Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011840653.1 RSPH17029_RS04415 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_000015985.1:WP_011840653.1 Length = 709 Score = 833 bits (2153), Expect = 0.0 Identities = 431/706 (61%), Positives = 528/706 (74%), Gaps = 8/706 (1%) Query: 20 DAARRF--EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYAT 77 DA R+ +EL K+ W T E IPV L+ M+ LD G+ PF G AT Sbjct: 6 DAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRAT 65 Query: 78 MYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVG 137 MYA RPWTIRQYAGFSTA+ SNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG Sbjct: 66 MYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVG 125 Query: 138 MAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQ 197 AGVAIDSI DM+ LF GIPL+++SVSMTMNGAV+PILA ++VT EEQGV L+GTIQ Sbjct: 126 KAGVAIDSIEDMKILFDGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTIQ 185 Query: 198 NDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMA 257 NDILKEFMVRNTYIYPP+PSMRII++I YTS MPK+NSISISGYHMQEAGA E+A Sbjct: 186 NDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQELA 245 Query: 258 YTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGP 317 YTLADG +Y+RA + G+NVD FA RLSFF+ IGMNFFME AKLRAAR+LW +++ +F P Sbjct: 246 YTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEFAP 305 Query: 318 KNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTD 377 K P S+ LRTH QTSG SL QD YNNV+RT EAM+A G TQSLHTN+LDEAIALPT+ Sbjct: 306 KKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPTE 365 Query: 378 FSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAI 437 FSARIARNTQ+ LQ+E+G TRV+DP +GS YVE LT +LA KAW I+EVE +GGM KA+ Sbjct: 366 FSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKAV 425 Query: 438 EKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLV 497 G+PK+RIEE+AAR QA ID G ++GVNKYRL E P+++L +DN V Q A+L Sbjct: 426 ASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLK 485 Query: 498 KLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFG 557 K+RA RD +AALD++T A NLL+ +DA RA A+VGE+S A+EKVFG Sbjct: 486 KMRATRDEAACQAALDELTRRAAE------GGNLLEAAVDASRARASVGEISMAMEKVFG 539 Query: 558 RYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVI 617 R+ A+++T+SGVY + + + VE F + EGRRPR+L+ KMGQDGHDRG KVI Sbjct: 540 RHRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVI 599 Query: 618 ATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGR 677 ATA+AD+GFDVDVG LFQTPEE A+ A++ DVHVVG+SSLA GH TL P L + L + G Sbjct: 600 ATAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGA 659 Query: 678 PDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723 +IL+ GGVIP+QD+D L++ G I+ PGT IP +A ++ +R Sbjct: 660 GEILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIR 705 Lambda K H 0.317 0.133 0.389 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: 1311 Number of extensions: 44 Number of successful extensions: 2 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: 728 Length of database: 709 Length adjustment: 40 Effective length of query: 688 Effective length of database: 669 Effective search space: 460272 Effective search space used: 460272 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 Apr 10 2024. 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