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Entamoeba Genome Structure Proteins

      

Synthetase and Modification Proteins

Genome structure proteins included in supplementary tables for tRNA synthetases, tRNA and rRNA modification proteins are presented here from the Structure and Content of the Entamoeba histolytica Genome (submitted, Advances in Parasitology).

We present Protein Name, Protein Accession linked to NCBI's Entrez Protein database, mRNA models (XM) included in the reannotation linked to TIGR's Annotation Display (Pathema Annotation Link) or mRNA models not included in the reannotation linked to NCBI's Nucleotide database (Models Excluded from the Reannotation).

tRNA Synthetase Proteins (section 2.12)

Protein Name Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
Isoleucyl-tRNA synthetase XP_655936 EHI_177660
Valyl-tRNA synthetase XP_650652 EHI_033680
Methionyl-tRNA synthetase XP_652867 EHI_079860
Leucyl-tRNA synthetase XP_649157 EHI_161970
Tyrosyl-tRNA synthetase XP_650212 EHI_009240
Tryptophanyl-tRNA synthetase XP_649189 EHI_020240
Tryptophanyl-tRNA synthetase XP_657052 EHI_110420
Tryptophanyl-tRNA synthetase XP_654266 EHI_110680
Glutaminyl-tRNA synthetase XP_650546 EHI_062700
Glutaminyl-tRNA synthetase XP_655785 EHI_155570
Glutamyl-tRNA synthetase XP_651552 EHI_127020
Arginyl-tRNA synthetase XP_650386 EHI_169700
Cysteinyl-tRNA synthetase XP_650600   XM_645508
Lysyl-tRNA synthetase XP_649894 EHI_175050
Aspartyl-tRNA synthetase XP_651543 EHI_126920
Asparaginyl-tRNA synthetase XP_656678 EHI_073460
Glycyl-tRNA synthetase XP_653365 EHI_103730
Threonyl-tRNA synthetase XP_650679 EHI_092640
Seryl-tRNA synthetase XP_650679 EHI_092640
Prolyl-tRNA synthetase XP_651857   XM_646765
Prolyl-tRNA synthetase XP_648621 EHI_040400
Histidyl-tRNA synthetase XP_655565 EHI_180020
Alanyl-tRNA synthetase XP_654998 EHI_198790
Phenylalanyl-tRNA synthetase XP_651987 EHI_078230

tRNA and rRNA Modification Proteins (section 2.12)

Protein Name Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
RNAse P subunit (POP1) XP_652185 EHI_127090  
RNAse P subunit (POP1) XP_651558   XM_646466
RNAse P subunit p30 XP_650994 EHI_179350  
RNAse P subunit p30 XP_650994 EHI_179350  
tRNA dihydrouridine synthase 1 XP_655221 EHI_164780  
tRNA dihydrouridine synthase 1 XP_655192   XM_650100
tRNA dihydrouridine synthase 3-like XP_651736 EHI_140340  
tRNA exportin XP_652648 EHI_029040  
tRNA intron endonuclease subunit (SEN2) XP_656546 EHI_042160  
tRNA intron endonuclease subunit (SEN2) XP_655617   XM_650525
tRNA intron endonuclease subunit (SEN2) XP_655597 EHI_042160  
RNA: NAD 2’ phosphotransferase (tRNA splicing) XP_650634    
RNA: NAD 2’ phosphotransferase (tRNA splicing) XP_648371   XM_643279  
tRNA nucleotidyltransferase XP_654783 EHI_167070  
tRNA nucleotidyltransferase XP_652076 EHI_054790  
tRNA delta(2)-isopentenylpyrophosphate transferase XP_655777 EHI_155640  
tRNA adenosine deaminase subunit XP_649973 EHI_019970  
tRNA (uracil-5) methyl transferase XP_650594   XM_645502
tRNA (uracil-5) methyl transferase XP_650606    
tRNA (1-methyladenosine) methyltransferase (poss) XP_653764 EHI_039210  
tRNA (1-methyladenosine) methyltransferase (poss) XP_650623 EHI_175220  
tRNA cytosine methyltransferase (poss) XP_653353 EHI_103830  
tRNA cytosine methyltransferase (poss) XP_656026 EHI_098500  
tRNA/rRNA C-5-methyltransferase XP_654608 EHI_140970  
N2N2-dimethylguanosine tRNA methyltransferase XP_657464 EHI_148760  
tRNA methyltransferase subunit TRM5 XP_650095 EHI_111740  
tRNA methyltransferase subunit TRM8 XP_656291 EHI_178940  
tRNA methyltransferase subunit TRM8 XP_656230   XM_651138
tRNA methyltransferase subunit TRM8 XP_649121 EHI_178940  
queuine tRNA-ribosyltransferase XP_656142 EHI_035660  
queuine tRNA-ribosyltransferase XP_652881 EHI_079900  
D-Tyr-tRNA (Tyr) deacylase (poss) XP_656041 EHI_118150  
rRNA pseudouridine synthase 1 XP_657416 EHI_151650  
rRNA pseudouridine synthase 1 XP_656284 EHI_179010  
rRNA pseudouridine synthase 2 XP_653636   XM_648544
rRNA pseudouridine synthase 2 XP_648050 EHI_088330  
rRNA pseudouridine synthase 2 XP_656733   XM_651641
tRNA adenosine deaminase subunit XP_657152 EHI_067570  
rRNA cytosine/adenosine deaminase XP_656002 EHI_169890  
rRNA methyltransferase XP_654474 EHI_006720  
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DNA Replication Initiation Proteins (section 2.13)

