Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_084456535.1 G494_RS0107590 hypothetical protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000429965.1:WP_084456535.1 Length = 1048 Score = 273 bits (697), Expect = 3e-77 Identities = 192/584 (32%), Positives = 305/584 (52%), Gaps = 48/584 (8%) Query: 17 KRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFT 74 K+W T + + + T +G+ + R+ P AD E ++ + G PG +P+ Sbjct: 468 KQWPATWQRLTGSQGAGEEGLITTANGYRLPRLGLPDPADRVESLRFLLEEGLPGVFPYA 527 Query: 75 RGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSD- 131 G+Y T RQ+AG E+N+R +L ++G LS+AFD T G DSD Sbjct: 528 TGIYPWRLPAAGKTTRQFAGLRGPGETNERLHFL-NRGIANPRLSIAFDGITLYGEDSDG 586 Query: 132 HPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVA------ 185 P + G++G+ GVA+DS DM+++ G + K+STSMTIN A +LAMY + A Sbjct: 587 DPGSRGKIGEGGVAVDSYEDMKLILKGFDVRKISTSMTINGPAPVILAMYFVAALELEEE 646 Query: 186 -----------EEQGVSQEK-----LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIM 229 E+G E LRGTVQ DILKE A+ IF +MR+ D+ Sbjct: 647 RLTAELGRALSPEEGAQLETETFTGLRGTVQADILKEVQAQNECIFAIDFAMRMVGDVQR 706 Query: 230 YCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLS 288 Y ++ + + +SISGYHI EAGA QE+AFTLA+G YV+ ++R M ++ FAP LS Sbjct: 707 YFIDHRINSFYSLSISGYHIGEAGATPAQELAFTLANGFTYVEYFLKRQMAINAFAPSLS 766 Query: 289 FFFAAHNNFLEEIAKFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPEN- 347 FFF + E +A R++WA +++ + A + RS +FHTQT+G L AQ+ + Sbjct: 767 FFFRVSHE-AEWLAYGPVCRKIWAIALRDRYGA-DSRSQRFKFHTQTSGRALQAQEWDTL 824 Query: 348 NIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPL 407 N +R A +L T SLH +S DE ++ P++K VR A + E+ + L Sbjct: 825 NPIRQTYHAYLGLLNNTNSLHIDSADEPMTTPSQKYVRQAAMIPNYLQEEAEAFAIQNLL 884 Query: 408 GGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKE------- 460 G+Y + + LK E+I ++GG+ A E GY + I E++ +Y++E Sbjct: 885 SGSYGFRAMARQLQAAILKEFERIDQLGGVAAATELGYQRNSIGESSARYEQERVPDPLS 944 Query: 461 IEEGKRIIVGVNAFVTDEPIEVEILKVDPSIR------EKQIERLKKLRSERDNKKVQEA 514 ++ +R I+G N ++ ++ E+ V +R ++QI R++ RS R ++ + A Sbjct: 945 MDLARRKIIGFNTYL-QPLVDQELPSVPQLVRPTQADWDRQISRVRDFRS-RHQQQAEAA 1002 Query: 515 LDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558 L +L A +D N+ ++ R ATL +++ LR++ G YR Sbjct: 1003 LQRLEAVAASDDGNIFAELLRTVR-CATLGQISARLRKVGGSYR 1045 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: 1162 Number of extensions: 51 Number of successful extensions: 8 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: 1048 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1007 Effective search space: 525654 Effective search space used: 525654 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: 55 (25.8 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