Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate SM_b20757 SM_b20757 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Smeli:SM_b20757 Length = 712 Score = 799 bits (2063), Expect = 0.0 Identities = 402/681 (59%), Positives = 505/681 (74%), Gaps = 5/681 (0%) Query: 35 GEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFST 94 G W T E I V L+ D + L++ G PFV GP ATMYA RPWT+RQYAGFST Sbjct: 23 GLVWHTPEGIDVKPLYTSDDMSGIGHLNSLPGFEPFVRGPRATMYAGRPWTVRQYAGFST 82 Query: 95 AKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFA 154 A+ SNAFYRRNLAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF Sbjct: 83 AEASNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVEDMKILFD 142 Query: 155 GIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPP 214 GIPLD++SVSMTMNGAV+PILA ++V EEQGV ++L+GTIQNDILKEFMVRNTYIYPP Sbjct: 143 GIPLDRISVSMTMNGAVIPILASFIVAGEEQGVSRDKLSGTIQNDILKEFMVRNTYIYPP 202 Query: 215 QPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVG 274 +PSMRI+++I YT+ MPK+NSISISGYHMQEAGAT E+A+TLADG +Y+RA + G Sbjct: 203 EPSMRIVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAALAKG 262 Query: 275 LNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGW 334 LNVD FA RLSFF+ IGMNFFME AKLRAAR+LW +++ +F P+ S+ LRTH QTSG Sbjct: 263 LNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMQEFKPEKASSLMLRTHCQTSGV 322 Query: 335 SLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQES 394 SL QD YNN+VRT EAM+A G TQSLHTNS DEA+ALPTDFSARIARNTQL LQ E+ Sbjct: 323 SLQEQDPYNNIVRTAFEAMSAVLGGTQSLHTNSFDEAMALPTDFSARIARNTQLILQHET 382 Query: 395 GTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQ 454 G T+V+DP +GS YVE LT +LA KAWG I+EVE +GGM KA+ G+PK IEEAA R Q Sbjct: 383 GVTKVVDPLAGSYYVESLTNELAEKAWGLIEEVEALGGMTKAVNAGLPKRLIEEAATRRQ 442 Query: 455 ARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDK 514 A +D + ++GVNKYRLE+E P+D+L++DN+ V Q ++ + R RD +K+K ALD Sbjct: 443 AAVDRAEEVIVGVNKYRLENEQPIDILQIDNAAVRTAQVKRIEETRRRRDSQKMKQALDA 502 Query: 515 ITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEV 574 + A + NLL ++A RA ATVGE++DA+ + FG YTA ++ +Y K Sbjct: 503 LADVA-----RSGKGNLLAAAVEAARARATVGEITDAMREAFGDYTAIPEVVTDIYGKAY 557 Query: 575 KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLF 634 + PE+ + E + G +P+I++AK+GQDGHDRG KVIA+A+ D+GFDV GPLF Sbjct: 558 EGDPELGVLAGRLGEATKRLGHKPKIMVAKLGQDGHDRGAKVIASAFGDIGFDVVAGPLF 617 Query: 635 QTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFD 694 QTPEE A A+ +V V+GVSSLA GH TL+P L + L K G DI++ GGVIP QD+D Sbjct: 618 QTPEEAADLALAEEVTVIGVSSLAAGHRTLMPQLAEALKKRGGEDIIVVCGGVIPRQDYD 677 Query: 695 ELRKDGAVEIYTPGTVIPESA 715 L ++G ++ PGT + ++A Sbjct: 678 YLMENGVAAVFGPGTQVLDAA 698 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: 1293 Number of extensions: 40 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: 712 Length adjustment: 40 Effective length of query: 688 Effective length of database: 672 Effective search space: 462336 Effective search space used: 462336 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