Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_092057248.1 BQ4888_RS10890 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_900111775.1:WP_092057248.1 Length = 714 Score = 872 bits (2252), Expect = 0.0 Identities = 443/678 (65%), Positives = 530/678 (78%), Gaps = 5/678 (0%) Query: 38 WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97 W+TAE I V L+ + + ++ DT G+ PFV GP A+MYA RPWT+RQYAGFSTA+E Sbjct: 30 WDTAEGIRVKPLYTKADVEKLETADTLPGVAPFVRGPMASMYAGRPWTVRQYAGFSTAEE 89 Query: 98 SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157 SNAFY+RNLAAGQ+GLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF+ IP Sbjct: 90 SNAFYKRNLAAGQQGLSVAFDLATHRGYDSDHPRVVGDVGKAGVAIDSVEDMKILFSDIP 149 Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217 LD++SVSMTMNGAVLPI+A Y+V AEEQGV E+LAGTIQNDILKEFMVRNTYIYPP+PS Sbjct: 150 LDKVSVSMTMNGAVLPIMANYIVAAEEQGVSQEKLAGTIQNDILKEFMVRNTYIYPPEPS 209 Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277 MRIIS+I YTS +MPK+NSISISGYH+QEAGA +E+A+TLADG++Y++A + GL+V Sbjct: 210 MRIISDIIEYTSKHMPKFNSISISGYHIQEAGANNALELAFTLADGLEYVKAAIAKGLDV 269 Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337 D FAPRLSFF+ IGMNFFME AKLRAAR LWA L+ QF PKNPKS+ LRTH QTSGWSLT Sbjct: 270 DAFAPRLSFFFAIGMNFFMEAAKLRAARFLWADLMQQFQPKNPKSLMLRTHCQTSGWSLT 329 Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397 QD YNNV+RT +EA+AA G TQSLHTN+LDEAIALPT+ SARIARNTQL +Q+ESG T Sbjct: 330 EQDPYNNVIRTTLEALAAVLGGTQSLHTNALDEAIALPTEQSARIARNTQLIIQEESGVT 389 Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457 V+DP GS YVE LT L +A + E++ +GGM KAIE G+PK+RIEE+AA+ QA I Sbjct: 390 NVVDPLGGSYYVESLTSALVEEARKILAEIDGLGGMTKAIESGMPKLRIEESAAKKQAAI 449 Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517 DSGR+ ++GVNKY+L E P+DVL +DN+ V Q A+L K+RAERD + AL IT Sbjct: 450 DSGREVIVGVNKYKLAKEEPIDVLDIDNTAVREGQIARLKKMRAERDEAACQKALAAITA 509 Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577 A D +NLL LC++A R A+VGE+SDA+EKVFGR+ A+I+ +SG Y V+ Sbjct: 510 ACA-----DTQQNLLGLCVEAARLRASVGEISDAMEKVFGRHRAEIKLVSGAYGSIVEKD 564 Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637 + + ++ F EGRRPRIL+AKMGQDGHDRG KV+ATAYAD GFDVD+GPLFQTP Sbjct: 565 QDFSALKARIDAFAATEGRRPRILVAKMGQDGHDRGAKVVATAYADAGFDVDMGPLFQTP 624 Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697 EE A+ AVE DVHVVGVSSLA GH TLVP L EL KLG DI+I GGVIP QD+DEL Sbjct: 625 EEAAKMAVENDVHVVGVSSLAAGHKTLVPQLAAELKKLGADDIVIVCGGVIPRQDYDELL 684 Query: 698 KDGAVEIYTPGTVIPESA 715 GA I+ PGT I SA Sbjct: 685 AAGAARIFGPGTPITVSA 702 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: 1331 Number of extensions: 41 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: 728 Length of database: 714 Length adjustment: 40 Effective length of query: 688 Effective length of database: 674 Effective search space: 463712 Effective search space used: 463712 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