5
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Functional classification of the Encephalitozoon cuniculi protein-coding genes.
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Gene identification number indicates the gene position with regard to one chromosomal sequence extremity and is preceded by the corresponding chromosome number. Each gene is listed in its functional role category with the common name assigned to the protein. The gene of the organism having the the best match is indicated in parentheses and abbreviated as in SWISSPROT-TrEMBL. The total number of genes associated with each major category is given. Ribosomal proteins are classified using the nomenclature adopted for mammals (an alternative appellation shown in parentheses is from the yeast nomenclature). Abbreviations for common names are as follows: Bprt, binding protein; cat, catalytic; CoA, coenzyme A; DAG, diacylglycerol; dep, dependent; DHase, dehydrogenase; elong, elongation; init, initiation; fam, family; mito, mitochondrial; P, phosphate; pol, polymerase; PP, pyrophosphate; prt, protein; put, putative; RDase, reductase; reg, regulatory; rel, related; rep, replication; Sase, synthetase, synthase; sub, subunit; subfam, subfamily; Tase, transferase; transp, transporter; w.sim, weak similarity.
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5
5
I. METABOLISM…………………………….79
Amino-acid metabolism
04.0840 asparagine Sase (ASNH METJA)
09.0910 deoxyhypusine Sase (DHYS SCHPO)
11.1430 diphthine Sase (DPH5 yeast)
08.0360 ornithine decarboxylase, w. sim
(DCOR yeast)
Nitrogen and sulfur metabolism
07.0100 NGG1-interacting factor 3 (NIF3 yeast)
11.1770 NIFS-like prt (NFS1 CANAL)
01.0510 NIFU-like prt (NIFU RICPR)
Nucleotide metabolism
Purine-ribonucleotide metabolism
01.0170 dihydrofolate RDase (DYR ENCCU)
01.1450 dihydrofolate RDase(DYR ENCCU)
08.0080 dihydrofolate RDase (DYR ENCCU)
01.1220 guanylate kinase (KGUA yeast)
01.0190 serine hydroxymethylTase (GLYC yeast)
01.1420 serine hydroxymethylTase (GLYC yeast)
Pyrimidine-ribonucleotide metabolism
11.0880 CTP Sase (PYRG MOUSE)
11.0480 CTP Sase (PYRG MOUSE)
03.1270 cytidylate kinase (KCY BACSU)
04.1220 thymidylate kinase (KTHY yeast)
Deoxyribonucleotide metabolism
09.1960 cytidine and dCMPdeaminase (TAD2 yeast)
05.0280 deoxyuridine 5'-triP nucleotidohydrolase
(DUT CHVP1)
06.0430 deoxyuridine 5'-triP nucleotidohydrolase
(DUT yeast)
08.1380 glutaredoxin (GLRX ORYZA)
09.1375 glutaredoxin (GLR2 SCHPO)
10.0920 ribonucleoside-diP RDase, large sub
(RIR1 CAEEL)
06.0730 ribonucleoside-diP RDase, small sub
(RIR2 BRARE)
01.0740 thymidine kinase (KITH ENCCU)
01.0180 thymidylate Sase (TYSY ENCCU)
