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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 120 TLTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMyGNALHKTHGDGSQDAIDLPLRVIVETSG 199
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRD-KKKEEANRGKPNWEHLNDDLHVLITVED 79

                        90       100
                ....*....|....*....|..
gi 17541280 200 PRREATARITAALETVQVLLVP 221
Cdd:cd22383  80 TENRAHIKLAKAVEEVKKLLIP 101

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 120 TLTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMyGNALHKTHGDGSQDAIDLPLRVIVETSG 199
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRD-KKKEEANRGKPNWEHLNDDLHVLITVED 79

                        90       100
                ....*....|....*....|..
gi 17541280 200 PRREATARITAALETVQVLLVP 221
Cdd:cd22383  80 TENRAHIKLAKAVEEVKKLLIP 101

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 17541280    122 TESIRIPVetyptyNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSN 168
Cdd:smart00322   4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE 44

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 120 TLTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMyGNALHKTHGDGSQDAIDLPLRVIVETSG 199
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRD-KKKEEANRGKPNWEHLNDDLHVLITVED 79

                        90       100
                ....*....|....*....|..
gi 17541280 200 PRREATARITAALETVQVLLVP 221
Cdd:cd22383  80 TENRAHIKLAKAVEEVKKLLIP 101

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; 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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 119 VTLTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMYGNAlHKTHGDGSQDAIDLPLRVIVETS 198
Cdd:cd22466   4 VTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKE-DLNRGKPNWEHLNDELHVLITVE 82

                        90       100
                ....*....|....*....|...
gi 17541280 199 GPRREATARITAALETVQVLLVP 221
Cdd:cd22466  83 DTENRAKVKLQRAVEEVRKLLVP 105

Splicing factor (branch point binding protein) [RNA processing and modification];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 122 TESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMYGNALHKTHGDGSQDAidlPLRVIVETS--- 198
Cdd:COG5176 149 QNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEA---VLHCLIEADsed 225

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 17541280 199 GPRREATARITAALETVQVllvppPDGRDELKRRQLVELAIMNGTYR 245
Cdd:COG5176 226 KICRLIKSQLNAIREARRN-----PEGQNDLKRFQLRWLAHLNGTLR 267

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 122 TESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMYGNAlHKTHGDGSQDAIDLPLRVIVETSGPR 201
Cdd:cd22467   3 VLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKE-EKLRDKPGYEHLNEPLHVLIEAELPA 81

                        90       100
                ....*....|....*....|
gi 17541280 202 REATARITAALETVQVLLVP 221
Cdd:cd22467  82 NIIDARLQHAQEIIEDLLKP 101

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 17541280 119 VTLTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMI--RGNHSNKMYGNALHKThGDGSQDAIDLPLRVIVE 196
Cdd:cd22384   3 IKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSIlgKGSMRDKAKEEELRKS-GDPKYAHLNEDLHVLIE 81

                        90       100
                ....*....|....*....|
gi 17541280 197 TSGPRREATARITAALETVQ 216
Cdd:cd22384  82 AFAPPAEAYARLAHALAELR 101

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        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17541280 121 LTESIRIPVETYPTYNFIGRIIGPRGTTAKQLEKDTGCRIMI--RGNHSNKMYGNALHKThGDGSQDAIDLPLRVIVETS 198
Cdd:cd22470   9 LGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSIlgKGSMRDKAKEEELRKS-GEAKYFHLNDDLHVLIEVF 87

                        90       100
                ....*....|....*....|...
gi 17541280 199 GPRREATARITAALETVQVLLVP 221
Cdd:cd22470  88 APPAEAYARMGHALEEIKKFLIP 110

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 17541280 121 LTESIRIPVETY-PTYNFIGRIIGPRGTTAKQLEKDTGCRIMIRGNHS 167
Cdd:cd22386   3 YQEKVFVGLEHApPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS 50

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 17541280 123 ESIRIPVEtyptynFIGRIIGPRGTTAKQLEKDTGCRIMI 162
Cdd:cd02393   6 TTIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDI 39

second 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 second one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 17541280 119 VTLTesIRIPVETyptynfIGRIIGPRGTTAKQLEKDTGCRIMI 162
Cdd:cd22447   4 QNLT--VPIPAST------RARIIGKKGANLKQIREKTGVRIDI 39

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17541280 134 TYNFI------GRIIGPRGTTAKQLEKDTGCRIMIRGNHSNKMYgnalhKT-HGDGSQDAIDLPLRVI 194
Cdd:cd22395   1 VYEFEvpselvGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNF-----QIcSIEGTQQQIDKALKLI 63

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 17541280 122 TESIRIPVETYptynfiGRIIGPRGTTAKQLEKDTGCRIMIRGnhsnkmygnalhkthgdgsQDAIDLPLRVivetSGPR 201
Cdd:cd22451   2 SIDIDIPKEYH------RAIIGKGGAVLRELEAETGCRIQVPK-------------------KDDPSGKIRI----TGAR 52

                        90
                ....*....|
gi 17541280 202 ---REATARI 208
Cdd:cd22451  53 dgvEAATAKI 62

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20
                ....*....|....*....|....*.
gi 17541280 140 RIIGPRGTTAKQLEKDTGCRIMIRGN 165
Cdd:cd22394  24 RLIGPNGSTLKAIELLTKCYILVQGN 49

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

                        10        20
                ....*....|....*....|....*
gi 17541280 138 IGRIIGPRGTTAKQLEKDTGCRIMI 162
Cdd:cd22459  13 AGSVIGKGGEIIKQLRQETGARIKV 37