Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate Ga0059261_3988 Ga0059261_3988 Methylmalonyl-CoA mutase, N-terminal domain/subunit
Query= SwissProt::Q3J4D7 (709 letters) >FitnessBrowser__Korea:Ga0059261_3988 Length = 712 Score = 974 bits (2518), Expect = 0.0 Identities = 498/700 (71%), Positives = 576/700 (82%), Gaps = 6/700 (0%) Query: 5 LDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRA 64 LDAW+ L+EKE+KG+ LTW T EGI VKPLYT D+ GLPG APFTRGVR Sbjct: 7 LDAWKALSEKEVKGRD---LTWRTPEGIDVKPLYTAEDVTADP---GLPGFAPFTRGVRG 60 Query: 65 TMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDV 124 +MYAGRPWTIRQYAGFSTAE SNAFYR+ LAAGQ+G+SVAFDLATHRGYDSDHPRV GDV Sbjct: 61 SMYAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVPGDV 120 Query: 125 GKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTI 184 GKAGVAIDS+EDMKILF+GIPL ++SVSMTMNGAVIPILA FIV GEEQGVPRA L GTI Sbjct: 121 GKAGVAIDSVEDMKILFDGIPLGEMSVSMTMNGAVIPILAFFIVAGEEQGVPRAQLDGTI 180 Query: 185 QNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQEL 244 QNDILKEFMVRNTYIYPPEPSMRII+DI YTS+EMPKFNSISISGYHMQEAGA VQEL Sbjct: 181 QNDILKEFMVRNTYIYPPEPSMRIISDIFGYTSREMPKFNSISISGYHMQEAGATQVQEL 240 Query: 245 AYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEFA 304 A+T+ADG EYV+ +A G+++D FAGRLSFFFAIGMNFFME AKLRAAR+LWHR+M++ Sbjct: 241 AFTIADGMEYVKYGVASGLDIDKFAGRLSFFFAIGMNFFMEVAKLRAARVLWHRVMTKLG 300 Query: 305 PKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPT 364 K S MLRTHCQTSGVSL EQDPYNNVIRT EAM+A LGGTQSLHTNALDEAIALPT Sbjct: 301 AKDERSKMLRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAMLGGTQSLHTNALDEAIALPT 360 Query: 365 EFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKA 424 +FSARIARNTQI++QEETG+T+VVDPL GSYYVE+LT EL +KAW +IE VEA GGM KA Sbjct: 361 DFSARIARNTQIVIQEETGMTKVVDPLGGSYYVEALTQELVDKAWEIIERVEAEGGMAKA 420 Query: 425 VASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARL 484 VA+G PK IEE++A A IDRGE VIVGVNKYR A+EDPI+ILD+DN AVR+AQIAR+ Sbjct: 421 VAAGWPKAMIEEASAATAARIDRGEQVIVGVNKYRKAEEDPIDILDVDNHAVREAQIARI 480 Query: 485 EKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGRHRAE 544 +K+++ RDEA CQAALD L A NLL AV+A+R RA++GEIS+AME VFGRH Sbjct: 481 KKVKSARDEAKCQAALDALREGARGTENLLALAVEAARHRATLGEISLAMEDVFGRHGTV 540 Query: 545 VKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFA 604 +SGVYG AY D + +++ V + GR+PRMLV KMGQDGHDRGA ++++AF Sbjct: 541 PTPVSGVYGGAYAEDRRWERLKDGVAATERRLGRKPRMLVAKMGQDGHDRGANLVSSAFG 600 Query: 605 DIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEILV 664 D+GF+V G LFQTP+EAA+ AI +V VVG SSLAAGHKTL P++I LK+ G G+I V Sbjct: 601 DLGFEVVPGPLFQTPQEAAELAIAENVDVVGASSLAAGHKTLIPQMIGHLKDAGRGDIKV 660 Query: 665 ICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLI 704 I GGVIP QDY FL+ AGV+AIFGPGTN+ +AA +L L+ Sbjct: 661 IAGGVIPAQDYQFLRDAGVQAIFGPGTNLVNAAADVLTLL 700 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: 1377 Number of extensions: 52 Number of successful extensions: 3 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