Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_075618392.1 GY23_RS06385 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_001939075.1:WP_075618392.1 Length = 1086 Score = 308 bits (789), Expect = 7e-88 Identities = 208/552 (37%), Positives = 309/552 (55%), Gaps = 43/552 (7%) Query: 43 GFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEE 100 G +I R+ P D GE ++ K PG +PFT GV+ G RQ+AG T E Sbjct: 539 GLKIPRVVLPKFVDYGEILRWVYKENVPGSFPFTAGVFPFKREGED-PKRQFAGEGTPER 597 Query: 101 SNKRYKYLLSQGQTG-LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDG 158 +N+R+ YL LS AFD T G D D P G+VG+ GV+I +L DM+ L+DG Sbjct: 598 TNRRFHYLSKDDNAKRLSTAFDSVTLYGEDPDTRPDIYGKVGESGVSICTLDDMKKLYDG 657 Query: 159 IPLDKVSTS--MTINSTAANLLAMYILVAEEQGV--SQEKL------------------- 195 L STS MTIN A +LAM++ A +Q V ++EKL Sbjct: 658 FNLCAPSTSVSMTINGPAPIILAMFMNTAIDQQVKINEEKLGRTLTVEEFSEVRETTMQV 717 Query: 196 -RGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGA 253 RGTVQ DILKE + T IF + ++R+ DI Y + V + +SISGYHI EAGA Sbjct: 718 VRGTVQADILKEDQGQNTCIFSTEFALRMMGDIQQYFIDTKVRNYYSVSISGYHIAEAGA 777 Query: 254 NAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWA 312 N + ++AFTL++G YV+ + RGM++D FAP LSFFF+ N E R ARR+WA Sbjct: 778 NPISQLAFTLSNGFTYVEYYLSRGMNIDDFAPNLSFFFS--NGLDPEYTVIGRVARRIWA 835 Query: 313 YIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSY 372 +M++ + A N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLHTN+Y Sbjct: 836 VVMRDKYGA-NDRSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALMALQDNCNSLHTNAY 894 Query: 373 DEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQ 432 DEA++ PTE+SVR A+ Q II E G+ +PL GA+ +E +TD + E L ++I Sbjct: 895 DEAITTPTEESVRRAMAIQMIITKEHGLSKNENPLQGAFIVEEMTDLVEEAVLSEFDRIN 954 Query: 433 KMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP------IEVEILK 486 GG++ A+E Y + +I E + Y+ G+ I+GVN ++ P +EI + Sbjct: 955 DRGGVLGAMETQYQRGKIQEESMHYEMLKHTGQLPIIGVNTYLNPNPPSAEDVDNMEIAR 1014 Query: 487 VDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEV 546 +E QI L+ + ER++ + + AL +L+ A N+ +++ + +A+L ++ Sbjct: 1015 ATIEEKESQILNLRAFQ-ERNSAESEAALKRLKEVA-VTGGNIFEQLMDTVK-VASLGQI 1071 Query: 547 TDVLREIWGEYR 558 T+ L E+ G+YR Sbjct: 1072 TNALYEVGGQYR 1083 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: 1278 Number of extensions: 69 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: 1086 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1045 Effective search space: 545490 Effective search space used: 545490 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