Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Dsui_0519 Dsui_0519 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__PS:Dsui_0519 Length = 721 Score = 861 bits (2225), Expect = 0.0 Identities = 442/723 (61%), Positives = 546/723 (75%), Gaps = 11/723 (1%) Query: 9 SVDLGNAPVP-ADAARRFEELAAKAGTGEA-----WETAEQIPVGTLFNEDVYKDMDWLD 62 S D +P +D + + AAK+ G W T E + V L+ + +D+ + D Sbjct: 2 SADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYAD 61 Query: 63 TYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTH 122 T G P++ GP ATMYA RPWTIRQYAGFSTA+ESNAFYR+ LAAG +G+SVAFDL TH Sbjct: 62 TLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATH 121 Query: 123 RGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTA 182 RGYDSDNPRV GDVG AGVAIDS+ DM+ LF GIPLD++SVSMTMNGAVLPILA Y+V A Sbjct: 122 RGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAA 181 Query: 183 EEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISG 242 EEQGV EQL+GTIQNDILKEFMVRNTYIYPP+PSM+IIS+IF YT+ +MPK+NSISISG Sbjct: 182 EEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISG 241 Query: 243 YHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLR 302 YH+QEAGA IE+A+TLADG++Y+R G + GL+VD FA RLSFFW +GMNF++E+AK+R Sbjct: 242 YHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMR 301 Query: 303 AARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQS 362 A RMLW +++ QF PK+ KS+ LRTHSQTSGWSLT QD YNNVVRT IEAMAA G TQS Sbjct: 302 AGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQS 361 Query: 363 LHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWG 422 LHTN+LDEAIALPT+FSARIARNTQL +Q+E+ V+DPW+GS +E+LT D+A KAW Sbjct: 362 LHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWS 421 Query: 423 HIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLK 482 IQE+E +GGM KA+E G KM++E AA QARIDSG+ ++GVNKY+L E +D+L Sbjct: 422 IIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILD 481 Query: 483 VDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAM 542 +DN V Q A+L K+RA RD V+AALD +T A + + NLL L + A R Sbjct: 482 IDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCA-----ESGEGNLLDLSVKAIRLR 536 Query: 543 ATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILL 602 ATVGE+SDALEKVFGR+ A +TISGVY V+ E + + +F + EGRRPRI++ Sbjct: 537 ATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMI 596 Query: 603 AKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHL 662 AK+GQDGHDRG KV+ATA+ADLGFD+D+GPLFQTPEE ARQAVE DVH +GVSSLA GH Sbjct: 597 AKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHK 656 Query: 663 TLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722 TL+PAL L + G DI++ GGVIP QD+D L GA I+ PGT I +SA +++++ Sbjct: 657 TLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEI 716 Query: 723 RAS 725 R S Sbjct: 717 RKS 719 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: 1361 Number of extensions: 47 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: 721 Length adjustment: 40 Effective length of query: 688 Effective length of database: 681 Effective search space: 468528 Effective search space used: 468528 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 17 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