Serine/threonine protein kinase [Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 780 DPVAYLMVPYYPKANLSA-VQASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGI-VGDYDFTK-- 855
Cdd:COG0515    79 DGRPYLVMEYVEGESLADlLRRRGPLPPAEALRILAQLAEALAAAHAAGIVHRDIKPANIL-LTPDGRVkLIDFGIARal 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1833563334 856 SESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWL 899
Cdd:COG0515   158 GGATLTQTGTVVGTPGYMAPEQARGEPVDPRSDVYSLGVTLYEL 201

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334   9 KVEDVVGSHVEDAVTFWAQNVSKNKDIMKIGCSLSEVCPLANSVFGNLDPKKIYGGLFSEDKCWYRCKVLKTISDDKCLV 88
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPKSDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVEV 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1833563334  89 RYIDYGNTEILNRSDIVEIPPELQF-SSIAKKYRLWG 124
Cdd:pfam00567  81 LFIDYGNTETVPLSDLRPLPPELESlPPQAIKCQLAG 117

Catalytic domain of bacterial Serine/Threonine kinases, PknB and similar proteins; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes many bacterial eukaryotic-type STKs including Staphylococcus aureus PknB (also called PrkC or Stk1), Bacillus subtilis PrkC, and Mycobacterium tuberculosis Pkn proteins (PknB, PknD, PknE, PknF, PknL, and PknH), among others. S. aureus PknB is the only eukaryotic-type STK present in this species, although many microorganisms encode for several such proteins. It is important for the survival and pathogenesis of S. aureus as it is involved in the regulation of purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, virulence, and antibiotic resistance. M. tuberculosis PknB is essential for growth and it acts on diverse substrates including proteins involved in peptidoglycan synthesis, cell division, transcription, stress responses, and metabolic regulation. B. subtilis PrkC is located at the inner membrane of endospores and functions to trigger spore germination. Bacterial STKs in this subfamily show varied domain architectures. The well-characterized members such as S. aureus and M. tuberculosis PknB, and B. subtilis PrkC, contain an N-terminal cytosolic kinase domain, a transmembrane (TM) segment, and mutliple C-terminal extracellular PASTA domains. The PknB subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 780 DPVAYLMVPYYPKANLSAV-QASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQGIVGDYDFTK--S 856
Cdd:cd14014    72 DGRPYIVMEYVEGGSLADLlRERGPLPPREALRILAQIADALAAAHRAGIVHRDIKPANILLTEDGRVKLTDFGIARalG 151

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1833563334 857 ESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWL 899
Cdd:cd14014   152 DSGLTQTGSVLGTPAYMAPEQARGGPVDPRSDIYSLGVVLYEL 194

Stk1 family PASTA domain-containing Ser/Thr kinase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 803 PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVfaLNREQGIVGDYDF----TKSESQRASVNAMVGGLSLLSPELK 878
Cdd:NF033483  103 PLSPEEAVEIMIQILSALEHAHRNGIVHRDIKPQNI--LITKDGRVKVTDFgiarALSSTTMTQTNSVLGTVHYLSPEQA 180

                          90
                  ....*....|....*...
gi 1833563334 879 TGKPPSASSDLYAYGCLF 896
Cdd:NF033483  181 RGGTVDARSDIYSLGIVL 198

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 275 AKIKQDQKLIEENEKLKTEKEVLLENYKALELKVEQTAQELQQEKTATMDLT-----KHLESTLKTcVGTRLKNLAAKVE 349
Cdd:COG4717    78 EELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPlyqelEALEAELAE-LPERLEELEERLE 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 350 LLKEIRHINISIRfgNDLSDAMQVLDE-GSFTTLASLNELEKIWAEYNVAQEKIQTCLNE-----NEGNILIAERNEVQQ 423
Cdd:COG4717   157 ELRELEEELEELE--AELAELQEELEElLEQLSLATEEELQDLAEELEELQQRLAELEEEleeaqEELEELEEELEQLEN 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 424 KLFVAVD----------------VFILEVDDLPLDKRLKTLQDLATSLESVYGKAKEGTNNSEETLRKfydwqctKREEF 487
Cdd:COG4717   235 ELEAAALeerlkearlllliaaaLLALLGLGGSLLSLILTIAGVLFLVLGLLALLFLLLAREKASLGK-------EAEEL 307

