Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Ac3H11_2278 Methylmalonyl-CoA mutase (EC 5.4.99.2)
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2278 Length = 722 Score = 845 bits (2182), Expect = 0.0 Identities = 432/719 (60%), Positives = 547/719 (76%), Gaps = 11/719 (1%) Query: 14 NAPVPADAA-RRFEELAAKAGTGEA-----WETAEQIPVGTLFNEDVYKDMDWLDTYAGI 67 NAP A A+ + + AAK+ G W T + I V L+ + + + +T G Sbjct: 8 NAPEFAAASLEAWAKAAAKSAPGGDVSALNWVTPDGITVKPLYTAEDTASLPYANTLPGF 67 Query: 68 PPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDS 127 P++ GP ATMYA RPWTIRQYAGFSTA+ESNAFYR+ LAAG +G+SVAFDL THRGYDS Sbjct: 68 EPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDS 127 Query: 128 DNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGV 187 D+PRV GDVG AGVAIDS+ DM+ LF IPLD++SVSMTMNGAVLP+LA YVV AEEQGV Sbjct: 128 DHPRVTGDVGKAGVAIDSVEDMKILFDQIPLDKVSVSMTMNGAVLPVLAGYVVAAEEQGV 187 Query: 188 KPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQE 247 ++L+GTIQNDILKEFMVRNTYIYPP+PSMRII +I YT+ NMPK+NSISISGYHMQE Sbjct: 188 SQDKLSGTIQNDILKEFMVRNTYIYPPKPSMRIIGDIIGYTAKNMPKFNSISISGYHMQE 247 Query: 248 AGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARML 307 AGA +E+A+TLADG +Y++ + GL+VD+FA RLSFFW IGMNF++EVAK+RAAR+L Sbjct: 248 AGANQALELAFTLADGKEYVKTAMASGLDVDEFAGRLSFFWAIGMNFYLEVAKMRAARLL 307 Query: 308 WAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNS 367 W +++ + G KNPKS+ LRTH QTSGWSLT QD YNNVVRT IEAMAA G TQSLHTN+ Sbjct: 308 WCRIMKETGAKNPKSLMLRTHCQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNA 367 Query: 368 LDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEV 427 LDEAIALPT+FSARIARNTQL +Q+E+ T VIDPW+GS +E+LT D+ AW I+EV Sbjct: 368 LDEAIALPTEFSARIARNTQLIIQEETHITNVIDPWAGSYMMEKLTQDMMDAAWKIIEEV 427 Query: 428 EKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNST 487 E +GGM +A++ G K++IE AAA QARIDSG+ ++GVNKY+L E P+D+L++DN Sbjct: 428 EAMGGMTQAVDSGWAKLKIEAAAAEKQARIDSGKDVIVGVNKYKLAKEDPVDILQIDNMK 487 Query: 488 VLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGE 547 V Q A+L K+RA RD KV+AALD +T AA + + NLL+L I+A R ATVGE Sbjct: 488 VRDGQIARLEKIRATRDAAKVQAALDALTAAA-----ESGEGNLLELSINAVRLRATVGE 542 Query: 548 MSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQ 607 +SDALEKVFGR+ A + ++GVY+ + ++ + + F + +GRRPR+++AK+GQ Sbjct: 543 VSDALEKVFGRHRADTQKVTGVYAAAYDSAEGWDKLKTEINAFAEEQGRRPRVMIAKLGQ 602 Query: 608 DGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPA 667 DGHDRG KV+ATA+ADLGFDVD+GPLFQTPEE ARQA+E DVH VGVS+LA GH TLVPA Sbjct: 603 DGHDRGAKVVATAFADLGFDVDMGPLFQTPEECARQAIENDVHAVGVSTLAAGHKTLVPA 662 Query: 668 LRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASL 726 + + L G DI++ VGGVIP QD+D L + G +Y PGT IP SA +++++R ++ Sbjct: 663 IIQSLRDQGADDIIVFVGGVIPAQDYDFLYESGVKGVYGPGTPIPASAKDVLEQIRKAV 721 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: 1404 Number of extensions: 45 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: 722 Length adjustment: 40 Effective length of query: 688 Effective length of database: 682 Effective search space: 469216 Effective search space used: 469216 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