Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_036834456.1 N784_RS09590 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000775615.1:WP_036834456.1 Length = 1079 Score = 310 bits (794), Expect = 2e-88 Identities = 208/552 (37%), Positives = 313/552 (56%), Gaps = 43/552 (7%) Query: 43 GFEIKRIYTPA--DLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEE 100 G +I ++ P D G+ ++ + PG +PFT GV+ +G T RQ+AG T + Sbjct: 532 GLQIPKVALPTYHDWGDRLLWVLRENIPGAFPFTAGVFPFKRKGEDPT-RQFAGEGTPDR 590 Query: 101 SNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRILFD 157 +N+R+ YL S+G+ LS AFD T G D D P G+VG+ GV+I +L DM+ L+ Sbjct: 591 TNRRFHYL-SEGEAAKRLSTAFDSVTLYGEDPDERPDIYGKVGESGVSICTLDDMQKLYA 649 Query: 158 GIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQEK--------------------- 194 G L S SMTIN A +LAM+ A +Q + K Sbjct: 650 GFDLCHPTTSVSMTINGPAPIILAMFFNTAIDQQIEMFKKQEGREPNQEERDRIKAETIS 709 Query: 195 -LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAG 252 +RGTVQ DILKE + T IF + ++R+ DI Y ++ V + +SISGYHI EAG Sbjct: 710 VVRGTVQADILKEDQGQNTCIFSTEFALRMMGDIQQYFIDHDVKNYYSVSISGYHIAEAG 769 Query: 253 ANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLW 311 AN + ++AFTLA+G YV+ + RGMD++KFAP LSFFF+ N E R ARR+W Sbjct: 770 ANPITQLAFTLANGFTYVEYYLSRGMDINKFAPNLSFFFS--NGLDPEYTVIGRVARRIW 827 Query: 312 AYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNS 371 A +M++ + A N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLHTNS Sbjct: 828 AIVMRDKYGA-NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALLAIQDNCNSLHTNS 886 Query: 372 YDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKI 431 YDEA++ PTE+SVR A+ Q II E G+ + L G++ +E LT + E L+ E++ Sbjct: 887 YDEAITTPTEESVRRAMAIQMIINKEFGLTKNENSLQGSFIVEELTHLVEEAVLQEFERM 946 Query: 432 QKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSI 491 GG++ A+ER Y + +I E + Y+ + G I+GVN ++ P E + Sbjct: 947 NDRGGVLGAMERQYQRGKIQEESLYYEGKKHSGDLPIIGVNTYLNPNPPSEEDIDSMELA 1006 Query: 492 REKQIERLKKLRSERD----NKKVQE-ALDKLRNAAEKEDENLMPYIIEAHRHLATLQEV 546 R Q E++ ++ S RD N +V E AL +L+ A K++ N+ ++E + +A+L ++ Sbjct: 1007 RASQEEKMHQIHSLRDFQERNAQVTENALQRLKQVA-KQNGNIFAELMETVK-VASLGQI 1064 Query: 547 TDVLREIWGEYR 558 T+ L E+ G+YR Sbjct: 1065 TNALYEVGGQYR 1076 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: 1195 Number of extensions: 62 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: 1079 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1038 Effective search space: 541836 Effective search space used: 541836 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