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 488 ASIRSETEASLQHLVAWFQSSQKVFDLSLDEPLTSEDLIGNIDEILEKTESCvCKELELSLIEQgvidkeiilsTYSQVL 567
Cdd:COG4717   308 QALPALEELEEEELEELLAALGLPPDLSPEELLELLDRIEELQELLREAEEL-EEELQLEELEQ----------EIAALL 376

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 568 QKIH--SEEKF--IATLLSKYKDSVEFKKQMIDCLNKNPNVDYLLSIKKTLKGLKAQLRWKLVEKSNLEESDDHDGTEIE 643
Cdd:COG4717   377 AEAGveDEEELraALEQAEEYQELKEELEELEEQLEELLGELEELLEALDEEELEEELEELEEELEELEEELEELREELA 456

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 1833563334 644 KIKQEITQLRNS-VFQEIYHEREEY-EKLNSLTQKW 677
Cdd:COG4717   457 ELEAELEQLEEDgELAELLQELEELkAELRELAEEW 492

Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 278 KQDQKLIE--ENEKLKTEKEVLLENYKALELKVEQTAQELQQE-KTATMDLTKHLESTLKTcvgtrlknlaAKVELlkei 354
Cdd:pfam09731 327 KLAEELSArlEEVRAADEAQLRLEFEREREEIRESYEEKLRTElERQAEAHEEHLKDVLVE----------QEIEL---- 392

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 355 rhiniSIRFGNDLSDamQVLDE-GSFTT-----LASLNELEKIWAEYNVAQEkiqtclnenegniliaERNEVQQkLFVA 428
Cdd:pfam09731 393 -----QREFLQDIKE--KVEEErAGRLLklnelLANLKGLEKATSSHSEVED----------------ENRKAQQ-LWLA 448

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 429 VDVFILEVDD-------LPLDKRLKTLQDLA-------TSLESVygkAKEGTNN---SEETLR-KFYDWQCTKREefASI 490
Cdd:pfam09731 449 VEALRSTLEDgsadsrpRPLVRELKALKELAsddevvkAALASL---PEEAYQRgvyTEAALReRFRRVAKEVRK--VSL 523

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1833563334 491 RSETEASL-QHLVAWFQSSQKvFDLSLDEPLTSEDligNIDEILEKTESCV 540
Cdd:pfam09731 524 IDPEGAGLlSHALSYLLSKLM-FKPKQGEADPAGD---DVESILARAEYYL 570

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334   9 KVEDVVGSHVEDAVTFWAQNVSKNKDIMKIGCSLSEVCPLANSVFGNLDPKKIYGGLFSEDKCWYRCKVLKTISDDKCLV 88
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPKSDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVEV 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1833563334  89 RYIDYGNTEILNRSDIVEIPPELQF-SSIAKKYRLWG 124
Cdd:pfam00567  81 LFIDYGNTETVPLSDLRPLPPELESlPPQAIKCQLAG 117

Serine/threonine protein kinase [Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 780 DPVAYLMVPYYPKANLSA-VQASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGI-VGDYDFTK-- 855
Cdd:COG0515    79 DGRPYLVMEYVEGESLADlLRRRGPLPPAEALRILAQLAEALAAAHAAGIVHRDIKPANIL-LTPDGRVkLIDFGIARal 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1833563334 856 SESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWL 899
Cdd:COG0515   158 GGATLTQTGTVVGTPGYMAPEQARGEPVDPRSDVYSLGVTLYEL 201

Catalytic domain of bacterial Serine/Threonine kinases, PknB and similar proteins; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes many bacterial eukaryotic-type STKs including Staphylococcus aureus PknB (also called PrkC or Stk1), Bacillus subtilis PrkC, and Mycobacterium tuberculosis Pkn proteins (PknB, PknD, PknE, PknF, PknL, and PknH), among others. S. aureus PknB is the only eukaryotic-type STK present in this species, although many microorganisms encode for several such proteins. It is important for the survival and pathogenesis of S. aureus as it is involved in the regulation of purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, virulence, and antibiotic resistance. M. tuberculosis PknB is essential for growth and it acts on diverse substrates including proteins involved in peptidoglycan synthesis, cell division, transcription, stress responses, and metabolic regulation. B. subtilis PrkC is located at the inner membrane of endospores and functions to trigger spore germination. Bacterial STKs in this subfamily show varied domain architectures. The well-characterized members such as S. aureus and M. tuberculosis PknB, and B. subtilis PrkC, contain an N-terminal cytosolic kinase domain, a transmembrane (TM) segment, and mutliple C-terminal extracellular PASTA domains. The PknB subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 780 DPVAYLMVPYYPKANLSAV-QASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQGIVGDYDFTK--S 856
Cdd:cd14014    72 DGRPYIVMEYVEGGSLADLlRERGPLPPREALRILAQIADALAAAHRAGIVHRDIKPANILLTEDGRVKLTDFGIARalG 151