01.1430 thymidylate Sase (TYSY ENCCU)
08.0090 thymidylate Sase (TYSY ENCCU)
Polynucleotide degradation
03.0200 deoxyribonuclease, TATD fam (TATD ECOLI)
03.0670 ribonuclease, HII fam (YNH2 yeast)
Other
08.0740 ATP-Bprt, MRP/MBP35 fam (NB35 yeast)
10.0480 bis (5'-adenosyl) triphosphatase, HIT fam
(FHIT HUMAN)
03.0880 bis (5'nucleosyl) tetraphosphatase, HIT fam
(APH1 SCHPO)
06.1530 nucleoside diP kinase A (NDKA FLABI)
04.1180 nucleoside triphosphatase, HAM1 fam
(HAM1 yeast)
05.0870 nucleoside triphosphatase, HAM1 fam
(NTPA METJA)
Phosphate metabolism
07.0180 acid phosphatase (PPAY CAEEL)
10.0340 inorganic pyrophosphatase (IPYR DROME)
10.1370 inositol polyphosphate-5 phosphatase, put (INP54 yeast)
05.1170 involved in polyphosphate metabolism
(PHM8 yeast)
06.1420 polyphosphate synthase, put (VTC4 yeast)
C-compound and carbohydrate metabolism
04.1130 a-1,2-mannosylTase, KTR fam (YUR1 yeast)
05.0310 acetyl-CoA Sase (ACS1 yeast)
09.1320 acidic endochitinase (CHIP BETVU)
01.0970 aldose RDase (ALDR MOUSE)
01.1390 chitin synthase 1 (CHS1 CRYNE)
07.1760 glucosamine-P N-acetylTase (GNA1 CAEEL)
07.1280 glucosamine-fructose-6-P aminoTase
(GFA2 HUMAN)
01.0650 phosphoacetylglucosamine mutase
(PCM1 SCHPO)
11.1780 UDP-N-acetylglucosamine
pyrophosphorylase (UAP1 yeast)
Lipid, fatty acid and isoprenoid metabolism
Biosynthesis
10.0310 1-acyl-sn-glycerol-3-P acylTase (PLSC yeast)
04.1280 1-acyl-sn-glycerol-3-P acylTase, put
(Y205 HUMAN)
10.1260 1-acyl-sn-glycerol-3-P acylTase, put
(YBP2 yeast)
11.0620 1,2-DAG ethanolamine phosphoTase
(EPT1 yeast)
10.1720 3-hydroxy-3-methylglutaryl-CoA RDase
(HMD1 DICDI)
10.0510 3-hydroxy-3-methylglutaryl-CoA Sase
(HMC2 BLAGE)
01.1000 CDP-DAG inositol 3-phosphatidylTase
(PIS HUMAN)
11.0850 CDP-DAG serine O-phosphatidylTase
( PEL1 yeast)
05.1250 CDP-DAG synthase (CDS1 yeast)
10.1590 choline-P cytidylylTase (CPCT MOUSE)
11.1810 farnesyl-PP Sase (FPPS HELAN)
02.0230 isopentenyl-diP d-isomerase II (IDI2 ARATH)
10.0890 long-chain-fatty-acid-CoA ligase (LCFX RAT)
10.0910 long-chain-fatty-acid-CoA ligase (LCFX RAT)
09.1780 mevalonate kinase (KIME yeast)
10.1510 mevalonate kinase, w.sim. (KIME PYRHO)
06.0490 mevalonate-PP decarboxylase (ER19 yeast)
09.1210 N-acetylglucosaminyl-phosphatidylinositol
biosynthetic protein (GPI3 yeast)
02.0860 serine palmitoylTase, sub 1 (LCB1 HUMAN)
05.0730 serine palmitoylTase, sub 2 (LCB2 HUMAN)
10.0300 sterol ester Tase (AREH SCHPO)
Degradation
06.0940 acetyl-CoA-C-acylTase (ATOB HAEIN)
05.1520 acyl-CoA thioesterase II (TESB ECOLI)
01.1380 glycerophosphoryldiester phosphodiesterase,
w.sim (GLPQ BACSU)
04.0660 lipase, put (CVT17 yeast)
11.1180 phospholipase D2 (PLD2 RAT)
