Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Dsui_1105 Dsui_1105 methylmalonyl-CoA mutase family protein
Query= BRENDA::Q8Y2U5 (1099 letters) >FitnessBrowser__PS:Dsui_1105 Length = 1093 Score = 1573 bits (4073), Expect = 0.0 Identities = 810/1105 (73%), Positives = 917/1105 (82%), Gaps = 18/1105 (1%) Query: 1 MTDLSAARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGH 60 MTDLS A+ P NKVRF+TAASLFDGHDASINIMRRILQS G EVIHLGH Sbjct: 1 MTDLSIAKKIVPYKPK------NKVRFITAASLFDGHDASINIMRRILQSTGSEVIHLGH 54 Query: 61 NRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPA 120 NRSV ++VNAALQEDVQGIA++SYQGGHVE+FKYMID L+ GGE+I+VFGGGGGVIVP+ Sbjct: 55 NRSVGDIVNAALQEDVQGIAITSYQGGHVEFFKYMIDLLKENGGENIKVFGGGGGVIVPS 114 Query: 121 EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDIDLAAYAPTTLEPVA----KGDRR 176 EI+EL +YGV RIYSPEDGQ +GL GMI D+V + D +L AP E V G+RR Sbjct: 115 EIKELHEYGVTRIYSPEDGQHLGLQGMINDVVEQSDYNLTTLAPQKPEEVMAALQSGNRR 174 Query: 177 ALAQLITALESGRIDPALR-QAVHARAATAHTPVLGITGTGGAGKSSLTDELIRRFRLDQ 235 ALA++++ALE+G LR Q V A A A TP LGITGTGGAGKSSLTDEL+RRFRLDQ Sbjct: 175 ALARIVSALENGAYPEGLRKQIVEAAALVATTPTLGITGTGGAGKSSLTDELVRRFRLDQ 234 Query: 236 HDRLRIAVISIDPSRRKSGGALLGDRIRMNAINHPNLFVRSLATREASSEISDALPDVIA 295 D L++A+ISIDPSR+++GGALLGDRIRMNAI HPN+F+RSLATRE SEIS ALP+VIA Sbjct: 235 EDGLKLAIISIDPSRKRTGGALLGDRIRMNAIEHPNIFMRSLATRETGSEISAALPEVIA 294 Query: 296 ACRAGGFDLIIVETSGIGQGDAAIVPHADLSLYVMTPEFGAASQLEKIDMLDFADLVAIN 355 AC+ GFDLIIVETSGIGQGDAAIVP D SLYVMTPEFGAASQLEKIDMLDFAD VAIN Sbjct: 295 ACKLSGFDLIIVETSGIGQGDAAIVPLVDASLYVMTPEFGAASQLEKIDMLDFADFVAIN 354 Query: 356 KFDRKGAQDAWRDVAKQVQRNREQWHAKPEDMPVFGTQASHFNDDGVTALYHALADRLAE 415 KFDRKGA+DA RDV KQ QRNRE + P++MPVFGT A+ FNDDGVTALY A+ +L E Sbjct: 355 KFDRKGAEDALRDVRKQYQRNRELFTQSPDEMPVFGTMAARFNDDGVTALYQAILPKLVE 414 Query: 416 RGMALAERTLPRPAGTCSTSHDAIVPPARVRYLAEVADTVRGYHRRVDAQSGLARERQQL 475 G+ LP S+ AIVP R RYLAE+ADT+R YH+ + Q +ARERQ L Sbjct: 415 FGLKAKAGKLPVVTVKESSRGRAIVPVERTRYLAEIADTLRAYHKHTEEQVKIARERQSL 474 Query: 476 QASRRMLEAAGAAADV-LTALDAQAAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIR 534 + S+ + + AA L D A +++ L A +KLL MWPD +AY+GDEYVVKIR Sbjct: 475 RISKDLFNSYDEAAKAALPKFDELIACKESELDAKAKKLLDMWPDTVKAYSGDEYVVKIR 534 Query: 535 DRELRTPLTYTTLSGTTLRKVVLPPYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDV 594 D+E+RT L +LSGT ++KVVLP + DDGE LR+LM+ENVPGSFPYTAGVFAFKR G Sbjct: 535 DKEIRTKLVSESLSGTKIKKVVLPRFTDDGETLRFLMKENVPGSFPYTAGVFAFKREG-- 592 Query: 595 GGEDPTRMFAGEGDALRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGN 654 EDPTRMFAGEGDA RTNRRFK VSEGM A RLSTAFDSVTLYG DPD RPDIYGK+GN Sbjct: 593 --EDPTRMFAGEGDAFRTNRRFKKVSEGMPAHRLSTAFDSVTLYGCDPDVRPDIYGKIGN 650 Query: 655 AGVSIATLDDLKVLYDGFDLTSPNTSVSMTINGPAPTILAMFMNTALDQNLARFRADNGR 714 +GVSIATLDD+KVLY GFDL P TSVSMTINGPAP ILA F NTA+DQ L +FRADNGR Sbjct: 651 SGVSIATLDDMKVLYSGFDLVCPTTSVSMTINGPAPIILACFFNTAIDQQLDKFRADNGR 710 Query: 715 EPTEGEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVR 774 EPTE E KIR WVL +VRGTVQADILKEDQGQNTCIFST F+LK+MGDIQE+FVH+QV+ Sbjct: 711 EPTEDEAEKIREWVLASVRGTVQADILKEDQGQNTCIFSTEFALKMMGDIQEFFVHNQVQ 770 Query: 775 NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMD 834 NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVE+YLARGMHIDDFAPNLSFFFSNGMD Sbjct: 771 NFYSVSISGYHIAEAGANPISQLAFTLANGFTYVESYLARGMHIDDFAPNLSFFFSNGMD 830 Query: 835 PEYSVLGRVARRIWAVTMRDKYGANERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALI 894 PEYSV+GRVARRIWAV M++KYGANERSQKLKYH+QTSGRSLHAQE+ FNDIRTTLQALI Sbjct: 831 PEYSVIGRVARRIWAVAMKNKYGANERSQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALI 890 Query: 895 AIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGLAKCENPNQGSFIIDELTD 954 AIYDNCNSLHTNAYDEAITTPT ESVRRA+AIQLIINREWG+AK ENPNQG+FIIDELTD Sbjct: 891 AIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINREWGVAKNENPNQGAFIIDELTD 950 Query: 955 LVEAAVLREFERLAERGGVLGAMETGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPE 1014 LVE AVL+EFE +A RGGVLGAMETGYQRG+IQEES+ YE +KHDGS PI+GVNTF NP+ Sbjct: 951 LVEEAVLKEFEAIASRGGVLGAMETGYQRGKIQEESLYYEHKKHDGSYPIIGVNTFLNPK 1010 Query: 1015 AGHAAPAHIELARSSEEEKQRQLARLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMD 1074 +A IELARS+EEEKQ Q+ARL DFH R+A +APAML +L++ VI++ NVFAVL++ Sbjct: 1011 G--SAQVEIELARSTEEEKQSQIARLKDFHQRNADKAPAMLAKLKQTVIENGNVFAVLVE 1068 Query: 1075 AVRVCSLGQITHALFEVGGQYRRNM 1099 AVRVCSLGQIT AL+EVGGQYRR+M Sbjct: 1069 AVRVCSLGQITGALYEVGGQYRRSM 1093 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: 2807 Number of extensions: 88 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: 1099 Length of database: 1093 Length adjustment: 46 Effective length of query: 1053 Effective length of database: 1047 Effective search space: 1102491 Effective search space used: 1102491 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: 58 (26.9 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