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 1040660609  65 KSVRVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRKGGDPKYAHLGMELHVHI 144
Cdd:cd22468     1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                          90       100
                  ....*....|....*....|....*.
gi 1040660609 145 EVFAPIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22468    81 EVFGPPCEAYARMAHAMEEVKKFLVP 106

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  65 KSVRVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRKGGDPKYAHLGMELHVHI 144
Cdd:cd22468     1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                          90       100
                  ....*....|....*....|....*.
gi 1040660609 145 EVFAPIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22468    81 EVFGPPCEAYARMAHAMEEVKKFLVP 106

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  70 KERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMrdknKEEELRKGGDPKYAHLGMELHVHIEVFAP 149
Cdd:COG5176   149 QNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEADSE 224

                  ....*...
gi 1040660609 150 IPDCYLRM 157
Cdd:COG5176   225 DKICRLIK 232

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1040660609  70 KERVLIPVKQyprfnfVGKILGPQGSTIKRLQEDTGAKISVLGKGS 115
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  65 KSVRVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRKGGDPKYAHLGMELHVHI 144
Cdd:cd22468     1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                          90       100
                  ....*....|....*....|....*.
gi 1040660609 145 EVFAPIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22468    81 EVFGPPCEAYARMAHAMEEVKKFLVP 106

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  63 ASKSVRVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRKGGDPKYAHLGMELHV 142
Cdd:cd22469     1 SNKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHV 80

                          90       100
                  ....*....|....*....|....*...
gi 1040660609 143 HIEVFAPIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22469    81 LIEVFAPPGEAYSRMSHALEEIKKFLVP 108

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 1040660609  69 VKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRkgGDPKYAHLGMELHVHIEVFA 148
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANR--GKPNWEHLNDDLHVLITVED 79

                          90       100
                  ....*....|....*....|..
gi 1040660609 149 PIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22383    80 TENRAHIKLAKAVEEVKKLLIP 101

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  68 RVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRkgGDPKYAHLGMELHVHIEVF 147
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 78

                          90       100
                  ....*....|....*....|...
gi 1040660609 148 APIPDCYLRMAHAMDEVKKFLMP 170
Cdd:cd22465    79 DAQNRAEIKLKRAVEEVKKLLVP 101

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 1040660609  72 RVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEELRkgGDPKYAHLGMELHVHIEVFAPIP 151
Cdd:cd22467     5 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLR--DKPGYEHLNEPLHVLIEAELPAN 82

                          90
                  ....*....|....*....
gi 1040660609 152 DCYLRMAHAMDEVKKFLMP 170
Cdd:cd22467    83 IIDARLQHAQEIIEDLLKP 101

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 1040660609  68 RVKERVLIPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMrdknKEEELRKGGDPKYAHLGMELHVHIEvf 147
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSV----KEGKVGRKDGQPLPGEDEPLHALVT-- 74

                          90
                  ....*....|....*....
gi 1040660609 148 apipdcylrmAHAMDEVKK 166
Cdd:cd22382    75 ----------ANTAESVKK 83

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  69 VKERVLIPVKQYPR-FNFVGKILGPQGSTIKRLQEDTGAKISVLGKGSmrdKNKEeelrkGGDPKYAHLGMelHVHIEvf 147
Cdd:cd22386     3 YQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIE-----PASGREADEPL--HLLIS-- 70

                  ....*..
gi 1040660609 148 APIPDCY 154
Cdd:cd22386    71 HPDPEGL 77

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1040660609  70 KERVLIPVKQyprfnfVGKILGPQGSTIKRLQEDTGAKISVLGKGS 115
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1040660609  84 NFVGKILGPQGSTIKRLQEDTGAKISVLGKG 114
Cdd:cd09031    10 NLVGAILGKGGKTLVEIQELTGARIQISKKG 40

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1040660609  72 RVLIPVKqyprfnFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMR 117
Cdd:cd22400     3 RILVPSE------FVGAIIGKGGATIRQITQQTGARIDIHRKENAG 42

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1040660609  71 ERVLIPVkqyprfNFVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22407     2 ERLDIPK------VYHPFIAGPNNENVKELQEETGVRINI 35

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1040660609  69 VKERVLIPVKqyprfnFVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22396     1 VTEEYKVPDK------MVGLIIGRGGEQINRLQAESGAKIQI 36

second 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 KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1040660609  72 RVLIPVKQyprfnfVGKILGPQGSTIKRLQEDTGAKISVLGKG 114
Cdd:cd22460     3 RLLVASSQ------AGSLIGKGGAIIKQIREESGASVRILPEE 39

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

                          10        20
                  ....*....|....*....|....*.
gi 1040660609  85 FVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd02394    12 FHGHIIGKGGANIKRIREESGVSIRI 37

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20
                  ....*....|....*....|....*
gi 1040660609  86 VGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22438    10 VGSIIGKKGETIKKFREESGARINI 34

type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) and similar proteins; PNPT1, also called 3'-5' RNA exonuclease OLD35, or PNPase old-35, or polynucleotide phosphorylase 1, or PNPase 1, or polynucleotide phosphorylase-like protein, is an RNA-binding protein implicated in numerous RNA metabolic processes. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'-to-5' direction. It acts as a mitochondrial intermembrane factor with RNA-processing exoribonulease activity. PNPT1 is a component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. It is involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules and required for correct processing and polyadenylation of mitochondrial mRNAs. PNPT1 also plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040660609  69 VKERVLIPVKQYPRFnfvgkiLGPQGSTIKRLQEDTGAKISVLGkgsmrdknkEEELrkggdpkyahlgmelhvhiEVFA 148
Cdd:cd09033     6 VTETLEVPPSKRAKF------VGPGGYNIKKLQAETGVTITQVD---------EETF-------------------SVFA 51

                          90       100
                  ....*....|....*....|
gi 1040660609 149 PIPDcylrmahAMDEVKKFL 168
Cdd:cd09033    52 PNQS-------AMDEAKEMI 64

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1040660609  75 IPVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22493     5 VPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITI 40

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1040660609  71 ERVLIPVKQyprfnfVGKILGPQGSTIKRLQEDTGAKISVLGKGSMrDKNKEEELRKGGDPKYAHLGMELHVHI 144
Cdd:cd22483     7 QEILIPASK------VGLVIGKGGETIKQLQERTGVKMIMIQDGPL-PTGADKPLRITGDPFKVQQAREMVLEI 73

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1040660609  76 PVKQYPRFNFVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22495     1 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 35

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20
                  ....*....|....*....|....*.
gi 1040660609  85 FVGKILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22437     9 SCGLIIGKGGSTIKELREDSNANIKI 34

first 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 first one.

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gi 1040660609  84 NFVGKILGPQGSTIKRLQEDTGAKISVLGKGSMRDKNKEEE 124
Cdd:cd22446    16 SVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDEDDD 56

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

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gi 1040660609  73 VLIPvKQYPRFnfvgkILGPQGSTIKRLQEDTGAKISV 110
Cdd:cd22406     9 VNIP-KEHHRF-----ILGKKGKKLQELELKTATKIVI 40

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

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gi 1040660609  87 GKILGPQGSTIKRLQEDTGAKISVLGKGSmRDKNKEEELRKGGDPKYAHLGMEL 140
Cdd:cd22482    14 GLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEM 66