Other
08.1150 oxidoRDase, short chain DHase/RDase fam,
put (YKF5 yeast)
10.0560 oxidoRDase, short-chain DHase/RDase fam,
put (DLTE BACSU)
11.1070 oxidoRDase, short-chain DHase/RDase fam,
put (YAEB SCHPO)
II. ENERGY…………………………………….23
Glycolysis
03.0680 6-phosphofructokinase A (K6PF CANFA)
10.1690 enolase (ENO FASHE)
01.0240 fructose-bisP aldolase (ALFB HUMAN)
05.0650 glucose-6-P isomerase (G6PI PIG)
07.0800 glyceraldehyde-3-P DHase (G3P2 BACSU)
05.0270 glycerol-3-P DHase A (GPDA FUGRU)
10.0870 glycerol-3-P DHase, mito. (GPDM CAEEL)
11.1540 hexokinase (HXK SCHMA)
05.0320 phosphoglycerate kinase (PGK KLULA)
10.1060 phosphoglycerate mutase (PGMI ANTSP)
09.1040 pyruvate DHase E1, a sub (ODPA SCHPO)
04.1160 pyruvate DHase E1, b sub (ODPB RICPR)
09.0640 pyruvate kinase (KPYK YARLI)
11.0230 triose phosphate isomerase (TPIS SCHJA)
Pentose phosphate pathway
05.0860 6-phosphogluconate DHase (6PGD SALTY)
10.0180 D-ribose-5-P isomerase (RPIA METTH)
06.1040 D-ribulose-5-P 3-epimerase (RPE METJA)
08.1850 glucose-6-P 1-DHase (G6PD yeast)
06.0120 transketolase 1 (TKT1 yeast)
Trehalose metabolism
02.1370 a,a-trehalase (TREA BOMMO)
01.0800 a,a-trehalose-P Sase, cat sub
(TPSA ASPNG)
01.0870 trehalose-6-P phosphatase (TPS2 yeast)
03.0280 UTP-glucose-1-P uridylTase (UDPG yeast)
III. CELL GROWTH, CELL DIVISION
AND DNA SYNTHESIS…………..…………135
Cell growth and cell polarity
08.0160 calcineurin, b sub (CALB NAEGR)
04.0810 calcium-Bprt, recoverin subfam (NCS1 yeast)
05.0410 GTP-Bprt, GTP1/OBG fam (DRG1 XENLA)
08.1270 GTP-Bprt, GTP1/OBG fam (DRG2 HUMAN)
05.0800 GTP-Bprt, GTP1/OBG fam (FEOB METJA)
02.0200 involved in plasmid maintenance, respiration
and cell proliferation (SMP2 yeast)
03.1560 RAS-related GTP-Bprt (RAC1 CAEEL)
03.0980 ser/thr protein kinase (KIN1 SCHPO)
09.1610 required for normal growth,SUA5/YRDC/
YC10/YWLC fam (YWLC BACSU)
11.0360 suppressor of temperature-sensitive growth
of yeast MRP1 mutants (SOH1 yeast)
09.0730 suppressor of BEM1/BUD5 (BE46 SCHPO)
Meiosis
04.1110 meiotic recombination prt (RE12 SCHPO)
06.0740 MEI2-related prt (MES1 SCHPO)
DNA synthesis and replication
DNA-directed DNA polymerases
05.0990 DNA pol a, sub A (DPOA SCHPO)
10.1080 DNA pol a, sub B (DPO2 rat)
05.1210 DNA pol / primase, large sub (PRI2 HUMAN)
08.0630 DNA pol / primase, small sub (PRI1 MOUSE)
09.0430 DNA pol d, large sub (DPOD CANAL)
09.0770 DNA pol d, small sub (DPD2 MOUSE)
05.1030 DNA pol d, PCNA (PCNA BRANR)
10.1210 DNA pol e, cat sub (DPOE SCHPO)
DNA replication factors A and C
10.0600 DNA rep factor A, prt 1 (RFA1 SCHPO)
06.0360 DNA rep factor A, prt 2 (RFA2 HUMAN)
07.0950 DNA rep factor A, prt 3, w.sim
(RFA3 SCHPO)
05.1530 DNA rep factor C sub (RFC1 yeast)
