Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate BPHYT_RS02085 BPHYT_RS02085 methylmalonyl-CoA mutase
Query= BRENDA::Q8Y2U5 (1099 letters) >FitnessBrowser__BFirm:BPHYT_RS02085 Length = 1298 Score = 931 bits (2405), Expect = 0.0 Identities = 473/608 (77%), Positives = 517/608 (85%), Gaps = 5/608 (0%) Query: 492 LTALDAQAAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTT 551 L LD A+R A LG ER LL WP AY+G E++V+IRDRE+RT LT TTLSG+ Sbjct: 696 LQQLDTLIAQRTASLGERERALLDTWPQTVAAYSGAEHIVRIRDREIRTALTVTTLSGSE 755 Query: 552 LRKVVLPPYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALR 611 +RKV LP + D GEILRWLM +N+PG FP+TAGVF F+R EDPTRMFAGEGD R Sbjct: 756 VRKVSLPKFADHGEILRWLMLDNLPGYFPFTAGVFPFRREN----EDPTRMFAGEGDPQR 811 Query: 612 TNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDG 671 TNRRFKL+SEGM AKRLSTAFDSVTLYGE+PD RPDIYGKVGN+GVS+ATLDD+K LYDG Sbjct: 812 TNRRFKLLSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMKTLYDG 871 Query: 672 FDLTSPNTSVSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQN 731 FDL +P TSVSMTINGPAPTILAMF N A+DQ +AR GR T E + R L+N Sbjct: 872 FDLCAPETSVSMTINGPAPTILAMFFNVAIDQQIARMTQQQGRPLTHDELSATRRAALEN 931 Query: 732 VRGTVQADILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGA 791 VRGTVQADILKEDQGQNTCIFST FSLKVMGDIQ YFV H VRNFYSVSISGYHIAEAGA Sbjct: 932 VRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHGVRNFYSVSISGYHIAEAGA 991 Query: 792 NPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVT 851 NPISQLA+TLANGFTYVEAYLARGM IDDFAPNLSFFFSNGMDPEY+VLGRVARRIWAV Sbjct: 992 NPISQLAYTLANGFTYVEAYLARGMSIDDFAPNLSFFFSNGMDPEYTVLGRVARRIWAVA 1051 Query: 852 MRDKYGANERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEA 911 MR++YGANERSQKLKYHVQTSGRSLHAQEI FNDIRTTLQALIAIYDNCNSLHTNA+DEA Sbjct: 1052 MRERYGANERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAFDEA 1111 Query: 912 ITTPTAESVRRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERG 971 ITTPT +SVRRA+AIQLIINREWGLAK +NPNQGSF+I+ELTDLVE AVL EF+RL ERG Sbjct: 1112 ITTPTEDSVRRAVAIQLIINREWGLAKNQNPNQGSFVIEELTDLVEEAVLAEFDRLTERG 1171 Query: 972 GVLGAMETGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPAHIELARSSEE 1031 GVLGAMETGYQRGRIQ+ESMLYE RKHDGS PIVGVNTF + H AP I LARS+++ Sbjct: 1172 GVLGAMETGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFLSAHP-HEAPQPIALARSTDD 1230 Query: 1032 EKQRQLARLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEV 1091 EKQ QL RL F ++H APA L+RL+RAVIDD+NVFAVLMD VRVCSLGQITHALFEV Sbjct: 1231 EKQSQLQRLRAFQSQHRDAAPAALERLKRAVIDDENVFAVLMDVVRVCSLGQITHALFEV 1290 Query: 1092 GGQYRRNM 1099 GGQYRRNM Sbjct: 1291 GGQYRRNM 1298 Score = 396 bits (1017), Expect = e-114 Identities = 223/348 (64%), Positives = 258/348 (74%), Gaps = 10/348 (2%) Query: 161 AYAPTTLEPVAKGDRRALAQLITALESGRIDPALRQAVHARA---ATAHTPVLGITGTGG 217 A T +P + RR LAQLI+A E+G +D + R+ + A+A ATA TPVLGITGTGG Sbjct: 271 ANTANTSDPASSTFRR-LAQLISAFEAGAVDASAREKLSAQAQAKATA-TPVLGITGTGG 