Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate GFF373 PGA1_c03840 methylmalonyl-CoA mutase large subunit
Query= SwissProt::P27253 (714 letters) >FitnessBrowser__Phaeo:GFF373 Length = 655 Score = 403 bits (1036), Expect = e-116 Identities = 245/657 (37%), Positives = 366/657 (55%), Gaps = 23/657 (3%) Query: 67 MYTAQPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVG 126 M +PW IR YAG STA SNA YR NLA GQ GLSVAFDL T GYDSD+ G+VG Sbjct: 4 MQKDRPWLIRTYAGHSTASASNALYRANLAKGQTGLSVAFDLPTQTGYDSDHVLARGEVG 63 Query: 127 KAGVAIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQ 186 K GV + + DM+ LFDQIPL++M+ SMT+N +L+ YI AEEQG KL GT+Q Sbjct: 64 KVGVPVCHLGDMRSLFDQIPLEQMNTSMTINATAPWLLSLYIAVAEEQGADVSKLQGTVQ 123 Query: 187 NDILKEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVA 246 ND++KEYL R TY+ PPKPS+++IAD+ +C N P++N +++ YH+ EAGA Q++A Sbjct: 124 NDLIKEYLSRGTYVCPPKPSLKMIADVAEYCYTNAPKWNPMNVCSYHLQEAGATPEQELA 183 Query: 247 FTLADGIEYIKAAISAGLKIDDF---APRLSFFFGIGMDLFMNVAMLRAARYLWSEAV-S 302 F LA + + + + +DF R+SFF G+ + +RA LW E Sbjct: 184 FALATA-QAVLDELKPRITPEDFPAMVGRISFFVNAGIRFVTEMCKMRAFVDLWDEICRD 242 Query: 303 GFGAQDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDE 359 +G +DPK R Q + LTEQ P NNV R IE LA TL +++ A++E Sbjct: 243 RYGVEDPKFRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKKARARAVQLPAWNE 302 Query: 360 ALGLPTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEA 419 ALGLP + + + Q I+ E++L D G+ +++ + + ARA + ++ Sbjct: 303 ALGLPRPWDQQWSMRMQQILAYETDLLEYGDLFDGNPAVDAKVEDLKTGARAELANLESM 362 Query: 420 GGMAKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDH----EDETDVLEIDNV 475 GG +IE K + +++A + I++ + ++VGVNK+ + E + + + Sbjct: 363 GGAVASIE--YMKGRLVDSNAERLNRIEKNETIVVGVNKWTEGEPSPLQTEDGGIMVVDP 420 Query: 476 MVRNEQIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDAL 535 V EQI L+ R+ RDD AV +AL AL AAQ+ +N++ ++ AA+ T GE ++ + Sbjct: 421 AVEQEQINRLDDWRSGRDDDAVQSALAALRAAAQNGDNIMPPSIAAAKAGVTTGEWAEEM 480 Query: 536 EVAFDRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQD 595 + Y P TGV + +++E D + A ++Q GRR + L+ K G D Sbjct: 481 RKVYGTYRGP----TGVSGSASNKTEGLDELRDKVNAVSDQL----GRRLKFLVGKPGLD 532 Query: 596 GHDRGAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPEL 655 GH GA+ IA D G D+ + TPEE+ A+ +D HVVG S L+ H LI EL Sbjct: 533 GHSNGAEQIAFRARDCGMDITYDGIRMTPEELVASAIADDAHVVGMSILSGSHLPLIEEL 592 Query: 656 VEALKKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVR-DVLNLISQ 711 + + + G + V+ GG+IP D L++ GVA +Y P L+++ D++ L Q Sbjct: 593 MGRMTEAGLSHVPVIVGGIIPDDDADRLKKMGVARVYTPKDFELNAIMGDIVELAKQ 649 Lambda K H 0.318 0.133 0.381 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: 960 Number of extensions: 46 Number of successful extensions: 7 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: 714 Length of database: 655 Length adjustment: 39 Effective length of query: 675 Effective length of database: 616 Effective search space: 415800 Effective search space used: 415800 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 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