Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate 351619 BT2091 methylmalonyl-CoA mutase small subunit (NCBI ptt file)
Query= SwissProt::O86028 (712 letters) >FitnessBrowser__Btheta:351619 Length = 633 Score = 211 bits (537), Expect = 9e-59 Identities = 142/463 (30%), Positives = 225/463 (48%), Gaps = 48/463 (10%) Query: 24 LVWHTPEGIDVKPLYTSDDMSGIGHLNSLPGFEPFVRGPRATMYAGRPWTVRQYAGFSTA 83 LVW T EG VKP Y +D+ G+ ++LPG P++RG T + W VRQ Sbjct: 37 LVWKTNEGFKVKPFYRMEDLEGLKTTDALPGEFPYLRG---TKKSNNEWLVRQEIKVECP 93 Query: 84 EASNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVEDMKILFDG 143 + +NA A D+ ++G DS V+ A E ++ L +G Sbjct: 94 KEANA--------------KALDIL-NKGVDSLSFHVKAKELNA-------EYIETLLNG 131 Query: 144 IPLDRISVSM-TMNGAVIPILASFIVAGEEQGVSRDKLSGTIQNDILKEFMVRNTYIYPP 202 I + + ++ T G V+ + + +++ KL G++ D + + R Sbjct: 132 IQAECVELNFSTCQGHVVELAGLLVAYFQKKDYDVKKLRGSVNYDFFNKMLTRGK----E 187 Query: 203 EPSMRIVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAALAKG 262 + M A + + +P + ++++ + AGA + QEL + LA G EY+ G Sbjct: 188 KGDMVQTAKALIEAIQPLPFYRVLNVNAISLNNAGAYISQELGYALAWGNEYMNQLTDAG 247 Query: 263 LNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMQEFKPEKAS------------- 309 + A ++ F F I N+F+E AK RAAR+LW I+ + PE Sbjct: 248 IPAATVAKKIKFNFGISSNYFLEIAKFRAARMLWANIVASYHPECLRDCDNKGANGECRC 307 Query: 310 SLMLRTHCQTSGVSLQEQDPYNNIVRTAFEAMSAVLGGTQSLHTNSFDEAMALPTDFSAR 369 + + H +TS +L D + N++RT EAMSA L G S+ FD+ + P +FS R Sbjct: 308 AAKMAVHAETSTFNLTLFDAHVNLLRTQTEAMSAALAGVDSMTVVPFDKTYSTPDEFSER 367 Query: 370 IARNTQLILQHETGVTKVVDPLAGSYYVESLTNELAEKAWGLIEEVEALGGMTKAVNAGL 429 +ARN QL+L+ E+ KV+DP AGSYY+E+LT +A++AW L VE GG A+ AG Sbjct: 368 LARNQQLLLKEESHFDKVIDPAAGSYYIENLTVSIAKQAWELFLAVEEAGGFYAALKAGT 427 Query: 430 PKRLIEEAATRRQAAVDRAEEVIVGVNKYRLENE-----QPID 467 + + E+ R AV + EV++G N++ NE QPI+ Sbjct: 428 VQAAVNESNKARHKAVAQRREVLLGTNQFPNFNEKAGEKQPIE 470 Lambda K H 0.318 0.134 0.379 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: 825 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 712 Length of database: 633 Length adjustment: 39 Effective length of query: 673 Effective length of database: 594 Effective search space: 399762 Effective search space used: 399762 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: 54 (25.4 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