Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate GFF2118 PGA1_c21510 methylmalonyl-CoA mutase BhbA
Query= SwissProt::Q3J4D7 (709 letters) >FitnessBrowser__Phaeo:GFF2118 Length = 707 Score = 1170 bits (3026), Expect = 0.0 Identities = 590/707 (83%), Positives = 641/707 (90%) Query: 1 MTEDLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTR 60 MT D WR LAEKEL+G+ D+LTWNTLEGI VKPLYT AD + H+ +PG PFTR Sbjct: 1 MTTKTDDWRALAEKELRGRPLDALTWNTLEGIDVKPLYTEADTKDLPHMGTMPGFGPFTR 60 Query: 61 GVRATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRV 120 GV+ATMYAGRPWTIRQYAGFSTAE SNAFYR+ LAAGQQGVSVAFDLATHRGYDSDHPRV Sbjct: 61 GVKATMYAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRV 120 Query: 121 VGDVGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAAL 180 +GDVGKAGVAIDS+EDMKILF+GIPL+++SVSMTMNGAVIPILA+FIV GEEQG ++ L Sbjct: 121 MGDVGKAGVAIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILASFIVAGEEQGHDKSLL 180 Query: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANL 240 +GTIQNDILKEFMVRNTYIYPPEPSMRII+DIIEYTS EMPKFNSISISGYHMQEAGANL Sbjct: 181 AGTIQNDILKEFMVRNTYIYPPEPSMRIISDIIEYTSNEMPKFNSISISGYHMQEAGANL 240 Query: 241 VQELAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM 300 VQELAYTLADGREYVRAA+ GM+VD FAGRLSFFFAIGMNFFME AKLRAAR LWHR+M Sbjct: 241 VQELAYTLADGREYVRAAMEAGMDVDKFAGRLSFFFAIGMNFFMEIAKLRAARTLWHRVM 300 Query: 301 SEFAPKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAI 360 ++F K S MLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSA LGGTQSLHTNALDEAI Sbjct: 301 TDFDAKNDRSKMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAI 360 Query: 361 ALPTEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGG 420 ALPT+FSARIARNTQ++LQEETGVT VVDPLAGSYYVESLT EL EKAWAL+EEVE MGG Sbjct: 361 ALPTDFSARIARNTQLVLQEETGVTNVVDPLAGSYYVESLTNELIEKAWALMEEVEEMGG 420 Query: 421 MTKAVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQ 480 MTKAVASGMPKLRIEESAARRQA IDRGE+VIVGVNKYR KEDPI+ILD+DNVAVRD+Q Sbjct: 421 MTKAVASGMPKLRIEESAARRQAMIDRGEEVIVGVNKYRKEKEDPIDILDVDNVAVRDSQ 480 Query: 481 IARLEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGR 540 IARLE +RA RD AAC+AALD LTR A EGGNLL AAV+A+RARASVGEISMAMEK FGR Sbjct: 481 IARLETLRADRDSAACEAALDNLTRVAKEGGNLLAAAVEAARARASVGEISMAMEKEFGR 540 Query: 541 HRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIA 600 H AEVKTL+GVYGAAYEGD+GFA IQ+ +E FAE EGRRPR+LVVKMGQDGHDRGAKVIA Sbjct: 541 HSAEVKTLAGVYGAAYEGDEGFAAIQKSIEDFAEAEGRRPRLLVVKMGQDGHDRGAKVIA 600 Query: 601 TAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAG 660 TAFADIGFDVDVG LFQTP+EAAQDAIDNDVHVVGISS AAGHKTLAP+L++ALKE+GA Sbjct: 601 TAFADIGFDVDVGPLFQTPDEAAQDAIDNDVHVVGISSQAAGHKTLAPQLVKALKEQGAE 660 Query: 661 EILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREA 707 +I+VICGGVIPQQDY FL GVKAIFGPGTNIP AA+ IL LIR++ Sbjct: 661 DIIVICGGVIPQQDYQFLYDNGVKAIFGPGTNIPEAAQDILKLIRQS 707 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: 1448 Number of extensions: 36 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: 707 Length adjustment: 39 Effective length of query: 670 Effective length of database: 668 Effective search space: 447560 Effective search space used: 447560 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