Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_076581961.1 BB347_RS05900 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_001971705.1:WP_076581961.1 Length = 560 Score = 673 bits (1737), Expect = 0.0 Identities = 335/556 (60%), Positives = 435/556 (78%), Gaps = 3/556 (0%) Query: 4 FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFE-IKRIYTPADLGEDWNYM 62 FD + L++I+ + W E V+ +++ ERKE F TD G + + R+YTPAD+ D +Y Sbjct: 2 FDPDDLEEIRAGKAEWHEEEVEPTVDRFGERKETFTTDTGGQTVDRLYTPADIS-DVDYQ 60 Query: 63 EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDL 122 E LG+PGE P+TRGVY+T YRGR+WTMRQYAG++T E++N+RY YLL QGQTGLS+AFDL Sbjct: 61 EDLGYPGEPPYTRGVYSTGYRGRLWTMRQYAGFSTPEDTNERYHYLLDQGQTGLSMAFDL 120 Query: 123 PTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYI 182 PTQ+G+DSD ++ GE+GK GVAIDSL DM +FDGIPLD+VSTSMTIN+ A+ LLAMYI Sbjct: 121 PTQMGHDSDASMSAGEIGKAGVAIDSLADMETVFDGIPLDEVSTSMTINAPASVLLAMYI 180 Query: 183 LVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPIS 242 V ++QGV +E+LRGT+QNDILKEYIAR TYI+PP+ SMR+ TDI +CA PK+N IS Sbjct: 181 AVGDQQGVDREQLRGTIQNDILKEYIARNTYIYPPESSMRIITDIFEFCASETPKFNTIS 240 Query: 243 ISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIA 302 ISGYHIREAG+ A QE+AFTL DGIEYV+ IE G+DVD FAP+LSFFF HNN EE+A Sbjct: 241 ISGYHIREAGSTAAQELAFTLGDGIEYVETAIEAGLDVDDFAPQLSFFFNGHNNIFEEVA 300 Query: 303 KFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362 KFRAARR+W I+ E F+A +P+S L+FHTQTAGS LTAQQ ENN+VRVA QALAAVLG Sbjct: 301 KFRAARRMWHDIIDERFDANDPKSKQLKFHTQTAGSMLTAQQIENNVVRVAYQALAAVLG 360 Query: 363 GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422 GTQSLHTN DEAL+LPTE+SVR ALRTQQI+A+ESG DT+DPL G+YY+E LTD + E Sbjct: 361 GTQSLHTNGKDEALALPTEESVRTALRTQQILAHESGAADTIDPLAGSYYVESLTDDVEE 420 Query: 423 EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEV 482 EA + +E++ + GGM AIE+ +VQ++I + ++ QKEI+ RIIVGVN F DE E+ Sbjct: 421 EAYEILEEVDERGGMREAIEQQWVQRQIQDTSFDRQKEIDSNDRIIVGVNEFEVDEDPEM 480 Query: 483 EILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLAT 542 ++ ++ +++QI+ L+ R++RD+ V+ LD LR AA+ ED NLMPYII+A + AT Sbjct: 481 DVQEITEEDQQRQIDSLESTRADRDDDAVEAKLDALREAAQGED-NLMPYIIDAVKVYAT 539 Query: 543 LQEVTDVLREIWGEYR 558 + E+ +VLR+ +GEY+ Sbjct: 540 VGEICNVLRDEFGEYQ 555 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: 858 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: 560 Length adjustment: 36 Effective length of query: 527 Effective length of database: 524 Effective search space: 276148 Effective search space used: 276148 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