Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 3607311 Dshi_0726 methylmalonyl-CoA mutase, large subunit (RefSeq)
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Dino:3607311 Length = 712 Score = 830 bits (2143), Expect = 0.0 Identities = 428/704 (60%), Positives = 529/704 (75%), Gaps = 11/704 (1%) Query: 27 ELAAKAGTGE-----AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAF 81 +LAAK G+ W+T E I V L+ + + +D L + G PF G ATMYA Sbjct: 10 DLAAKELRGKPLETLTWKTLEGIDVKPLYTAEDLEGLDHLGSVPGQAPFTRGVKATMYAG 69 Query: 82 RPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGV 141 RPWTIRQYAGFSTA+ESNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGV Sbjct: 70 RPWTIRQYAGFSTAEESNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVEGDVGKAGV 129 Query: 142 AIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDIL 201 AIDS+ DM+ LF GIPLDQ+SVSMTMNGAV+PILA ++VT EEQG L+GTIQNDIL Sbjct: 130 AIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILANFIVTGEEQGHDRSVLSGTIQNDIL 189 Query: 202 KEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLA 261 KEFMVRNTY+YPP+PSMRII++I YTSA MPK+NSISISGYHMQEAGA E+A+TLA Sbjct: 190 KEFMVRNTYVYPPEPSMRIIADIIEYTSAEMPKFNSISISGYHMQEAGANLVQELAFTLA 249 Query: 262 DGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPK 321 DG +Y+RA + G++VD+FA RLSFF+ IGMNFFME AKLRAARMLW K++ +F PKNP+ Sbjct: 250 DGREYVRAAIARGMDVDKFAGRLSFFFAIGMNFFMEAAKLRAARMLWHKIMSEFEPKNPR 309 Query: 322 SMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSAR 381 SM LRTH QTSG SL QD YNNV+RT EAM+A G TQSLHTN+LDEAIALPT+FSAR Sbjct: 310 SMMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAIALPTEFSAR 369 Query: 382 IARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGI 441 IARNTQL LQ+E+G T V+DP +GS YVE LT +LA KAW I+EVE++GGM KA+ G+ Sbjct: 370 IARNTQLILQEETGVTNVVDPLAGSYYVESLTNELAEKAWALIEEVEELGGMTKAVASGM 429 Query: 442 PKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRA 501 PK+RIEE+AAR QA ID G + ++GVNKYR + E P+D+L++DN+ V Q A+L K+RA Sbjct: 430 PKLRIEESAARRQAMIDKGTEVIVGVNKYRKDKEDPIDILEIDNAKVRDGQVARLAKIRA 489 Query: 502 ERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTA 561 ERD +AL ++ A NLL ++A RA A+VGE+S A+EKVFGR+ A Sbjct: 490 ERDEAACDSALAEVERCAAE------GGNLLAAAVEAARARASVGEISMAMEKVFGRHRA 543 Query: 562 QIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAY 621 +++T++GVY + ++ VE+F EGRRPR+L+ KMGQDGHDRG KVIATA+ Sbjct: 544 EVKTLAGVYGAAYEGDDGFAAIQKSVEDFAAEEGRRPRMLVVKMGQDGHDRGAKVIATAF 603 Query: 622 ADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDIL 681 AD+GFDVDVGPLFQTPEE A+ A++ DVHV+G+SS A GH TL P L L G DIL Sbjct: 604 ADIGFDVDVGPLFQTPEEAAQDAIDNDVHVIGISSQAAGHKTLAPKLVDALKAQGAGDIL 663 Query: 682 ITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRAS 725 + GGVIP+QD+ L G I+ PGT IPE+A +++ +R S Sbjct: 664 VICGGVIPQQDYQYLYDRGVKAIFGPGTNIPEAAQDILRLIRES 707 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: 1308 Number of extensions: 42 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