Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 351618 BT2090 methylmalonyl-CoA mutase large subunit (NCBI ptt file)
Query= BRENDA::Q84FZ1 (721 letters) >FitnessBrowser__Btheta:351618 Length = 715 Score = 935 bits (2417), Expect = 0.0 Identities = 472/678 (69%), Positives = 552/678 (81%), Gaps = 2/678 (0%) Query: 29 WMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAED 88 W TPE I VK Y ED EG E + GLPPYLRGPY MY +PWTIRQYAGFSTAE+ Sbjct: 32 WNTPEHIDVKPVYTKEDLEGMEHLGYAAGLPPYLRGPYSVMYTLRPWTIRQYAGFSTAEE 91 Query: 89 SNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIP 148 SNAFYRRNLA+GQKGLSVAFDLATHRGYD DH RV GDVG AGV+I S+ +M+ LF GIP Sbjct: 92 SNAFYRRNLASGQKGLSVAFDLATHRGYDPDHERVVGDVGKAGVSICSLENMKVLFDGIP 151 Query: 149 LDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGS 208 L +M+VSMTMNGAVLP +A YI A EQG E++AGTIQNDILKEFMVRNTYIYPP S Sbjct: 152 LSKMSVSMTMNGAVLPIMAFYINAGLEQGAKLEEMAGTIQNDILKEFMVRNTYIYPPAFS 211 Query: 209 MRIISDIFGYTSKNMPKFNSISISGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTI 268 M+IISDIF YTS+ MPKFNSISISGYHMQEAGAT D+ELAYTLADG+EY++AG AAG+ I Sbjct: 212 MKIISDIFEYTSQKMPKFNSISISGYHMQEAGATADIELAYTLADGLEYLRAGTAAGIDI 271 Query: 269 DQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLT 328 D FAPRLSFFWAIG N FMEIAKMRAAR++WAK+VK+F PK+ KSL LRTHSQTSGWSLT Sbjct: 272 DAFAPRLSFFWAIGTNHFMEIAKMRAARMLWAKIVKQFNPKNPKSLALRTHSQTSGWSLT 331 Query: 329 AQDVFNNVTRTCIEAMAATQGGTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTT 388 QD FNNV RTCIEAMAA G TQSLHTNALDEA+ALPTDFSARIARNTQ+++Q+E+ Sbjct: 332 EQDPFNNVGRTCIEAMAAALGHTQSLHTNALDEAIALPTDFSARIARNTQIYIQEETYIC 391 Query: 389 RIIDPWGGSYYVERLTRDIAARAWEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARI 448 + +DPWGGSYYVE LT ++A +AWE I EVE LGGMAKAIE GIPK+RIEEAAAR QARI Sbjct: 392 KNVDPWGGSYYVEALTNELAHKAWERIEEVEKLGGMAKAIETGIPKMRIEEAAARTQARI 451 Query: 449 DSGRQTIVGINKYKPDDEMKIDLLRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTK 508 DSG QTIVG+NKY+ + E ID+L +DN VR +QI+ LKRL+ RNQA+VD ALAA+T+ Sbjct: 452 DSGSQTIVGVNKYRLEKEAPIDILEIDNTAVRLEQIENLKRLKEGRNQAEVDKALAAITE 511 Query: 509 AAD-GEGNLLELAVNAARAKATVGEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVE 567 + G+GNLLELAV AAR +AT+GEIS A EK GR++A IR+ISGVY E + Sbjct: 512 CVETGKGNLLELAVEAARVRATLGEISYACEKVVGRYKAIIRTISGVYSSESKNDGD-FK 570 Query: 568 KVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAA 627 + L E F + +GR+PRI+VAKMGQDGHDRG KV+A+ +AD GFDVD+GPLF TP EAA Sbjct: 571 RACELAEKFAKKEGRQPRIMVAKMGQDGHDRGAKVVATGYADCGFDVDMGPLFQTPAEAA 630 Query: 628 RQAVENDVHIVGVSSLAAGHLTLVPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGA 687 R+AVENDVH+VGVSSLAAGH TL+P++ LK+ GR+D++++ GGVIP DYD LY AG Sbjct: 631 REAVENDVHVVGVSSLAAGHKTLIPQIMEELKKLGREDIVVIAGGVIPAQDYDFLYKAGV 690 Query: 688 SAIFPPGTVIAEAAVNLL 705 +AIF PGT +A+AA +L Sbjct: 691 AAIFGPGTPVAKAACQIL 708 Lambda K H 0.318 0.134 0.391 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: 1289 Number of extensions: 42 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: 721 Length of database: 715 Length adjustment: 40 Effective length of query: 681 Effective length of database: 675 Effective search space: 459675 Effective search space used: 459675 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