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1833563334 857 ESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWL 899
Cdd:cd14014   152 DSGLTQTGSVLGTPAYMAPEQARGGPVDPRSDIYSLGVVLYEL 194

Catalytic domain of Protein Kinases; PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. PKs make up a large family of serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins. Majority of protein phosphorylation occurs on serine residues while only 1% occurs on tyrosine residues. Protein phosphorylation is a mechanism by which a wide variety of cellular proteins, such as enzymes and membrane channels, are reversibly regulated in response to certain stimuli. PKs often function as components of signal transduction pathways in which one kinase activates a second kinase, which in turn, may act on other kinases; this sequential action transmits a signal from the cell surface to target proteins, which results in cellular responses. The PK family is one of the largest known protein families with more than 100 homologous yeast enzymes and more than 500 human proteins. A fraction of PK family members are pseudokinases that lack crucial residues for catalytic activity. The mutiplicity of kinases allows for specific regulation according to substrate, tissue distribution, and cellular localization. PKs regulate many cellular processes including proliferation, division, differentiation, motility, survival, metabolism, cell-cycle progression, cytoskeletal rearrangement, immunity, and neuronal functions. Many kinases are implicated in the development of various human diseases including different types of cancer. The PK family is part of a larger superfamily that includes the catalytic domains of RIO kinases, aminoglycoside phosphotransferase, choline kinase, phosphoinositide 3-kinase (PI3K), and actin-fragmin kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 773 FLFLCKSDPVAYLMVPYYPKANLSAV--QASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGIV-G 849
Cdd:cd00180    56 LYDVFETENFLYLVMEYCEGGSLKDLlkENKGPLSEEEALSILRQLLSALEYLHSNGIIHRDLKPENIL-LDSDGTVKlA 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1833563334 850 DYDFTK---SESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWLS 900
Cdd:cd00180   135 DFGLAKdldSDDSLLKTTGGTTPPYYAPPELLGGRYYGPKVDIWSLGVILYELE 188

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1833563334   66 FSEDKCWYRCKVLKTISDDKCLVRYIDYGNTEILNRSDIVEIPPEL 111
Cdd:smart00333  12 RWEDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57

fifth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334  11 EDVVGSHVEDAVTFWAQnVSKNKDIM-KIGCSLSEVCPLANSVFGNLDPKKIYGGLFSeDKCWYRCKVLKTISDDKclVR 89
Cdd:cd20424    14 EEVYITYVNDPWTFYCQ-LARNAGVLdQLASAISRLSSEIRKLELSVNPGTLCLAKYS-DQHWYRGIIITNKNSTE--VF 89

                          90       100
                  ....*....|....*....|...
gi 1833563334  90 YIDYGNTEILNRSDIVEIPPELQ 112
Cdd:cd20424    90 FVDYGNTEKVEKEDMLPIPSDAY 112

Catalytic domain of the Serine/Threonine kinases, Interleukin-1 Receptor Associated Kinases and related STKs; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. Some IRAKs may also play roles in T- and B-cell signaling, and adaptive immunity. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK-1, -2, and -4 are ubiquitously expressed and are active kinases, while IRAK-M is only induced in monocytes and macrophages and is an inactive kinase. Variations in IRAK genes are linked to diverse diseases including infection, sepsis, cancer, and autoimmune diseases. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain (a pseudokinase domain in the case of IRAK3), and a C-terminal domain; IRAK-4 lacks the C-terminal domain. This subfamily includes plant receptor-like kinases (RLKs) including Arabidopsis thaliana BAK1 and CLAVATA1 (CLV1). BAK1 functions in BR (brassinosteroid)-regulated plant development and in pathways involved in plant resistance to pathogen infection and herbivore attack. CLV1, directly binds small signaling peptides, CLAVATA3 (CLV3) and CLAVATA3/EMBRYO SURROUNDING REGI0N (CLE), to restrict stem cell proliferation: the CLV3-CLV1-WUS (WUSCHEL) module influences stem cell maintenance in the shoot apical meristem, and the CLE40 (CLAVATA3/EMBRYO SURROUNDING REGION40) -ACR4 (CRINKLY4) -CLV1- WOX5 (WUSCHEL-RELATED HOMEOBOX5) module at the root apical meristem. The IRAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 775 FLCKSDPvaYLMV-PYYPKANLS----AVQASMPLTSEEALKVMKGVARGLHTLHSAN---IIHGSLHQNNVFaLNRE-Q 845
Cdd:cd14066    58 YCLESDE--KLLVyEYMPNGSLEdrlhCHKGSPPLPWPQRLKIAKGIARGLEYLHEECpppIIHGDIKSSNIL-LDEDfE 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 846 GIVGDY----DFTKSESQrASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLwlsvqnqEFETnedGIPKVDQFHL 921
Cdd:cd14066   135 PKLTDFglarLIPPSESV-SKTSAVKGTIGYLAPEYIRTGRVSTKSDVYSFGVVLL-------ELLT---GKPAVDENRE 203