Entamoeba histolytica genes encoding homologues of Saccharomyces cerevisiae and Homo sapiens genes involved in DNA replication initiation.
The Saccharomyces cerevisiae Gene Homologues table includes : Yeast Protein Length (aa), protein Function, Entamoeba Homologue protein models (XP) linked to NCBI's Entrez Protein database, mRNA models (XM) included in the reannotation linked to TIGR's Annotation Display (Pathema Annotation Link), Entamoeba Homologue Length (aa), E-value, Stretch of Homology, % Identity, % Similarity, Conserved Domain, and span of the domain Region in parentheses.


The Homo sapiens Gene Homologues table includes : Human Protein Length (aa), protein Function, Entamoeba Homologue protein models (XP) linked to NCBI's Entrez Protein database, mRNA models (XM) included in the reannotation linked to TIGR's Annotation Display (Pathema Annotation Link), Entamoeba Homologue Length (aa), E-value, Stretch of Homology, % Identity, % Similarity, Conserved Domain, and span of the domain Region in parentheses.

Footnotes:
Saccharomyces cerevisiae homologous genes sought but not found: MCM1, MCM10, Cdc7, DBF4, Orc2, Orc3, Orc4, Orc5, Orc6, Cdt1, geminin and DNA pol ε
Please note that entries with ** have multiple Pathema Annotation Links.

Saccharomyces cerevisiae Gene Homologues

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
MCM2 (868) Component of replicative helicase XP_656059 EHI_117970 883 1.50E-154 245-460 51 69 Mcm (351-861)
MCM3 (972) ** Component of replicative helicase XP_653372 EHI_103600 601 4.70E-105 71-391 53 69 Mcm (6-529)

  XP_653372 EHI_103600




 

  XP_653372 EHI_103600




 