02.0680 DNA rep factor C sub (RFC2 yeast)
02.0290 DNA rep factor C sub (RFC3 yeast)
10.0780 DNA rep factor C sub (AC13 HUMAN)
09.1330 DNA rep factor C sub (RFC5 yeast)
DNA replication licensing factors, MCM family
04.0850 MCM2 (CC19 SCHPO)
08.0290 MCM3 (MCM3 SCHPO)
02.1150 MCM4 (MCM4 SCHPO)
11.0800 MCM4 (MCM4 DROME)
06.0340 MCM5 (MCM5 yeast)
05.0780 MCM6 (MCM6 MOUSE)
07.0490 MCM7 (MCM7 MOUSE)
09.1360 MCM7 (MCM7 XENLA)
DNA topoisomerases
06.1520 DNA topoisomerase I (TRF5 yeast)
04.0350 DNA topoisomerase II (TOP2 SCHPO)
04.1070 DNA topoisomerase III (TOP3 SCHPO)
Other
02.1090 ATP-dept DNA-binding helicase,
RAD3/XPD fam (CHL1 yeast)
08.1120 ATP-dept DNA-binding helicase,
RAD3/XPD fam (CHL1 yeast)
09.1800 DNA helicase (DNA2 yeast)
02.1220 DNA ligase (DNL1 MOUSE)
03.1030 origin recognition complex, sub 1
(ORC1 DROME)
10.1130 origin recognition complex, sub 2
(ORC2 ARATH)
09.0310 telomerase, cat sub (TERT SCHPO)
Recombination and DNA repair
07.1130 ATP-dep DNA helicase (HUS2 SCHPO)
03.0910 casein kinase I (HHP2 SCHPO)
11.1980 casein kinase I, a sub (KC1A BOVIN)
01.0350 chromodomain DNA-Bprt, SNF2/RAD54 fam
(CHD2 HUMAN)
05.0300 DNA mismatch repair prt, MUTL/HEXB fam
(MLH1 HUMAN)
11.1260 DNA mismatch repair prt, MUTL/HEXB fam
(HEXB STRPN)
03.0540 DNA mismatch repair prt, MUTS fam
(MSH2 HUMAN)
10.0710 DNA mismatch repair prt, MUTS fam
(MSH6 yeast)
06.0200 DNA repair helicase, RAD3/XPD subfam
(RAD3 yeast)
01.1060 DNA repair helicase RAD25 (RA25 yeast)
01.0450 DNA repair prt, RAD4/XPC fam
(XPC MOUSE)
10.1170 DNA repair prt, RAD14/XPA fam
(XPA XENLA)
07.0610 DNA repair prt RAD50 (RA50 yeast)
08.0760 DNA repair prt, XPF/ERCC4/RAD1 fam
(MEI9 DROME)
05.1280 double-strand break DNA repair prt,
MRE11/RAD32 fam (RA32 SCHPO)
11.0760 exonuclease 1 (EXO1 SCHPO)
07.0380 exonuclease, put (YSM4 CAEEL)
07.0390 recombination and DNA repair prt RAD18
(RA18 SCHPO)
09.0410 recombination and DNA repair prt RAD26
(RA26 yeast)
06.0820 recombination and DNA repair prt
SNF2/RAD54 fam (YA83 SCHPO)
09.1390 RUVB-like DNA helicase (RUVB MYCLE)
10.0530 uracyl-DNA glycosylase (UNG HUMAN)
Cell cycle control and mitosis
Protein kinases
05.1510 casein kinase II, a sub (KC2A CAEEL)
10.1200 casein kinase II, b sub KC2B DROME)
03.0420 CDC 68 (Start, general transcription)
(CC68 yeast)
11.0960 cell cycle protein kinase CDC2
(CC2A ANTMA)
08.1920 cell cycle protein kinase CDK2
(CDK2 CARAU)
08.0230 cell cycle protein kinase, CDC2/CDKX
subfam (CC22 MEDSA)
11.1290 cell cycle protein kinase, CDC2/CDKX
subfam (CDKA HUMAN)
08.1790 cell cycle protein kinase, CDC2/CDKX
subfam (CDK9 CAEEL)
08.1960 cell cycle protein kinase, CDC7 subfam
(HSK1 SCHPO)