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1833563334 922 DDNVKSLlcsliyfRSSMTAEQVLNAECFLLPK-GKSVPIPEKEIE--------CTQHSREDESKMESLDRYSEK 987
Cdd:cd14066   204 NASRKDL-------VEWVESKGKEELEDILDKRlVDDDGVEEEEVEallrlallCTRSDPSLRPSMKEVVQMLEK 271

Catalytic domain of the Dual-specificity protein kinase, Testicular protein kinase; Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TESK proteins phosphorylate cofilin and induce actin cytoskeletal reorganization. In the Drosphila eye, TESK is required for epithelial cell organization. Mammals contain two TESK proteins, TESK1 and TESK2, which are highly expressed in testis and play roles in spermatogenesis. TESK1 is found in testicular germ cells while TESK2 is expressed mainly in nongerminal Sertoli cells. TESK1 is stimulated by integrin-mediated signaling pathways. It regulates cell spreading and focal adhesion formation. The TESK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 771 LIFLFLCKSDPVAYLMVPYYPKANLSA-VQASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQG--- 846
Cdd:cd14155    51 LRFMGVCVHQGQLHALTEYINGGNLEQlLDSNEPLSWTVRVKLALDIARGLSYLHSKGIFHRDLTSKNCLIKRDENGyta 130

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1833563334 847 IVGDYDFTK---SESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWLSVQnqeFETNEDGIPKVDQFHLD 922
Cdd:cd14155   131 VVGDFGLAEkipDYSDGKEKLAVVGSPYWMAPEVLRGEPYNEKADVFSYGIILCEIIAR---IQADPDYLPRTEDFGLD 206

Stk1 family PASTA domain-containing Ser/Thr kinase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 803 PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVfaLNREQGIVGDYDF----TKSESQRASVNAMVGGLSLLSPELK 878
Cdd:NF033483  103 PLSPEEAVEIMIQILSALEHAHRNGIVHRDIKPQNI--LITKDGRVKVTDFgiarALSSTTMTQTNSVLGTVHYLSPEQA 180

                          90
                  ....*....|....*...
gi 1833563334 879 TGKPPSASSDLYAYGCLF 896
Cdd:NF033483  181 RGGTVDARSDIYSLGIVL 198

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1833563334  64 GLFSEDKCWYRCKVLKTISDDKCLVRYiDYGNTEILNRSDIV 105
Cdd:cd04508     6 AKWSDDGQWYPATVVAVNDDGKYTVLF-DDGNEEEVSEDDIR 46

Catalytic domain of the LIM domain kinase-like protein kinases; PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. Members of this subfamily include LIMK, Testicular or testis-specific protein kinase (TESK), and similar proteins. LIMKs are characterized as serine/threonine kinases (STKs) while TESKs are dual-specificity protein kinases. Both LIMK and TESK phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They are implicated in many cellular functions including cell spreading, motility, morphogenesis, meiosis, mitosis, and spermatogenesis. The LIMK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 773 FLFLCKSDPVAYLMVPYYPKANLSAVQASM--PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNN--VFALNREQ-GI 847
Cdd:cd14065    53 FIGVCVKDNKLNFITEYVNGGTLEELLKSMdeQLPWSQRVSLAKDIASGMAYLHSKNIIHRDLNSKNclVREANRGRnAV 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1833563334 848 VGDY-------DFTKSESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYG 893
Cdd:cd14065   133 VADFglarempDEKTKKPDRKKRLTVVGSPYWMAPEMLRGESYDEKVDVFSFG 185

Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii CNK2 and similar proteins; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chlamydomonas reinhardtii CNK2 has both cilliary and cell cycle functions. It influences flagellar length through promoting flagellar disassembly, and it regulates cell size, through influencing the size threshold at which cells commit to mitosis. This subfamily belongs to the (NIMA)-related kinase (Nek) family, which includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily includes CNK1, and -2. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 803 PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQGIVGDYDFTKSeSQRASVNAMVGGLSLLSPELKTGKP 882
Cdd:cd08530    99 LFPEDDIWRIFIQMLRGLKALHDQKILHRDLKSANILLSAGDLVKIGDLGISKV-LKKNLAKTQIGTPLYAAPEVWKGRP 177

                          90
                  ....*....|...
gi 1833563334 883 PSASSDLYAYGCL 895
Cdd:cd08530   178 YDYKSDIWSLGCL 190

Catalytic domain of the Dual-specificity Protein Kinase, Dusty; Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. Dusty protein kinase is also called Receptor-interacting protein kinase 5 (RIPK5 or RIP5) or RIP-homologous kinase. It is widely distributed in the central nervous system, and may be involved in inducing both caspase-dependent and caspase-independent cell death. The Dusty subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 804 LTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQGIVGDYDFTKSESQRASvnAMVGGLSLLSPELKTGKPP 883
Cdd:cd13975    99 LSLEERLQIALDVVEGIRFLHSQGLVHRDIKLKNVLLDKKNRAKITDLGFCKPEAMMSG--SIVGTPIHMAPELFSGKYD 176

                          90
                  ....*....|....*.
gi 1833563334 884 SaSSDLYAYGCLFLWL 899
Cdd:cd13975   177 N-SVDVYAFGILFWYL 191

seventh Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the seventh one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1833563334  66 FSEDKCWYRCKVlKTISDDKCLVRYIDYGNTEILNRSDIVEIPPEL 111
Cdd:cd20426    57 YSEDNHWYRALV-TKINDNLVSVRFVDYGNEEDVVREQVRALPSEL 101

Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 4; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK4, also called SAK or STK18, is structurally different from other PLKs in that it contains only one polo box that can form two adjacent polo boxes and a functional PDB by homodimerization. It is required for late mitotic progression, cell survival, and embryonic development. It localizes to centrosomes and is required for centriole duplication and chromosomal stability. Overexpression of PLK4 may be associated with colon tumors. The PLK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 803 PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGI-VGDYDF-TKSESQRASVNAMVGGLSLLSPELKTG 880
Cdd:cd14186    98 PFTEDEARHFMHQIVTGMLYLHSHGILHRDLTLSNLL-LTRNMNIkIADFGLaTQLKMPHEKHFTMCGTPNYISPEIATR 176

                          90       100
                  ....*....|....*....|....*....
gi 1833563334 881 KPPSASSDLYAYGCLFLWLSVQNQEFETN 909
Cdd:cd14186   177 SAHGLESDVWSLGCMFYTLLVGRPPFDTD 205

Catalytic domain of STE family Protein Kinases; PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. This family is composed of STKs, and some dual-specificity PKs that phosphorylate both threonine and tyrosine residues of target proteins. Most members are kinases involved in mitogen-activated protein kinase (MAPK) signaling cascades, acting as MAPK kinases (MAPKKs), MAPKK kinases (MAPKKKs), or MAPKKK kinases (MAP4Ks). The MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising of the MAPK, which is phosphorylated and activated by a MAPKK, which itself is phosphorylated and activated by a MAPKKK. Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAPKKK to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. Other STE family members include p21-activated kinases (PAKs) and class III myosins, among others. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. Class III myosins are motor proteins containing an N-terminal kinase catalytic domain and a C-terminal actin-binding domain, which can phosphorylate several cytoskeletal proteins, conventional myosin regulatory light chains, as well as autophosphorylate the C-terminal motor domain. They play an important role in maintaining the structural integrity of photoreceptor cell microvilli. The STE family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 775 FLCKSDPvaYLMVPYYPKANLSAV--QASMPLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVfALNREQGI-VGDY 851
Cdd:cd05122    66 YLKKDEL--WIVMEFCSGGSLKDLlkNTNKTLTEQQIAYVCKEVLKGLEYLHSHGIIHRDIKAANI-LLTSDGEVkLIDF 142