  XP_653372 EHI_103600




 
MCM4 (934) Component of replicative helicase XP_649080 EHI_187720 608 2.30E-135 225-607 49 71 Mcm (92-576)
MCM5 (775) Component of replicative helicase XP_648784 EHI_069980 639 1.60E-134 310-625 61 78 Mcm (130-622)
MCM6 (1018) Component of replicative helicase XP_654108 EHI_118870 682 8.20E-152 310-655 56 73 Mcm (130-655)
MCM7 (846) Component of replicative helicase XP_650807 EHI_158110 690 1.80E-124 66-657 41 62 Mcm (157-653)
Cdc45 (651) DNA replication initiation factor; recruited to pre-RC complexes XP_657172 EHI_049900 543 1.40E-26 176-365 23 41 Cdc45 (24-537)
Cdc28 (298) Cyclin-dependent kinase (CDK) XP_652398 EHI_065280 291 4.30E-74 1-283 50 60 S-Tkc
Pol1 (1468) Catalytic subunit of the DNA polymerase alpha-primase complex XP_657373 EHI_151520 1132 7.80E-72 593-929 34 55 Pol_B (593-929)
Psf1 (208) Subunit of the GINS complex XP_652581 EHI_136990 189 0.00085 94-185 29 53 Psf1 (8-188)
Psf2 (213) Subunit of the GINS complex XP_655297 EHI_069340 199 2.70E-15 51-191 31 51 Psf2 (20-160)
Psf3 (194) Subunit of the GINS complex XP_648782 EHI_069960 216 0.73 66-185 30 49 Psf3 (68-188)
Sld5 (294) Subunit of the GINS complex XP_648113 EHI_048430 204 1.00E-04 82-204 24 43 COG5086 (20-204)

Homo sapiens Gene Homologues

Human Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Cdc6/ORC1 (560) ** DNA replication licensing XP_650362 EHI_105150 371 1.20E-07 24 44 20-233 Cdc6 (18-360)

  XP_650362 EHI_105150




 
MCM8 (840) Component of replicative helicase XP_654207 EHI_140670 733 1.70E-109 42 62 178-731 MCM2 (50-733)
MCM9 (391) ** Component of replicative helicase XP_654939 EHI_076880 810 1.60E-46 39 55 14-285 MCM (25-500)

  XP_654939 EHI_076880




 
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Checkpoint Gene Homologues (section 2.13)

Checkpoint Gene Homologues have been characterized in Entamoeba histolytica and presented in four tables:

DNA Replication Checkpoint Genes: E. histolytica genes encoding homologues of S. cerevisiae DNA replication checkpoint genes. Footnote: Genes sought but not found: Tof1 and Dpb11.

G1-S Phase Transition Saccharomyces cerevisiae Gene Homologues: E. histolytica genes encoding homologues of S. cerevisiae G1-S phase transition. Footnote: Genes sought but not found: p21, p27, p53, Chk1, PRB, Cln4, Sic1, CDC25, and DHH1.

G1-S Phase Transition Homo sapiens Gene Homologues: E. histolytica genes encoding homologues of Homo sapiens G1-S phase transition.

Spindle Formation Saccharomyces cerevisiae Gene Homologues: E. histolytica genes encoding homologues of S. cerevisiae checkpoint genes required for spindle formation. Footnote: Genes sought but not found: Mad1/3, Bub1,3, Cep3, Dma1, Bim1, and Gac1.

Footnote:
Please note that entries with ** have multiple Pathema Annotation Links.

DNA Replication Checkpoint Genes

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Mec1 (2369) ** Central regulator of the Mec1p/Tel1p XP_653989 EHI_197310 946 1.40E-56 453-945 29 50 PI3Kc_related (614-886)

  XP_653989 EHI_197310





Mrc1 (1097) S-phase checkpoint XP_653447 EHI_072050 1813 7.00E-07 586-1200 19 37 Autophagy protein Apg6 (707-827), Smc (611-853)

G1-S Phase Transition Saccharomyces cerevisiae Gene Homologues

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Cdc28 (298) Cyclin-dependent kinase (CDK) XP_652398 EHI_065280 291 4.30E-74 1-283 50 60 S-Tkc (3-283)
Skp1 (195) kinetochore protein, component of SCF ligase XP_654128 EHI_118670 162 1.00E-34 45-160 49 69 Skp1 (8-110)
Cdc34 (295) Ubiquitin-conjugating enzyme or E2; component of SCF ligase XP_652735 EHI_048700 165 1.40E-36 5-162 45 69 Ubiquitin-conjugating enzyme E2 (9-159)
Cdc53 (816) Cullin, structural protein of SCF complexes XP_652735 EHI_048700 721 3.70E-52 326-624 27 47 Cullin (80-720)
Cln1 (547) G1 cyclin XP_651788 EHI_121830 319 0.35 15-125 26 42 Cyclin (69-157)
Cln2 (545) G1 cyclin XP_648667 EHI_030880 307 0.015 85-163 22 51 Cyclin (183-272)
Cln3 (580) G1 cyclin XP_651788 EHI_121830 319 0.001 49-175 24 46 Cyclin (69-157)
RecQl4 helicase (1208) Role in cell cycle START XP_653505 EHI_023090 509 2.10E-40 35-354 31 52 DexHC (28-200)

