Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_041102537.1 SUTH_RS17165 methylmalonyl-CoA mutase
Query= BRENDA::P11653 (728 letters) >NCBI__GCF_000828635.1:WP_041102537.1 Length = 721 Score = 862 bits (2226), Expect = 0.0 Identities = 435/688 (63%), Positives = 537/688 (78%), Gaps = 5/688 (0%) Query: 38 WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97 W T E + V L+ + + W DT G PF+ GP ATMYA RPWTIRQYAGFSTA+ Sbjct: 33 WVTPEGLTVKPLYTRADVEGLPWADTLPGFAPFLRGPQATMYAVRPWTIRQYAGFSTAEA 92 Query: 98 SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157 SNAFYR+ LAAG +G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF GIP Sbjct: 93 SNAFYRQALAAGAQGVSVAFDLATHRGYDSDHPRVTGDVGKAGVAIDSVEDMKILFDGIP 152 Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217 LD++SVSMTMNGAVLPILA YVV AEEQGV EQL+GTIQNDILKEFMVRNTYI+PP+PS Sbjct: 153 LDKVSVSMTMNGAVLPILAGYVVAAEEQGVTQEQLSGTIQNDILKEFMVRNTYIFPPEPS 212 Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277 MRII++I YT+ NMPK+NSISISGYHMQEAGAT +E+A+TLADG +Y++ + G++V Sbjct: 213 MRIIADIIGYTAQNMPKFNSISISGYHMQEAGATQALELAFTLADGREYVKTAIASGMDV 272 Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337 D FA RLSFFW IGMNF++E+AK+RAAR+LW +++ +F PKNPKSM LRTH QTSGWSLT Sbjct: 273 DAFAGRLSFFWAIGMNFYLEIAKMRAARLLWWRIMDEFKPKNPKSMMLRTHCQTSGWSLT 332 Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397 QD YNNVVRT IEAMAA G TQSLHTNSLDEAIALPT+FS+RIARNTQL +Q+E+ T Sbjct: 333 EQDPYNNVVRTTIEAMAAVFGGTQSLHTNSLDEAIALPTEFSSRIARNTQLIIQEETHIT 392 Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457 VIDPW+GS +E+LT D+A +AW I++V+K+GGM +A++ G K++IE AA+ QARI Sbjct: 393 SVIDPWAGSYMMEKLTQDIADEAWRIIEDVDKMGGMTQAVQSGWAKLQIETCAAQKQARI 452 Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517 DSG+ ++GVNKY+L+ E P++ L VDN V Q +L ++RA RD V++AL +T Sbjct: 453 DSGQDVIVGVNKYKLKEEAPIETLDVDNHAVRDAQIVRLKQIRATRDGAAVQSALAALTE 512 Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577 AA K NLL L I A R ATVGE+SDALE V+GR+ A +T+SGVYS Sbjct: 513 AA-----KTGQGNLLDLAIKASRQRATVGEISDALEAVWGRHRATNQTVSGVYSAAFGED 567 Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637 ++E R+L++ F AEGRRPRI++AK+GQDGHDRG KV+ATA+ADLGFDVDVGPLFQTP Sbjct: 568 GTMQEIRDLIDNFAAAEGRRPRIMIAKLGQDGHDRGAKVVATAFADLGFDVDVGPLFQTP 627 Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697 EE ARQA+E DVH +GVS+LA GH TLVPAL K L + G DI++ VGGVIP QD+ +L Sbjct: 628 EEAARQAIENDVHAIGVSTLAAGHKTLVPALVKALREQGANDIVVFVGGVIPAQDYGQLY 687 Query: 698 KDGAVEIYTPGTVIPESAISLVKKLRAS 725 KDGA I+ PGT IP+ A +++ +RA+ Sbjct: 688 KDGAAGIFGPGTPIPQCAHEVLRAIRAA 715 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: 1349 Number of extensions: 53 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: 721 Length adjustment: 40 Effective length of query: 688 Effective length of database: 681 Effective search space: 468528 Effective search space used: 468528 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 09 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