Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_065401015.1 BBI00_RS21385 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_001684965.1:WP_065401015.1 Length = 707 Score = 857 bits (2214), Expect = 0.0 Identities = 430/672 (63%), Positives = 528/672 (78%), Gaps = 6/672 (0%) Query: 56 KDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSV 115 KD T GI P++ GPY+TMY +PWTIRQYAGFSTA+ESNAFYRRNLAAGQKGLSV Sbjct: 41 KDESLTQTSPGIEPYLRGPYSTMYVQKPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSV 100 Query: 116 AFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPIL 175 AFDL THRGYDSD+ RV GDVG AGVAIDS+ DM+ LF IPLDQ+SVSMTMNGAVLPIL Sbjct: 101 AFDLATHRGYDSDHSRVVGDVGKAGVAIDSVEDMKILFNEIPLDQISVSMTMNGAVLPIL 160 Query: 176 ALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKW 235 + Y+V AEEQGVK EQL+GTIQNDILKEFMVRNTYIYPP PSM+II++IF YTS N+PK+ Sbjct: 161 SFYIVAAEEQGVKQEQLSGTIQNDILKEFMVRNTYIYPPAPSMKIIADIFEYTSQNIPKF 220 Query: 236 NSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFF 295 NSISISGYHMQEAGAT +EMAYTLADG++Y+R G G+NVD FAPRLSFFW IGMN F Sbjct: 221 NSISISGYHMQEAGATPVLEMAYTLADGLEYVRTGIKAGMNVDDFAPRLSFFWAIGMNHF 280 Query: 296 MEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAA 355 ME+AK+RAAR +WA L+ QF P+NPKS++LRTHSQTSGWSLT Q+ +NN+ RT IEA+++ Sbjct: 281 MEIAKMRAARYIWANLLKQFNPQNPKSLALRTHSQTSGWSLTEQEPFNNITRTAIEALSS 340 Query: 356 TQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWD 415 G TQSLHTN+LDEAIALPTD+SA+IARNTQ+ LQQESG V+DP GS VE LT Sbjct: 341 ALGGTQSLHTNALDEAIALPTDYSAKIARNTQIILQQESGICDVVDPMGGSNLVESLTQQ 400 Query: 416 LARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLE-H 474 + +A +I EVE+ GGM KAIE GIPKMRIEEAAA+ QA+IDSG + +IGVN ++ Sbjct: 401 MIEEAMRYIDEVEQEGGMTKAIEAGIPKMRIEEAAAKKQAKIDSGEEFIIGVNSFKSSLK 460 Query: 475 EPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKL 534 + +++L +DN+ V +Q +L ++AER+ E V L+ I +A K NLL L Sbjct: 461 QDAIEILDIDNTEVRRKQIERLNNIKAERNSEAVTQILNDIRESA-----KTGKGNLLAL 515 Query: 535 CIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAE 594 CI+A R T+GEMSDA+E+ FGRY A I+TISGVY+ E+A L ++FE+ E Sbjct: 516 CIEAARRRVTLGEMSDAMEETFGRYKANIKTISGVYAMNAGKNEYFEKALHLTQKFEEEE 575 Query: 595 GRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGV 654 GRRPRI++AKMGQDGHDRG KV+ATA+AD+GFDVDV PLFQTPEE A+QA+E D+H++GV Sbjct: 576 GRRPRIMVAKMGQDGHDRGAKVVATAFADMGFDVDVAPLFQTPEEVAKQAIENDIHILGV 635 Query: 655 SSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPES 714 SSLA GH TLVP + +EL KLG DI I VGGVIP+QD++ L +GA I+ PGT +P+ Sbjct: 636 SSLAAGHKTLVPQVVEELSKLGADDITIVVGGVIPQQDYEFLYANGADFIFGPGTNLPKC 695 Query: 715 AISLVKKLRASL 726 A+ ++++L A + Sbjct: 696 AVEILERLLAKI 707 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: 1272 Number of extensions: 38 Number of successful extensions: 3 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: 707 Length adjustment: 40 Effective length of query: 688 Effective length of database: 667 Effective search space: 458896 Effective search space used: 458896 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