G1-S Phase Transition Homo sapiens Gene Homologues

Human Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Models Excluded
from the Reannotation
Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
ATM kinase (3056) Intra S-phase checkpoint protein XP_650784   XM_645692 2410 6.30E-70 2042-2409 37 57 PI3Kc_related, Proteins related to phosphoinositide 3-kinase (2049-2327)
ATR kinase (2644) G1/S transition, G2/M transition XP_651798   XM_646706 1032 1.40E-56 249-981 24 46 PI3Kc_related (700-972)
Chk2 (543) G1/S transition XP_653200 EHI_011510
424 4.10E-53 4-406 33 50 S_TKc (123-386)

Spindle Formation Saccharomyces cerevisiae Gene Homologues

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Models Excluded
from the Reannotation
Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Glc7 (312) Involved in mitosis XP_651611 EHI_176170
303 1.70E-88 3-296 51 72 Protein phosphatase 2A homologues (32-294)
Pph21 (370) Catalytic subunit of protein phosphatase XP_656214   XM_651122 297 5.30E-92 7-294 53 72 Protein phosphatase 2A homologues (22-276)
Cdc55 (527) Catalytic subunit of phosphatase involved in mitosis XP_657525 EHI_148170
440 5.30E-70 150-347 35 53 WD40 28-359, Cdc55 (28-434)
Mps1 (764) Dual-specificity kinase required for spindle pole body (SPB) duplication XP_653959 EHI_073650
353 2.20E-23 23-309 29 52 S_TKc (23-306)
Bub2 (307) Spindle checkpoint protein XP_649751 EHI_135170
319 2.80E-22 35-298 28 46 TBC, Domain in Tre-2, BUB2p, and Cdc16p (50-251)
Tpd3 (635) Regulatory subunit A of the heterotrimeric protein phosphatase 2A,involved in mitosis XP_649444 EHI_124870
549 6.50E-40 27-548 27 45 COG1413, FOG: HEAT repeat (205-327)
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Chromosome Segregation Saccharomyces cerevisiae Gene Homologues (section 2.13)

E. histolytica genes encoding homologues of S. cerevisiae genes required for chromosome segregation

Footnote: Genes sought but not found: Bir1, Cbf1, Cbf2, Chl4, Ctf19, Ctf3, Ctf13, Cep3, Ctr9, Dsn1, Dam1,MCM 16, MCM21, MCM22, MTw1, NNf1,2, APC1(9; Brn1, Bur2, Cik1, Cse2, Doc1, Dyn1, Pds1, Src.
Please note that entries with ** have multiple Pathema Annotation Links.

