K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGS 162
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKgSMRDKK 53

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGS 162
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKgSMRDKK 53

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267617  113 TETIMVPVekfpdyNFVGRLLGPRGTTAKQLEVTTGCRITIlgrtKRDGSSSNPDVTTGP 172
Cdd:smart00322   4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI----PGPGSEERVVEITGP 53

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGS 162
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKgSMRDKK 53

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267617 111 MLTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDG-------SSSNPDVT--TGPLRVQISVP 180
Cdd:cd22384     4 KLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKgSMRDKakeeelrKSGDPKYAhlNEDLHVLIEAF 83

                          90
                  ....*....|....*...
gi 1972267617 181 ADMPQAAKLLKGGVGHIQ 198
Cdd:cd22384    84 APPAEAYARLAHALAELR 101

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267617 113 TETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGSSSNPDVTTG----PLRVQISvpADMPQAa 187
Cdd:cd02395     3 QRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKgSVKEGKGRSDPQPDPdeeeDLHVLIT--ADTEEK- 79

                          90
                  ....*....|....*
gi 1972267617 188 klLKGGVGHIQAILD 202
Cdd:cd02395    80 --VDKAAKLIEKLLI 92

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGSSSNPDVTTG-----PLRVQISVPadmpq 185
Cdd:cd22382     2 VSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKgSVKEGKVGRKDGQPLpgedePLHALVTAN----- 76

                          90
                  ....*....|....*.
gi 1972267617 186 AAKLLKGGVGHIQAIL 201
Cdd:cd22382    77 TAESVKKAVDKIKEII 92

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR-TKRDGS 162
Cdd:cd22468     5 LKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKgSMRDKA 56

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1972267617 112 LTETIMVPVEKFPDYNFVGRLLGPRGTTAKQLEVTTGCRITILGR 156
Cdd:cd22470     9 LGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGK 53

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1972267617 114 ETIMVPVEkfpdynFVGRLLGPRGTTAKQLEVTTGCRITILGRTKRDGS 162
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGE 43

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267617 113 TETIMVPVEkfpdynFVGRLLGPRGTTAKQLEVTTGCRITIlgrTKRDGSSSnpdvttgplRVQISVPADMPQAAKllkg 192
Cdd:cd22451     2 SIDIDIPKE------YHRAIIGKGGAVLRELEAETGCRIQV---PKKDDPSG---------KIRITGARDGVEAAT---- 59

                          90
                  ....*....|
gi 1972267617 193 gvGHIQAILD 202
Cdd:cd22451    60 --AKILNISD 67

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1972267617 113 TETIMVPVEkfpdynFVGRLLGPRGTTAKQLEVTTGCRITI 153
Cdd:cd22395     1 VYEFEVPSE------LVGRLIGKQGRNVKQLKQKSGAKIYI 35

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1972267617 114 ETIMVPVEKfpdynfVGRLLGPRGTTAKQLEVTTGCRITI 153
Cdd:cd02393     6 TTIKIPPDK------IGDVIGPGGKTIRAIIEETGAKIDI 39