Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 16996 b2917 methylmalonyl-CoA mutase (NCBI)
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Keio:16996 Length = 714 Score = 812 bits (2097), Expect = 0.0 Identities = 414/680 (60%), Positives = 513/680 (75%), Gaps = 10/680 (1%) Query: 39 ETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKES 98 +TAE I + L+ E +++ T G+PP+V GP ATMY +PWTIRQYAGFSTAKES Sbjct: 28 QTAEGIAIKPLYTEADLDNLEVTGTLPGLPPYVRGPRATMYTAQPWTIRQYAGFSTAKES 87 Query: 99 NAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPL 158 NAFYRRNLAAGQKGLSVAFDL THRGYDSDNPRVAGDVG AGVAID++ DM+ LF IPL Sbjct: 88 NAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGVAIDTVEDMKVLFDQIPL 147 Query: 159 DQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSM 218 D+MSVSMTMNGAVLP+LA Y+V AEEQGV P++L GTIQNDILKE++ RNTYIYPP+PSM Sbjct: 148 DKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDILKEYLCRNTYIYPPKPSM 207 Query: 219 RIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVD 278 RII++I A+ S NMP++N+ISISGYHM EAGA ++A+TLADG++YI+A S GL +D Sbjct: 208 RIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLADGIEYIKAAISAGLKID 267 Query: 279 QFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTA 338 FAPRLSFF+GIGM+ FM VA LRAAR LW++ V FG ++PKS++LRTH QTSGWSLT Sbjct: 268 DFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEAVSGFGAQDPKSLALRTHCQTSGWSLTE 327 Query: 339 QDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTR 398 QD YNNV+RT IEA+AAT G TQSLHTN+ DEA+ LPTDFSARIARNTQ+ +Q+ES R Sbjct: 328 QDPYNNVIRTTIEALAATLGGTQSLHTNAFDEALGLPTDFSARIARNTQIIIQEESELCR 387 Query: 399 VIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARID 458 +DP +GS Y+E LT + ++A IQ++++ GGMAKAIE G+PK IEEA+AR Q+ ID Sbjct: 388 TVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMAKAIEAGLPKRMIEEASAREQSLID 447 Query: 459 SGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWA 518 G++ ++GVNKY+L+HE DVL++DN V EQ A L ++RA RD V AAL+ +T A Sbjct: 448 QGKRVIVGVNKYKLDHEDETDVLEIDNVMVRNEQIASLERIRATRDDAAVTAALNALTHA 507 Query: 519 AGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGV----YSKEV 574 A + + NLL ++A R AT+GE+SDALE F RY + ++GV Y + Sbjct: 508 AQH------NENLLAAAVNAARVRATLGEISDALEVAFDRYLVPSQCVTGVIAQSYHQSE 561 Query: 575 KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLF 634 K+ E + E+F GRRPRIL+AKMGQDGHDRG KVIA+AY+DLGFDVD+ P+F Sbjct: 562 KSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDRGAKVIASAYSDLGFDVDLSPMF 621 Query: 635 QTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFD 694 TPEE AR AVE DVHVVG SSLA GH TL+P L + L K GR DI + GGVIP QD+ Sbjct: 622 STPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEALKKWGREDICVVAGGVIPPQDYA 681 Query: 695 ELRKDGAVEIYTPGTVIPES 714 L++ G IY PGT + +S Sbjct: 682 FLQERGVAAIYGPGTPMLDS 701 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: 1287 Number of extensions: 37 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 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