Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_097028688.1 CRO07_RS00240 methylmalonyl-CoA mutase
Query= SwissProt::Q3J4D7 (709 letters) >NCBI__GCF_900207575.1:WP_097028688.1 Length = 709 Score = 1324 bits (3426), Expect = 0.0 Identities = 671/709 (94%), Positives = 697/709 (98%) Query: 1 MTEDLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTR 60 MT+ L AW+KLAEKELKG+SPDSLTWNTLEGIPVKPLYTRAD+ G++HLDG+PGVAPFTR Sbjct: 1 MTDKLAAWQKLAEKELKGRSPDSLTWNTLEGIPVKPLYTRADIEGLDHLDGVPGVAPFTR 60 Query: 61 GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120 GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV Sbjct: 61 GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120 Query: 121 VGDVGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAAL 180 VGDVGKAGVAIDS+EDMKILF+GIPLEKISVSMTMNGAVIPILA+FIVTGEEQGVPRA L Sbjct: 121 VGDVGKAGVAIDSVEDMKILFDGIPLEKISVSMTMNGAVIPILASFIVTGEEQGVPRAEL 180 Query: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANL 240 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYT+KEMPKFNSISISGYHMQEAGANL Sbjct: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTAKEMPKFNSISISGYHMQEAGANL 240 Query: 241 VQELAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM 300 VQELAYTLADGREYVRAA+ARGMNVD+FAGRLSFFFAIGMNFFMEAAKLRAAR+LWHRIM Sbjct: 241 VQELAYTLADGREYVRAAIARGMNVDEFAGRLSFFFAIGMNFFMEAAKLRAARMLWHRIM 300 Query: 301 SEFAPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAI 360 SEF PKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEA++AALGGTQSLHTNALDEAI Sbjct: 301 SEFEPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEALAAALGGTQSLHTNALDEAI 360 Query: 361 ALPTEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGG 420 ALPTEFSARIARNTQ+ILQEETGVT+VVDPLAGSYYVESLT ELAEKAWALIEEVEAMGG Sbjct: 361 ALPTEFSARIARNTQLILQEETGVTKVVDPLAGSYYVESLTNELAEKAWALIEEVEAMGG 420 Query: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ Sbjct: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480 Query: 481 IARLEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540 IARLEKMRATRDEAACQ ALDELTRRA+EGGNLLEAAVDASRARASVGEISMAMEKVFGR Sbjct: 481 IARLEKMRATRDEAACQKALDELTRRASEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540 Query: 541 HRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600 HRAEVKTLSGVYGAAYEGDDGFA IQ+DVE+FAEEEGRRPRMLVVKMGQDGHDRGAKVIA Sbjct: 541 HRAEVKTLSGVYGAAYEGDDGFAAIQKDVETFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600 Query: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAG 660 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALK +GAG Sbjct: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKAQGAG 660 Query: 661 EILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709 +ILVICGGVIPQQDYDFL +GVKAIFGPGTNIPSAAK ILDLIR+AR+ Sbjct: 661 DILVICGGVIPQQDYDFLYNSGVKAIFGPGTNIPSAAKQILDLIRQARA 709 Lambda K H 0.318 0.133 0.377 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: 1586 Number of extensions: 42 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: 709 Length of database: 709 Length adjustment: 39 Effective length of query: 670 Effective length of database: 670 Effective search space: 448900 Effective search space used: 448900 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