Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate 3607311 Dshi_0726 methylmalonyl-CoA mutase, large subunit (RefSeq)
Query= SwissProt::Q3J4D7 (709 letters) >FitnessBrowser__Dino:3607311 Length = 712 Score = 1201 bits (3107), Expect = 0.0 Identities = 608/709 (85%), Positives = 652/709 (91%) Query: 1 MTEDLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTR 60 MT+ DAW LA KEL+GK ++LTW TLEGI VKPLYT DL G++HL +PG APFTR Sbjct: 1 MTKGKDAWADLAAKELRGKPLETLTWKTLEGIDVKPLYTAEDLEGLDHLGSVPGQAPFTR 60 Query: 61 GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120 GV+ATMYAGRPWTIRQYAGFSTAE SNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV Sbjct: 61 GVKATMYAGRPWTIRQYAGFSTAEESNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120 Query: 121 VGDVGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAAL 180 GDVGKAGVAIDS+EDMKILF+GIPL+++SVSMTMNGAVIPILANFIVTGEEQG R+ L Sbjct: 121 EGDVGKAGVAIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILANFIVTGEEQGHDRSVL 180 Query: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANL 240 SGTIQNDILKEFMVRNTY+YPPEPSMRIIADIIEYTS EMPKFNSISISGYHMQEAGANL Sbjct: 181 SGTIQNDILKEFMVRNTYVYPPEPSMRIIADIIEYTSAEMPKFNSISISGYHMQEAGANL 240 Query: 241 VQELAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM 300 VQELA+TLADGREYVRAA+ARGM+VD FAGRLSFFFAIGMNFFMEAAKLRAAR+LWH+IM Sbjct: 241 VQELAFTLADGREYVRAAIARGMDVDKFAGRLSFFFAIGMNFFMEAAKLRAARMLWHKIM 300 Query: 301 SEFAPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAI 360 SEF PK P S+MLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSA LGGTQSLHTNALDEAI Sbjct: 301 SEFEPKNPRSMMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAI 360 Query: 361 ALPTEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGG 420 ALPTEFSARIARNTQ+ILQEETGVT VVDPLAGSYYVESLT ELAEKAWALIEEVE +GG Sbjct: 361 ALPTEFSARIARNTQLILQEETGVTNVVDPLAGSYYVESLTNELAEKAWALIEEVEELGG 420 Query: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480 MTKAVASGMPKLRIEESAARRQA ID+G +VIVGVNKYR KEDPI+IL+IDN VRD Q Sbjct: 421 MTKAVASGMPKLRIEESAARRQAMIDKGTEVIVGVNKYRKDKEDPIDILEIDNAKVRDGQ 480 Query: 481 IARLEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540 +ARL K+RA RDEAAC +AL E+ R AAEGGNLL AAV+A+RARASVGEISMAMEKVFGR Sbjct: 481 VARLAKIRAERDEAACDSALAEVERCAAEGGNLLAAAVEAARARASVGEISMAMEKVFGR 540 Query: 541 HRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600 HRAEVKTL+GVYGAAYEGDDGFA IQ+ VE FA EEGRRPRMLVVKMGQDGHDRGAKVIA Sbjct: 541 HRAEVKTLAGVYGAAYEGDDGFAAIQKSVEDFAAEEGRRPRMLVVKMGQDGHDRGAKVIA 600 Query: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAG 660 TAFADIGFDVDVG LFQTPEEAAQDAIDNDVHV+GISS AAGHKTLAPKL++ALK +GAG Sbjct: 601 TAFADIGFDVDVGPLFQTPEEAAQDAIDNDVHVIGISSQAAGHKTLAPKLVDALKAQGAG 660 Query: 661 EILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709 +ILVICGGVIPQQDY +L GVKAIFGPGTNIP AA+ IL LIRE+R+ Sbjct: 661 DILVICGGVIPQQDYQYLYDRGVKAIFGPGTNIPEAAQDILRLIRESRA 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: 1496 Number of extensions: 37 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: 712 Length adjustment: 39 Effective length of query: 670 Effective length of database: 673 Effective search space: 450910 Effective search space used: 450910 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