PIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDK 517 +E+E G R +VGVN FV DE P ++ ++D R+KQ++RL K++++RD+ V+EAL Sbjct: 425 QEVESGVRPVVGVNKFVVDEPPPDLATYELDAEGRDKQLKRLAKVKADRDDVAVKEALAA 484 Query: 518 LRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYRAPLIF 563 L AAE D+NLM +I+ T+ E+ L+ +WGE++ P++F Sbjct: 485 LARAAE-GDDNLMHKLIDCANAYCTVGEMVSTLKSVWGEFQQPVVF 529 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: 782 Number of extensions: 27 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: 529 Length adjustment: 35 Effective length of query: 528 Effective length of database: 494 Effective search space: 260832 Effective search space used: 260832 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 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