Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_092482543.1 BM299_RS05960 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_900115975.1:WP_092482543.1 Length = 554 Score = 681 bits (1757), Expect = 0.0 Identities = 340/542 (62%), Positives = 436/542 (80%), Gaps = 6/542 (1%) Query: 21 ETTVKKFLEKAPERKEK---FMTDDGFEIKRIYTPADLGEDWNYMEKLGFPGEYPFTRGV 77 + T +K+L + +RK++ F T G ++ IYTP D+ + ++Y++ LGFPGEYPFTRGV Sbjct: 10 KATREKWLTQRSKRKDRDINFDTVSGMPVQDIYTPEDI-KGFDYLQDLGFPGEYPFTRGV 68 Query: 78 YATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEG 137 MYRGR+WTMRQ+AG+ATAEESN+RYKYLL +GQTGLSVAFD+PT +GYDSDHP + G Sbjct: 69 QHNMYRGRLWTMRQFAGFATAEESNQRYKYLLEKGQTGLSVAFDMPTIMGYDSDHPRSLG 128 Query: 138 EVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRG 197 EVG+VGVAIDSL DM LFDGIPLD+VSTSMT N+ A+ L MYI E+QGV EKL G Sbjct: 129 EVGRVGVAIDSLADMETLFDGIPLDQVSTSMTTNAPASILWCMYIATGEKQGVPSEKLTG 188 Query: 198 TVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQ 257 T+QNDILKEYIA+ ++IFPP+PSMRL T+I Y A +VPKWN +SISGYHIREAG+ AVQ Sbjct: 189 TIQNDILKEYIAQKSWIFPPEPSMRLITNIFEYAARHVPKWNTVSISGYHIREAGSTAVQ 248 Query: 258 EVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKE 317 E+AFTLADG YV+A I G+DVD FAPRLSFFF +H +F EEIAK+RAARR+WA MKE Sbjct: 249 ELAFTLADGFAYVEAGIAAGLDVDDFAPRLSFFFNSHIDFFEEIAKYRAARRIWARRMKE 308 Query: 318 WFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALS 377 + AKNP+S +LRFHTQTAG +LTAQQPENNI+R A +ALAAVLGGTQSLHTNS DE L+ Sbjct: 309 KYGAKNPKSWLLRFHTQTAGCSLTAQQPENNIIRTAYEALAAVLGGTQSLHTNSMDEVLA 368 Query: 378 LPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGM 437 LPTEKSV+IALRTQQIIAYE+GV + +DPL G+Y++E LT+ + EEA KY +I++ GG+ Sbjct: 369 LPTEKSVQIALRTQQIIAYETGVANVIDPLAGSYFVEALTNKMEEEAEKYFAEIERRGGV 428 Query: 438 MRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVT-DEPIEVEILKVDPSIREKQI 496 + AI++ + Q+EIA+AAY+YQ+ I++ +RI VGVN F+ DE +++EIL +DP+I KQ+ Sbjct: 429 LAAIDQNFFQQEIADAAYQYQRAIDKKQRIQVGVNEFINPDEQMDIEILTIDPAIERKQV 488 Query: 497 ERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGE 556 E+++KLR +RDN +VQE L+ LR AAE EN++PYI+E R AT E+ +RE++GE Sbjct: 489 EKVQKLRRDRDNIRVQETLEALRKAAE-GTENMIPYILECVRAYATEGEIVQTMREVFGE 547 Query: 557 YR 558 Y+ Sbjct: 548 YK 549 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: 879 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: 554 Length adjustment: 36 Effective length of query: 527 Effective length of database: 518 Effective search space: 272986 Effective search space used: 272986 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 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