Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_046008375.1 OLEAN_RS05325 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_000967895.1:WP_046008375.1 Length = 720 Score = 873 bits (2255), Expect = 0.0 Identities = 434/688 (63%), Positives = 539/688 (78%), Gaps = 5/688 (0%) Query: 38 WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97 W T E +P+ L+ +D KD+++ +T G+ P+V GP ATMYA RPWTIRQYAGFSTA+E Sbjct: 30 WHTPEGVPIKVLYTQDDVKDLEFTNTMPGLAPYVRGPQATMYAGRPWTIRQYAGFSTAEE 89 Query: 98 SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157 SNAFYR+NLAAG +G+SVAFDL THRGYDSD+PRV+GDVG AGVAIDS+ DM+ LF IP Sbjct: 90 SNAFYRKNLAAGAQGVSVAFDLATHRGYDSDHPRVSGDVGKAGVAIDSVEDMKILFNEIP 149 Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217 LD++SVSMTMNGAVLPILA Y+V AEEQGV ++L+GTIQNDILKEFMVRNTYIYPP PS Sbjct: 150 LDKVSVSMTMNGAVLPILANYIVAAEEQGVSQDKLSGTIQNDILKEFMVRNTYIYPPTPS 209 Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277 MRII +I AYTS NMPK+NSISISGYH+QEAGA A +E+AYTL+DG +Y+R + GL+V Sbjct: 210 MRIIGDIIAYTSGNMPKYNSISISGYHIQEAGADAALELAYTLSDGREYVRTALAAGLDV 269 Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337 D FAPRLSFFWGI MNF+ME+AKLRA R+LW +++ +F PKNPKS LRTHSQTSGWSLT Sbjct: 270 DAFAPRLSFFWGISMNFYMEIAKLRAGRLLWNRIMAEFKPKNPKSSMLRTHSQTSGWSLT 329 Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397 QD YNNVVRT IEAMAA G TQSLHTN+LDEA+ALPT+FSARIARNTQ+ +Q+E+G T Sbjct: 330 EQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAVALPTEFSARIARNTQIIIQEETGIT 389 Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457 +V+DPW GS +E LT +A KAW I+E+E+ GGMAKAIE+G+PK+RIEE+AAR QARI Sbjct: 390 QVVDPWGGSYMMESLTQQMADKAWALIEEIEEKGGMAKAIEEGLPKLRIEESAARKQARI 449 Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517 D G ++GVNK++L E LD+L+VDN V Q +L ++++ RD E V AAL IT Sbjct: 450 DRGEDVIVGVNKHQLNEEADLDILEVDNVAVRESQIKRLTEIKSTRDNEAVNAALSAITA 509 Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577 AA K + NLL L + A R ATVGE+SDA+E+ FGRY A+ RTISGVY ++ Sbjct: 510 AA-----KTGEGNLLDLSVKAARLRATVGEISDAMEEEFGRYKAEARTISGVYGASYEDD 564 Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637 + + + +E FE +GRRPR+L+ KMGQDGHDRG KVIATA+AD+GFD+D+ P+F TP Sbjct: 565 ADWQTIKSDIESFETEQGRRPRMLVCKMGQDGHDRGAKVIATAFADVGFDIDLSPMFSTP 624 Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697 EE A+QAVE DVHVVGVSS A GH TL+P+L L G DI++ GGVIP+QD+D L Sbjct: 625 EEVAKQAVENDVHVVGVSSQAAGHKTLIPSLIAALKAQGADDIIVVAGGVIPKQDYDYLW 684 Query: 698 KDGAVEIYTPGTVIPESAISLVKKLRAS 725 G I+ PGT IP SA ++++ ++A+ Sbjct: 685 DAGVKGIFGPGTKIPISARAVLEAIKAA 712 Lambda K H 0.317 0.133 0.389 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: 1348 Number of extensions: 53 Number of successful extensions: 2 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: 728 Length of database: 720 Length adjustment: 40 Effective length of query: 688 Effective length of database: 680 Effective search space: 467840 Effective search space used: 467840 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