Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_073040518.1 BUB04_RS13745 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_900129305.1:WP_073040518.1 Length = 562 Score = 613 bits (1581), Expect = e-180 Identities = 307/563 (54%), Positives = 414/563 (73%), Gaps = 5/563 (0%) Query: 4 FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63 F + L++++ E + W +K L++ PER E+F T E+K +YTP D+ E +Y E Sbjct: 2 FSESQLERMEREYQDWLGE-YQKALQRLPERLERFSTVSDMEVKSLYTPLDIKEK-DYFE 59 Query: 64 KLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLP 123 LGFPG+YPFTRGV TMYR R+WTMR +AG TAE++NKR+ YL+ G+TGLS AFD P Sbjct: 60 DLGFPGQYPFTRGVQPTMYRARLWTMRMFAGLGTAEDTNKRFHYLIEHGETGLSTAFDFP 119 Query: 124 TQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYIL 183 T +GYD+D P+A GE GK GVAID++ DMR LF GI L++V+TSMTIN A+ + AMYI Sbjct: 120 TLMGYDTDAPVARGECGKCGVAIDTIDDMRRLFAGINLEEVTTSMTINPPASVIWAMYIA 179 Query: 184 VAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISI 243 AE +G ++KL GT+QND LKE+IA+ T + PP+PS+RL D + + VP+WN ISI Sbjct: 180 NAENEGYDRKKLGGTIQNDCLKEFIAQKTLMLPPEPSLRLVVDTVEFGTYEVPRWNTISI 239 Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303 SGYHIREAGA AVQE+AFT+ DGI YV+ I+RG+ VD FA RLSFF+ +H +F EEIAK Sbjct: 240 SGYHIREAGATAVQELAFTIYDGITYVEECIKRGLKVDDFAGRLSFFWNSHIDFFEEIAK 299 Query: 304 FRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGG 363 RAARR+WA IMKE F A+ PRSM+ RFHTQTAG +LTAQ+P NNI+R +ALAAVLGG Sbjct: 300 MRAARRMWARIMKERFKAQKPRSMLCRFHTQTAGCSLTAQEPYNNIIRTTTEALAAVLGG 359 Query: 364 TQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEE 423 TQSLHTNS DE +P+E++VRIALRTQQI+A E+GV + +DPL G+Y++E LTD + EE Sbjct: 360 TQSLHTNSLDEVYMIPSEEAVRIALRTQQILADETGVANVIDPLAGSYFVEALTDKMEEE 419 Query: 424 ALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVE 483 A+ YI K+ ++GGM+ AIE+ Y Q EIA+AAY++Q+++E G++II+GVN F ++ P Sbjct: 420 AMAYIRKLDELGGMVAAIEKDYPQMEIADAAYQFQQQVERGEKIIIGVNKFPSERPELEF 479 Query: 484 ILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKE---DENLMPYIIEAHRHL 540 +L++D + QIER ++ + +RD K+Q+A+D+LR E + N+MP +I+A R Sbjct: 480 VLRIDDELENFQIERTRQFKEKRDKVKLQKAMDELRRRCEGPPCWENNVMPALIDAVRAG 539 Query: 541 ATLQEVTDVLREIWGEYRAPLIF 563 AT QE D+ RE++G Y P F Sbjct: 540 ATEQECCDLYREVFGTYTDPGTF 562 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: 838 Number of extensions: 38 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: 562 Length adjustment: 36 Effective length of query: 527 Effective length of database: 526 Effective search space: 277202 Effective search space used: 277202 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