328 Query: 218 AGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAINH----PNLF 273 AGKSSLTDELIRRFRLD D L IAV++IDPSRRKSGGALLGDRIRMNAI ++ Sbjct: 329 AGKSSLTDELIRRFRLDYGDALTIAVLAIDPSRRKSGGALLGDRIRMNAIGDWGGGARVY 388 Query: 274 VRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVPHADLSLYVMTPE 333 +RS+ATREASSE+SD+LPD + C+A GFDLI+VETSGIGQG+AAIVP D SLYVMTPE Sbjct: 389 MRSMATREASSEVSDSLPDALMLCKAAGFDLIVVETSGIGQGNAAIVPFVDESLYVMTPE 448 Query: 334 FGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWHAKPEDMPVFGTQ 393 FGAASQLEKIDMLDFA VAINKFDRKGA DA RDVAKQVQRNR + PE MPVFGT Sbjct: 449 FGAASQLEKIDMLDFAGFVAINKFDRKGAPDALRDVAKQVQRNRADFAKPPEAMPVFGTI 508 Query: 394 ASHFNDDGVTALYHALADRLAERGMALAERTLPRPAG-TCSTSHDAIVPPARVRYLAEVA 452 AS FNDDGVTALY +A+ L + G+ L P G S+ +AIVPPARVRYLA++A Sbjct: 509 ASRFNDDGVTALYRHVAEALRKHGLRSGGGRLAAPEGLRFSSGRNAIVPPARVRYLADIA 568 Query: 453 DTVRGYHRRVDAQSGLARERQQLQASRRMLEAAGAAADVLTALDAQAA 500 T+ Y R DAQ+ LARER QL +RRML AG A +T A A+ Sbjct: 569 QTIHAYRERADAQARLARERWQLVEARRMLGEAGTQAGAVTQSRASAS 616 Score = 221 bits (563), Expect = 3e-61 Identities = 152/364 (41%), Positives = 193/364 (53%), Gaps = 22/364 (6%) Query: 1 MTDLSAARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGH 60 MTDLS + A S ++RFVTAA+LFDGHDASINIMRRILQ+ G EVIHLGH Sbjct: 1 MTDLSTPQRA----GSHKLPAGRRLRFVTAAALFDGHDASINIMRRILQASGVEVIHLGH 56 Query: 61 NRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPA 120 NRSVDEV AALQED G+AVSSYQGGH EYF+Y++D LRARGGE I+VFGGGGGVIVP Sbjct: 57 NRSVDEVATAALQEDADGVAVSSYQGGHNEYFRYLVDLLRARGGERIKVFGGGGGVIVPE 116 Query: 121 EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDIDLAAYAPT----TLEPVAKGDRR 176 EI EL+ YGV +IYSP+DGQR+GL GMI DM+ RC A E V + +R Sbjct: 117 EISELESYGVEKIYSPQDGQRLGLQGMIDDMIARCAEGARAAEAVGQSRVGEWVDEFSKR 176 Query: 177 ALAQLITALESGRIDPALR----QAVHARAATAHTPVLGITGTGGAGKSSLT-DELIRRF 231 L + + ++G + A+R QA H AT+ V T A ++ T D Sbjct: 177 GLPRFDSRGDAGGDEDAVRNPFSQASHVGCATSVGHVANAADTADAADTADTADAADTAD 236 Query: 232 RLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAINHPNLFVRSLATREASSEISDALP 291 D D A +I + + N N N + T + +S L Sbjct: 237 AADTADTADTADTAIAANTANTANT-------ANTANTANT-ANTANTSDPASSTFRRLA 288 Query: 292 DVIAACRAGGFDLIIVE-TSGIGQGDAAIVPHADLSLYVMTPEFGAASQLEKIDMLDFAD 350 +I+A AG D E S Q A P ++ + +L + LD+ D Sbjct: 289 QLISAFEAGAVDASAREKLSAQAQAKATATPVLGITGTGGAGKSSLTDELIRRFRLDYGD 348 Query: 351 LVAI 354 + I Sbjct: 349 ALTI 352 Lambda K H 0.320 0.134 0.388 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: 3243 Number of extensions: 111 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 1099 Length of database: 1298 Length adjustment: 47 Effective length of query: 1052 Effective length of database: 1251 Effective search space: 1316052 Effective search space used: 1316052 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (27.3 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