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Models Excluded
from the Reannotation
Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Cse4 (230) Centromere protein that resembles histones, homologue of human CENP-A XP_653386 EHI_051840
147 1.60E-26 55-145 63 76 Histone H3 (51-147)
HRR25 (495) Protein kinase regulates DNA repair and chromosome segregation XP_657385 EHI_151950
335 9.70E-84 2-305 53 68 S_TKc (9-282)
Smc2 (1171) Component of the condensin complex, essential SMC chromosomal ATPase family member XP_657185 EHI_049770
1135 8.50E-158 1-379 41 61 Smc (1-1104)
Ipl1 (368) Aurora kinase XP_649507   XM_644415 317 2.10E-63 29-314 41 61 S-TKc (62-311)
Tub1 (448) Alpha-tubulin XP_653419 EHI_005950
455 2.1e-120 1-445 46 66 Tubulin/Ftsz (1-452)
Tub3 (446) Alpha-tubulin XP_653419 EHI_005950
455 8.4e-117 1-448 48 66 Tubulin/Ftsz (1-452)
Tub2 (458) Beta-tubulin XP_657170 EHI_049920
459 3.50E-134 1-429 54 74 Tub/Ftsz (2-398)
Mck1 (376) Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis XP_657520 EHI_148220
370 2.30E-59 30-328 41 58 S-TKc (32-316)
Apc 11 (166) Catalytic core subunit of the Anaphase-Promoting Complex/Cyclosome (APC/C), which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors XP_651657   XM_646565 87 2.40E-19 38-87 45 63 Apc11 (1-85)
Cin8 (1001) Kinesin motor protein XP_649446 EHI_124890
863 1.20E-56 133-780 27 47 Kinesin motor domain (2-321)
Smc4 (1449) Subunit of the condensin complex, which reorganizes chromosomes during cell division XP_654748 EHI_199700
1226 8.40E-101 150-1186 27 49 Smc (357-1215)
Kin3 (436) Chromosome segregation, protein kinase XP_648115 EHI_048410
484 5.80E-28 144-254 36 57 S-TKc (30-258)
Cdc20 (611) Activator of anaphase-promoting complex, required for metaphase/anaphase transition XP_657064 EHI_051010
377 4.90E-41 14-328 33 51 WD40 (52-327)
Cdh1 (567) ** CDC20 homologue XP_657064 EHI_051010
377 6.30E-41 34-328 31 53 WD40 (52-327)

  XP_657064 EHI_051010






  XP_657064 EHI_051010





Smc1 (1226) Subunit of the multiprotein cohesin complex, essential protein involved in chromosome segregation and in double-strand DNA break repair XP_656581 EHI_050790
1197 9.30E-118 54-1195 27 51 Smc (786-1196)
Cdc16 (840) Component of APC XP_656055 EHI_118010
497 4.40E-06 190-482 21 43 TPR (381-484)
Esp1 (1631) Separase with cysteine protease activity (related to caspases) that promotes sister chromatid separation by mediating dissociation of the cohesin Scc1p from chromatin XP_651118 EHI_120330
1503 1.00E-28 1246-1484 30 53 Peptidase (1239-1427), esp1 (1258-1484)
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Mitosis Saccharomyces cerevisiae Gene Homologues (section 2.13)

E. histolytica genes encoding homologues of S. cerevisiae involved in mitosis

Footnote: Genes sought but not found: Cik1, Dma2, Dad3, 4; Dyn1.

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Act (375) Actin XP_653735   376 1.40E-176 3-376 83 92 Actin (8-374)
Kip3 (806) Kinesin-related motor protein XP_656748 EHI_140230 629 2.50E-48 41-535 31 49 Kinesin motor domain (4-333)
HRR25 (495) Protein kinase regulates, DNA repair, and chromosome segregation; binds the CTD of RNA pol II XP_657385 EHI_151950 335 9.70E-84 2-305 53 68 S_TKc (9-282)
KAR3 (730) Minus-end-directed microtubule motor that functions in mitosis XP_651294   567 1.80E-80 211-556 31 49 Kinesin C terminal (236-560)
BNI1 (1954) Formin, nucleates the formation of linear actin filaments XP_653884 EHI_192460 1212 5.60E-14 683-1072 21 41 Formin (718-1097)
SAC3 (1302) Nuclear pore-associated protein, involved in transcription, mRNA export from the nucleus XP_655223 EHI_136450 670 0.011 322-491 23 42 Sac3 (437-653)
TOR1 (2471) Involved in cell cycle signaling and meiosis, controls cell growth XP_648644 EHI_104570 2417 0 497-1681 41 61 FAT (1940-2214), Tel1 (415-2296)
Ark1 (638) Serine/threonine protein kinase involved in regulation of the cortical actin cytoskeleton; involved in control of endocytosis XP_652314 EHI_127410 519 8.00E-41 4-388 30 48 S/Tkc (17-272)
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Exit from Mitosis Saccharomyces cerevisiae Gene Homologues (section 2.13)

E. histolytica genes encoding homologues of S. cerevisiae genes that regulate exit from mitosis

Footnote: Genes sought but not found: Spo12, Net1, Cdc14, Rio1.