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1833563334 852 DFTKSESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGC 894
Cdd:cd05122   143 GLSAQLSDGKTRNTFVGTPYWMAPEVIQGKPYGFKADIWSLGI 185

Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 1; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK1 functions as a positive regulator of mitosis, meiosis, and cytokinesis. Its localization changes during mitotic progression; associating first with centrosomes in prophase, with kinetochores in prometaphase and metaphase, at the central spindle in anaphase, and in the midbody during telophase. It carries multiple functions throughout the cell cycle through interactions with differrent substrates at these specific subcellular locations. PLK1 is overexpressed in many human cancers and is associated with poor prognosis. The PLK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 804 LTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGI-VGDYDF-TKSESQRASVNAMVGGLSLLSPELKTGK 881
Cdd:cd14187   104 LTEPEARYYLRQIILGCQYLHRNRVIHRDLKLGNLF-LNDDMEVkIGDFGLaTKVEYDGERKKTLCGTPNYIAPEVLSKK 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 882 PPSASSDLYAYGCLFLWLSVQNQEFET------------NEDGIPKvdqfHLDDNVKSLLCSLIYFRSSM--TAEQVLNA 947
Cdd:cd14187   183 GHSFEVDIWSIGCIMYTLLVGKPPFETsclketylrikkNEYSIPK----HINPVAASLIQKMLQTDPTArpTINELLND 258

                  ...
gi 1833563334 948 ECF 950
Cdd:cd14187   259 EFF 261

Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek family is composed of 11 different mammalian members (Nek1-11) with similarity to the catalytic domain of Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was identified in a screen for cell cycle mutants that were prevented from entering mitosis. Neks contain a conserved N-terminal catalytic domain and a more divergent C-terminal regulatory region of various sizes and structures. They are involved in the regulation of downstream processes following the activation of Cdc2, and many of their functions are cell cycle-related. They play critical roles in microtubule dynamics during ciliogenesis and mitosis. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 803 PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFaLNREQGI-VGDYDFTKS-ESQRASVNAMVGGLSLLSPELKTG 880
Cdd:cd08215    99 PFPEEQILDWFVQICLALKYLHSRKILHRDLKTQNIF-LTKDGVVkLGDFGISKVlESTTDLAKTVVGTPYYLSPELCEN 177

                          90
                  ....*....|....*
gi 1833563334 881 KPPSASSDLYAYGCL 895
Cdd:cd08215   178 KPYNYKSDIWALGCV 192

Catalytic domain of the Serine/Threonine Kinase, LIM domain kinase; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LIMKs phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They act downstream of Rho GTPases and are expressed ubiquitously. As regulators of actin dynamics, they contribute to diverse cellular functions such as cell motility, morphogenesis, differentiation, apoptosis, meiosis, mitosis, and neurite extension. LIMKs contain the LIM (two repeats), PDZ, and catalytic kinase domains. Vertebrate have two members, LIMK1 and LIMK2. The LIMK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 785 LMVPYYPKANLSAVQASM--PLTSEEALKVMKGVARGLHTLHSANIIHGSLHQNNVFALNREQGIVGDY----------- 851
Cdd:cd14154    67 LITEYIPGGTLKDVLKDMarPLPWAQRVRFAKDIASGMAYLHSMNIIHRDLNSHNCLVREDKTVVVADFglarliveerl 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833563334 852 ----------DFTKSESQRASVNAMVGGLSLLSPELKTGKPPSASSDLYAYGCLFLWLSVQnqeFETNEDGIPKVDQFHL 921
Cdd:cd14154   147 psgnmspsetLRHLKSPDRKKRYTVVGNPYWMAPEMLNGRSYDEKVDIFSFGIVLCEIIGR---VEADPDYLPRTKDFGL 223

                  .
gi 1833563334 922 D 922
Cdd:cd14154   224 N 224

Tudor domain found in survival motor neuron protein (SMN) and similar proteins; SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Mutations in human SMN lead to motor neuron degeneration and spinal muscular atrophy. SMN contains a central, highly conserved Tudor domain that is required for U snRNP assembly and Sm protein binding and has been shown to bind arginine-glycine-rich motifs in an methylarginine-dependent manner.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1833563334  66 FSEDKCWYRCKVLKTI-SDDKCLVRYIDYGNTEILNRSDIveIPP 109
Cdd:cd20398    11 YSEDGIIYEATIVSIDaERGTCVVRYTGYGNEEEQNLSDL--LPP 53