Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Dsui_0519 Dsui_0519 methylmalonyl-CoA mutase
Query= reanno::PS:Dsui_0519 (721 letters) >FitnessBrowser__PS:Dsui_0519 Length = 721 Score = 1419 bits (3672), Expect = 0.0 Identities = 721/721 (100%), Positives = 721/721 (100%) Query: 1 MSADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYA 60 MSADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYA Sbjct: 1 MSADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYA 60 Query: 61 DTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLAT 120 DTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLAT Sbjct: 61 DTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLAT 120 Query: 121 HRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVA 180 HRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVA Sbjct: 121 HRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVA 180 Query: 181 AEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISIS 240 AEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISIS Sbjct: 181 AEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISIS 240 Query: 241 GYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKM 300 GYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKM Sbjct: 241 GYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKM 300 Query: 301 RAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQ 360 RAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQ Sbjct: 301 RAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQ 360 Query: 361 SLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAW 420 SLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAW Sbjct: 361 SLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAW 420 Query: 421 SIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDIL 480 SIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDIL Sbjct: 421 SIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDIL 480 Query: 481 DIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVG 540 DIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVG Sbjct: 481 DIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVG 540 Query: 541 EVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLG 600 EVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLG Sbjct: 541 EVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLG 600 Query: 601 QDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLP 660 QDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLP Sbjct: 601 QDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLP 660 Query: 661 ALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR 720 ALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR Sbjct: 661 ALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR 720 Query: 721 G 721 G Sbjct: 721 G 721 Lambda K H 0.317 0.132 0.380 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: 1662 Number of extensions: 58 Number of successful extensions: 1 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: 721 Length of database: 721 Length adjustment: 40 Effective length of query: 681 Effective length of database: 681 Effective search space: 463761 Effective search space used: 463761 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 (21.6 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