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Tem1 (246) GTP-binding protein of the ras superfamily involved in termination of M-phase XP_657549 EHI_027640 189 1.80E-52 2-188 51 76 Rab/Rho (6-171/4-163)
Cdc15 (975) Protein kinase promotes mitotic exit XP_654672 EHI_009590 1760 2.30E-50 411-683 40 62 S-Tkc (420-676)
Mob1 (314) transcriptional regulator involved in mitosis XP_650241 EHI_159630 211 1.10E-41 22-196 38 60 Mob1 (27-199)
Mob2 (288) Directs daughter cell-specific transcription of several genes involved in cell separation XP_650241 EHI_159630 211 1.60E-35 23-199 38 60 Mob1 (27-199)
Lte1 (1435) Putative GDP/GTP exchange factor required for mitotic exit XP_651306 EHI_139450 491 4.20E-11 216-449 24 48 RasGEF (224-445)
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Cytokinesis Saccharomyces cerevisiae Gene Homologues (section 2.13)

E. histolytica genes encoding homologues of S. cerevisiae genes required for cytokinesis

Footnote: All known homologues were present.

Yeast Protein Length (aa) Function Entamoeba Homologue Pathema Annotation Link Entamoeba Homologue Length (aa) E-value Stretch of Homology % Identity % Similarity Conserved Domain (Region)
Actin (375) Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions XP_653735   376 1.40E-176 3-376 83 92 Actin (8-374)
Ark1 (638) Serine/threonine protein kinase involved in regulation of the cortical actin cytoskeleton XP_652314 EHI_127410 519 8.00E-41 4-388 30 48 S/Tkc (17-272)
Bir1 (954) Protein involved in cell cycle regulation and chromosome segregation, contains BIR domain XP_657286 EHI_093850 1387 1.90E-05 645-1382 25 46 CH, Calponin homology domain; actin-binding domain (28-123)
Cdc15 (975) Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase XP_654672 EHI_009590 1760 2.30E-50 411-683 38 60 S-Tkc (420-676)
Cla4 (843) Involved in localizing cell growth with respect to the septin ring; protein kinase, homologous to Ste20p, interacts with CDC42 XP_657512 EHI_148280 467 1.40E-82 215-460 48 65 S_TKc 192-447, PAK (p21 activated kinase) Binding Domain (88-127)
Exo70 (623) Essential 70kDa subunit of the exocyst complex XP_650775 EHI_142040 765 0.00048 549-611 23 38 Exo70 exocyst complex subunit (428-636)
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CDKs and Cyclins (section 2.13)

E. histolytica genes for CDKs and cyclins: Amino acid sequences of modified PSTAIRE motifs in CDS homologues. Identification of cyclin homologues is presented in two tables.

In the Amino Acid Sequences of Modified PSTAIRE Motifs in CDK Homologues table, Entamoeba CDK Homologues with protein models (XP) linked to NCBI's Entrez Protein database , mRNA models (XM) included in the reannotation linked to TIGR's Annotation Display (Pathema Annotation Link) or mRNA models not included in the reannotation linked to NCBI's Nucleotide database (Models Excluded from the Reannotation) and PSTAIRE Motif are presented. The protein models (XP) under the header Entamoeba Cyclin Homologues, the model mRNA (XM) link to TIGR's Annotation Display under the header Pathema Annotation Link, or mRNA models not included in the reannotation linked to NCBI's Nucleotide database (Models Excluded from the Reannotation), the Best Match, % Identify and % Similarity are presented in the Identification of Cyclin Homologues table.

Footnote: Genes sought but not found: Spo12, Net1, Cdc14, and Rio1.

