Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_075618030.1 GY23_RS04780 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_001939075.1:WP_075618030.1 Length = 717 Score = 921 bits (2380), Expect = 0.0 Identities = 459/698 (65%), Positives = 567/698 (81%), Gaps = 6/698 (0%) Query: 25 FEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPW 84 F+E+A+ + T +++ T E I V + + ++ + ++ + GI P GPY TMY RPW Sbjct: 15 FQEVASTS-TRDSFLTNEGIHVSSRYGKEDAESLNHMSDLPGIAPNTRGPYPTMYVSRPW 73 Query: 85 TIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAID 144 T+RQYAGFSTA+ESNAFYRRNLA GQKGLSVAFDL THRGYDSD+PRV GDVG AGVAID Sbjct: 74 TVRQYAGFSTAEESNAFYRRNLAMGQKGLSVAFDLATHRGYDSDHPRVTGDVGKAGVAID 133 Query: 145 SIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEF 204 SI DM+ LF GIPLDQMSVSMTMNGAVLPILA Y+VTAEEQGV E+LAGTIQNDILKE+ Sbjct: 134 SIEDMKILFDGIPLDQMSVSMTMNGAVLPILAFYIVTAEEQGVSLEKLAGTIQNDILKEY 193 Query: 205 MVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGV 264 MVRNTYIYPP+ SM+II++IF YTS +MPK+NSISISGYHMQEAGATADIE+AYTLADG+ Sbjct: 194 MVRNTYIYPPKMSMKIIADIFEYTSNHMPKFNSISISGYHMQEAGATADIELAYTLADGL 253 Query: 265 DYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMS 324 +Y+R G G+++D FAPRLSFFW IGMN+FMEVAK+RAAR +WA+++ F PKNPKS++ Sbjct: 254 EYVRTGLQAGIDIDSFAPRLSFFWAIGMNYFMEVAKMRAARRIWAQMMQTFDPKNPKSLA 313 Query: 325 LRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIAR 384 LRTHSQTSGWSLT QD +NNV RT IEA AAT GHTQSLHTN+LDEAIALPTDFSARIAR Sbjct: 314 LRTHSQTSGWSLTEQDPFNNVTRTLIEANAATMGHTQSLHTNALDEAIALPTDFSARIAR 373 Query: 385 NTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKM 444 NTQLFLQ+E+ T+VIDPW GS VE+LT +L +KAW I+E+E++GGMAKAIE G+PKM Sbjct: 374 NTQLFLQEETMMTKVIDPWGGSYAVEKLTDELMKKAWALIEEIEELGGMAKAIETGLPKM 433 Query: 445 RIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERD 504 +IEEAAA+ QA+IDSG++ +IGVNK+RL+ E P+D+L +DNS V +Q ++ ++ R+ Sbjct: 434 KIEEAAAKKQAQIDSGKEIIIGVNKFRLQEEEPIDILNIDNSVVRQKQIERIETMKNMRN 493 Query: 505 PEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIR 564 E V+ AL +T AA + + NLL + A R AT+GE+SDA+EKV GR+ A IR Sbjct: 494 EEAVQLALSALTKAA-----ESGEENLLACAVQAARVRATLGEISDAIEKVSGRHKAVIR 548 Query: 565 TISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADL 624 ++SGVYS N E++ +++ E+F++ EGRRPRIL+AKMGQDGHDRG KVIATA+ADL Sbjct: 549 SVSGVYSANFSNEEEIQTVKDMTEDFKENEGRRPRILIAKMGQDGHDRGAKVIATAFADL 608 Query: 625 GFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITV 684 GFDVD+GPLFQTPEETARQA E DVHV+GVSSLA GH+TLVP L EL K+GR DILI V Sbjct: 609 GFDVDIGPLFQTPEETARQAAENDVHVIGVSSLAAGHMTLVPELLSELKKIGREDILIVV 668 Query: 685 GGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722 GGVIP QD+ LR++GA I+ PGTVIP +A +++++ Sbjct: 669 GGVIPAQDYAFLRENGASAIFGPGTVIPVAAAKVIEEI 706 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: 1295 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: 717 Length adjustment: 40 Effective length of query: 688 Effective length of database: 677 Effective search space: 465776 Effective search space used: 465776 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 24 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