10.0120 cell cycle protein kinase, CDC7 subfam
(HSK1 SCHPO)
02.1450 cyclin-dep ser/thr protein kinase (KI28 yeast)
10.0830 mitogen-activated protein kinase
(MK16 yeast)
03.0620 ser/thr protein kinase (CHK1 SCHPO)
07.1270 ser/thr protein kinase (MRK1 yeast)
05.0630 ser/thr protein kinase (PKPA PHYB)
02.0550 ser/thr protein kinase (SPK1 yeast)
08.1620 ser/thr protein kinase (WEE1 XENLA)
07.0360 ser/thr/tyr protein kinase (IPL1 yeast)
02-0510 thr/tyr protein kinase (MPS1 yeast)
Protein phosphatases
04.0300 protein tyrosine phosphatase (PTPE MOUSE)
09.0980 ser/thr protein phosphatase 1-1, cat sub
(PP11 yeast)
11.0660 ser/thr protein phosphatase 1-1, cat sub
(PP11 CAEEL)
05.0440 ser/thr protein phosphatase 1-1, g cat sub
(PPP5 HUMAN)
04.0690 ser/thr protein phosphatase 2-A, a sub
(P2AA CHICK)
04.0200 ser/thr protein phosphatase 2-A, b sub
(2A5G HUMAN)
09.1490 ser/thr protein phosphatase 2-A, reg sub A
(2AAA DROME)
05.0810 ser/thr protein phosphatase 2-A, reg sub B
(2ABD RAT)
07.1520 ser/thr protein phosphatase 2-C
(P2C1 ARATH)
Cyclins
08.0260 cyclin B, G2/M specific (CG2B MEDSA)
04.1460 cyclin B-like prt (CG2B CARAU)
09.0840 cyclin C-like prt, G1/S transition
(CG1C ORYZA)
01.1150 cyclin C-like (or K) prt (CYCK HUMAN)
Chromosome segregation proteins, SMC family
07.0680 chromosome segregation prt (CUT3 SCHPO)
01.1160 chromosome segregation prt (CUT4 SCHPO)
09.1910 chromosome segregation prt (P115 MYCPN)
04.0930 chromosome segregation prt (SMC1 yeast)
11.2000 chromosome segregation prt, put
(YDZ2 SCHPO)
Other
06.1430 anaphase promoting complex sub
(CC23 yeast)
06.0150 anaphase promoting complex sub
(CUT9 SCHPO)
06.1450 CDC50-like prt, put (YCY4 yeast)
05.1020 centromere/microtubule-Bprt (CBF5 SCHPO)
07.0860 cullin (CUL2 CAEEL)
06.0880 cullin (CUL6 CAEEL)
01.0210 interacts with B-type cyclin, NAP/SET fam
(SET DROME)
01.1400 interacts with B-type cyclin, NAP/SET fam
(SET DROME)
11.0170 RAS suppressor (RSU1 HUMAN)
04.1250 required for microtubule-dep processes prior
to anaphase (CC20 yeast)
07.0350 required for spindle pole body duplication
(CUT1 SCHPO)
02.1270 required for mitosis (D1B1 yeast)
03.1380 required for mitosis and meiosis
(PELO DROME)
01.1300 similarity to CDC4 (CC4 yeast)
03.1520 similarity to CDC20, put (YGA3 yeast)
11.1590 spindle pole body prt (SAD1 SCHPO)
Cytokinesis
03.1230 periodic tryptophan prt 1 (PWP1 HUMAN)
05.0190 periodic tryptophan prt 2 (PWP2 yeast)
11.1950 septin (C10H MOUSE)
09.0820 septin (CC10 yeast)
01.1370 septin-like prt (SPN4 SCHPO)
01.0630 ser/thr protein kinase required for actin ring
and septation (PLO1 SCHPO)
11.0430 similarity to SKT5 (interacts with septins),
put (YAIA SCHPO)