Amino Acid Sequences of Modified PSTAIRE Motifs in CDK Homologues

Entamoeba CDK Homologue Pathema Annotation Link Models Excluded
from the Reannotation
PSTAIRE Motif
XP_652398 EHI_065280
PVTSVRE
XP_656401 EHI_153140
PSTALRE
XP_651330 EHI_108670
PVTSLRE
XP_656968 EHI_152430
SCSSLRE
XP_656764 EHI_068070
QSCNLRE
XP_653941 EHI_105300
SSTSLRE
XP_651418 EHI_054090
TSSALRE
XP_652736 EHI_048710
CSATIRE
XP_650467   XM_645375 PLEILRE

Identification of Cyclin Homologues

Entamoeba Cyclin Homologue Pathema Annotation Link Models Excluded
from the Reannotation
Best Match % Identity % Similarity
XP_652267 EHI_166420
Dreissena polymorpha B/A type cyclin 35 57
XP_648667 EHI_166420
Dictyostelium discodeum B type cyclin 34 58
XP_648916 EHI_003890
Nicotiana tabacum A/B type cyclin 23 46
XP_651788 EHI_121830
Nicotiana tabacum A/B type cyclin 25 47
XP_655949 EHI_087830
Xenopus laevis B type cyclin 26 43
XP_655180   XM_650088 Apis mellifera E type cyclin 24 40
XP_652067 EHI_054710
Gallus gallus H type cyclin 41 21
XP_650431   XM_645339 Oryza sativa H type cyclin 30 51
XP_653258 EHI_159560
Dictyostelium discodeum C type cyclin 29 52
XP_650240  
Dictyostelium discodeum C type cyclin 31 52
XP_648710 EHI_090030
Strongylocentrotus purpuratus K type cyclin 30 48
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Cleavage and Polyadenylation Specificity Factors (CPSF) (section 2.14)

Cleavage and Polyadenylation Specificity Factors (CPS), their subunits or proteins, the corresponding E. histolytica protein models (XP), mRNA models (XM) included in the reannotation linked to TIGR's Annotation Display (Pathema Annotation Link) or mRNA models not included in the reannotation linked to GenBank (Models Excluded from Reannotation) are presented in the following six tables:
Global Regulatory Subunits of the Ccr4/Not Complex in Entamoeba histolytica
Members of the Chromatin Remodeling Complexes of Entamoeba histolytica
Unidentified Bromodomain Proteins (PF00439) Found in the Entamoeba histolytica Genome
Entamoeba histolytica Homologues of General Transcription Factor Subunits
Splicing Machinery of Entamoeba histolytica
Entamoeba histolytica Homologues of Cleavage and Polyadenylation Specificity Factors (CPSF)
Other Transcription-related Proteins Mentioned

Footnote:
Please note that entries with ** have multiple Pathema Annotation Links.

Global Regulatory Subunits of the Ccr4/Not Complex in Entamoeba histolytica

Subunits of the Ccr4/Not Complex Protein Accession Pathema Annotation Link
CAF1 XP_652713 EHI_048150
CAF1 XP_656835 EHI_039000
CAF40 XP_653602 EHI_093570
CDC73 ** XP_652813  

XP_652813  
NOT1/CDC39 XP_652682 EHI_200810
NOT1/CDC39 XP_656253 EHI_178720
NOT1/CDC39 XP_648795 EHI_184570
NOT3 XP_651476 EHI_119550
NOT4 XP_654312 EHI_080710

Members of the Chromatin Remodeling Complexes of Entamoeba histolytica

Subunits Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
ehELP3 transcription elongation factor XP_657379 EHI_152010  
ehESA1 XP_654629 EHI_142000  
ehGCN5 XP_654208 EHI_140660  
RPD3 his/ehHDAC XP_650263 EHI_119320  
ehhat1 XP_653967 EHI_073570  
ehTra1 XP_650639   XM_645547

XP_650638 EHI_155160  
ehRbap46 ** XP_648975 EHI_020290  

XP_648975 EHI_020290  

XP_648975 EHI_020290  

XP_648352   XM_643260
ehRbAp46_2 XP_655352 EHI_052160  
RVB1/TBP interacting protein TIP49 XP_651853 EHI_040360  

