Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_076578503.1 BB347_RS03070 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_001971705.1:WP_076578503.1 Length = 566 Score = 625 bits (1612), Expect = 0.0 Identities = 298/560 (53%), Positives = 424/560 (75%), Gaps = 8/560 (1%) Query: 4 FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63 +D E L+ I+E ++WE T+ LE+ ER+E F T ++ R+YTP D+ D +Y+E Sbjct: 2 YDDEDLEAIRESGEKWETDTLDPVLERHGERQEDFATVSNIDVDRLYTPEDVA-DLDYLE 60 Query: 64 KLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLP 123 LGFPGE P+TRG Y TMYRGR WTMRQ+AG+ TAEE+N+R+ YL+ +GQTGLSVAFD+P Sbjct: 61 DLGFPGEEPYTRGPYPTMYRGRTWTMRQFAGFGTAEETNERFHYLIDEGQTGLSVAFDMP 120 Query: 124 TQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYIL 183 T +G DSD ++EGE+GK GVA+D+L DM ILFDGI L+++STS TIN +A + AMY+ Sbjct: 121 TLMGLDSDDRMSEGEIGKEGVAVDTLRDMEILFDGIDLEEISTSFTINPSAPVIYAMYVA 180 Query: 184 VAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISI 243 +A++QGV +E +RGT+QND+ KE+IA+ ++ PP+PS+ L TD++ + E P+++PIS+ Sbjct: 181 MADQQGVPRENIRGTLQNDMFKEFIAQKEWVVPPEPSLDLVTDVLEFSTEETPQFHPISV 240 Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303 SGYHIREAG+ AVQE+AFTLADG YV+ +ERG+ VD+FAPRLSFFF HN+F EEIAK Sbjct: 241 SGYHIREAGSTAVQELAFTLADGFAYVEDAMERGLAVDEFAPRLSFFFNCHNSFFEEIAK 300 Query: 304 FRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGG 363 +RAARR++A +M EW++A+ S L+FHTQTAG +LTAQQP NN+VRV IQALA VLGG Sbjct: 301 YRAARRIYARVMDEWYDAQRDESKRLKFHTQTAGQSLTAQQPMNNVVRVTIQALAGVLGG 360 Query: 364 TQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEE 423 TQSLHTNS+DEAL+LP+E +VR+ALRTQQIIA ESG D VDP+GG++ +E LTD E Sbjct: 361 TQSLHTNSFDEALALPSEDAVRVALRTQQIIAEESGAADIVDPMGGSFAVEALTDETEER 420 Query: 424 ALKYIEKIQKMG------GMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTD 477 ++Y+ +I++MG G+++ I+ GY +EI +A+Y+YQ+ +E G+ ++VGVN F + Sbjct: 421 TMRYLTEIREMGEGSMRDGVLKGIDDGYFLREIQDASYEYQERVERGEEVVVGVNEFTLE 480 Query: 478 EPIEVEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAH 537 E E LK+D + E+Q+ERL++++++RD+ V++AL++L+ ++ EN +P ++EA Sbjct: 481 EDTSPETLKIDETTAERQLERLEQVKAQRDDAAVEDALEELQRTIDR-GENTIPVLVEAV 539 Query: 538 RHLATLQEVTDVLREIWGEY 557 + AT+ E+ V + G Y Sbjct: 540 KAYATVGEIMQVFEDEHGAY 559 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: 846 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: 566 Length adjustment: 36 Effective length of query: 527 Effective length of database: 530 Effective search space: 279310 Effective search space used: 279310 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