02.1030 similarity to SKT5 (interacts with septins),
put (YBEQ ECOLI)
06.0540 similarity to SKT5 (interacts with septins),
put (YBEQ ECOLI)
Other
11.0650 DNA hexamer-Bprt (HEXP LEIMA)
06.0610 N6-adenine-specific DNA methylase
(N6M1 HUMAN)
08.1860 N6-adenine methylTase, put (Y284 METJA)
11.1190 nucleotide-Bprt (NB35 yeast)
IV. TRANSCRIPTION……………………..171
rRNA transcription
rRNA synthesis
04.1400 RNA pol I, first largest sub (RPA1 SCHPO)
03.0440 RNA pol I, second largest sub (RPA2 yeast)
01.0600 RNA pol I, 40K sub (RPA5 HUMAN)
08.1330 RNA pol I, 13.7K sub (RPA9 yeast)
rRNA processing
10.0690 ATP-dep RNA helicase (25S maturation),
DEAD box fam (SPB4 yeast)
08.1080 ATP-dep RNA helicase (P68-like),
DEAD box fam (DBP2 yeast)
06.1250 ATP-dep RNA helicase (25S maturation),
put (YA47 SCHPO)
10.0440 ATP-dep RNA helicase (18S maturation),
put (YN21 CAEEL)
06.0390 belongs to the RNase PH (exosome) fam, put
(YBX3 SCHPO)
10.0270 belongs to the RNase PH (exosome) fam, put
(YG2N yeast)
03.0700 component of the 3', 5' exoribonuclease for 3'
end formation of 5.8S rRNA (DIS3 yeast)
09.0830 component of the 3', 5' exoribonuclease for 3'
processing of 5.8S rRNA (RNPH CAEEL)
10.0820 fibrillarin (FBR2 yeast)
07.0320 nucleolar prt (NOP2 yeast)
04.0820 nucleolar prt, pre-18S splicing (NOP5 yeast)
09.1600 nucleolar prt, pre-18S splicing (NOP5 yeast)
01.1080 nucleolar prt, NOL1/NOP2 fam
(p120 HUMAN)
04.0460 rRNA adenine-N6,N6-dimethylTase
(DIM1 yeast)
07.1340 rRNA methylTase (SPB1 yeast)
09.0920 rRNA methylTase, put (YEK3 SCHPO)
01.1360 small nucleolar prt (GAR1 yeast)
03.0730 small nucleolar prt (GAR2 SCHPO)
05.1320 U3 snoRNP, 18S production (IMP3 yeast)
02.0240 U3 snoRNP, 18S production (SOF1 yeast)
11.1910 U3 snoRNP, IMP4-like prt (YEE7 SCHPO)
tRNA transcription
tRNAsynthesis
07.0090 RNA pol III, 160K sub (RPC1 yeast)
11.0370 RNA pol III, 130K sub (RPC2 SCHPO)
10.0210 RNA pol III, 34K sub (RPC6 yeast)
08.0650 RNA pol III, 25K sub (RPCY yeast)
03.0490 RNA pol III, 12.5K sub (RPCZ yeast)
11.0590 RNA pol I and III, 14K sub (RPC9 HUMAN)
05.0500 transcrption init factor TFIIIB, 70K sub
(TF3B yeast)
tRNA processing
07.1650 ribonuclease P sub (RP29 HUMAN)
03.0920 tRNA intron endonuclease (ENDA METTH)
tRNA modification
08.1450 N2,N2-dimethylguanosine-tRNA methylTase
(TRM1 yeast)
11.1610 tRNA pseudouridylate Sase 1(TRUA METTH)
04.0890 tRNA pseudouridylate Sase 2 (PSU2 yeast)
05.1350 tRNA pseudouridylate Sase 2 (TRUB METJA)
03.1440 tRNA adenylylTrase (CCA1 yeast)
06.0310 tRNA ribosylTase (TGT DROME)
mRNA transcription
General activities
DNA-directed RNA polymerase II
03.0290 RNA pol II, first sub (RPB1 SCHPO)
10.0250 RNA pol II, second sub (RPB2 SCHPO)