XP_651853 EHI_040360  
RVB2/TBP interacting protein TIP49 XP_650562 EHI_091070  
ADA2 XP_651177   XM_646085
EAF3 XP_656783 EHI_067880  
Sir2 family with N terminal zinc binding domains XP_657434 EHI_151300  

XP_652007   XM_646915
Most similar to archaeal SIR proteins XP_654806 EHI_007500  

XP_651122   XM_646030

Unidentified Bromodomain Proteins Found in the Entamoeba histolytica Genome

Bromodomain Containing Proteins (PF00439) Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
Bromodomain protein & contains WD40 repeats XP_650909   XM_645817
Bromodomain protein & contains ANK repeats XP_654384 EHI_008050  
Bromodomain protein XP_655875 EHI_049490  
Bromodomain protein XP_655396 EHI_200210  
Bromodomain protein XP_657183 EHI_049790  
Bromodomain protein XP_654384 EHI_008050  

Entamoeba histolytica Homologues of General Transcription Factor Subunits

Subunits Protein Accession Pathema Annotation Link
TFIIE: TFA1 XP_649330 EHI_113420
TFIIE: TFA1 XP_656831  
TFIE: TFA2 XP_656544 EHI_042180
TFIIF auxiliary subunit XP_655411 EHI_088040
TFIIH:TFB2 XP_648469 EHI_192400

XP_648469 EHI_192400
TFIIH: TFB4 XP_650390 EHI_091540
TFIIH: SSL1 XP_655488 EHI_182880
TFIIH: SSL2 XP_649651 EHI_088430
TFIIH: SSL2 XP_654948 EHI_077260
TFIIH: RAD3 XP_650832 EHI_197850
TFIIH: RAD3 XP_649489 EHI_132410

Splicing Machinery of Entamoeba histolytica

Subunits Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
Core snRNP proteins      
Smb1 XP_653239 EHI_060400  
Smd1 XP_655345 EHI_113690  
Smd2 XP_651333 EHI_108640  
Smd3 XP_655862   XM_650770  
SME1 XP_654638 EHI_141910  
SMX2 XP_651637   XM_646545  
LSM2 XP_654174 EHI_068580  
LSM3 XP_657435   XM_652343
LSM6 XP_655404   XM_650312
LSM7 XP_648790 EHI_025840  
U1 snRNP specific proteins      
SNP1 XP_656357 EHI_153670  
YHC1 XP_656390   XM_651298
U5 snRNP specific proteins      
MSL1 XP_656582 EHI_050780  
PRP9 XP_656858 EHI_038600  
PRP11 XP_656062 EHI_117940  
HSH49 XP_655332   XM_650240
CUS1 XP_650882   XM_645790
RSE1 XP_652013 EHI_144720  
HSH155 XP_647865 EHI_049170  
U4/U6 snRNP specific proteins      
PRP8 XP_653245 EHI_060350  
BRR2 ** XP_657324 EHI_045170  

XP_657324 EHI_045170  
SNU114 XP_656072   XM_650980
PRP6 XP_657274 EHI_093960  
DIB1 XP_657315 EHI_045260  
Prp Complex 19      
CEF1 XP_653186 EHI_000550  
ISY1 XP_656460 EHI_187260  
SYF1 XP_656694 EHI_073300  
CLF1 XP_650622 EHI_175230  
PRP46 XP_657543   XM_652451

Entamoeba histolytica Homologues of Cleavage and Polyadenylation Specificity Factors (CPSF)

Other Transcription-related Proteins Mentioned

Proteins Protein Accession Pathema Annotation Link Models Excluded
from the Reannotation
TBP motif proteins XP_654950   XM_649858
TBP motif proteins XP_654951   XM_649859
SPT6 XP_654539 EHI_092290  
SPT16 XP_652208 EHI_109860  
SNF2 XP_649984 EHI_115350  
SNF2 XP_653178 EHI_000780  
CEG1 XP_652201 EHI_109940  
CEG1 XP_656137   XM_651045
ABD1 XP_649365   XM_644273
ABD1 XP_653474    
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