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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71988874 683 RTEVSVPTRIIGRIIGKGGQNVRELQRITGAVVKIPEEERNGgevyrhddglEEDMTMIRTIGNMYSTHNVQFRL 757
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPD----------EGDEVPVEIIGNFYATQSAQRRI 65

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 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEEKTQRE 586
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPE 46

fourth 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 fourth one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71988874 683 RTEVSVPTRIIGRIIGKGGQNVRELQRITGAVVKIPEEERNGgevyrhddglEEDMTMIRTIGNMYSTHNVQFRL 757
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPD----------EGDEVPVEIIGNFYATQSAQRRI 65

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874   313 IRCVVEGKYHAVIIGPNGSTIKDIASSTRCRVDFVNLSKKErtvlgnNDRILTVHGVAEQATKAVARILD 382
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEG------NERIVTITGTPEAVEAAKALIEE 65

third 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 third one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEEKTQRE 586
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPE 46

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874    542 QVRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEEKT-----QREAEEAEKKRKL 596
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEErvveiTGPPENVEKAAEL 63

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 71988874   543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEEKTQRE 586
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNER 45

putative RNA-processing protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874  323 AVIIGPNGSTIKDIASSTRCRVDF---VNLSKKERTVLGNNDRILTvhgvAEQATKAVAR---------------ILDVI 384
Cdd:PRK13763  15 GVLIGKKGETKKEIEERTGVKLEIdseTGEVIIEPTDGEDPLAVLK----ARDIVKAIGRgfspekalrlldddyVLEVI 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 71988874  385 QSEAVKDDVNvgadTVLRMRahnqlcGRLIGKAGSSIKEIMQKTGTNITV 434
Cdd:PRK13763  91 DLSDYGDSPN----ALRRIK------GRIIGEGGKTRRIIEELTGVDISV 130

fourth 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 fourth one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71988874 683 RTEVSVPTRIIGRIIGKGGQNVRELQRITGAVVKIPEEERNGgevyrhddglEEDMTMIRTIGNMYSTHNVQFRL 757
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPD----------EGDEVPVEIIGNFYATQSAQRRI 65

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        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 397 ADTV-LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKyieppggISGLTanelLGLMERTIMVRGpSIEAVVQAEA 475
Cdd:cd22493   2 ADEVpLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISP-------LQDLT----LYNPERTITVKG-SIEACCRAEQ 69

                        90       100
                ....*....|....*....|..
gi 71988874 476 LISAKLKKCYESDsqLRAQSMQ 497
Cdd:cd22493  70 EIMKKVREAYEND--VAAMNLQ 89

K homology RNA-binding domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71988874    313 IRCVVEGKYHAVIIGPNGSTIKDIASSTRCRVDFVNlskkertvLGNNDRILTVHGVAEQATKAVARILDVI 384
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--------PGSEERVVEITGPPENVEKAAELILEIL 68

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        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 401 LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPPGGISgltanellglmERTIMVRGpSIEAVVQAEALISAK 480
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSS-----------ERIVTITG-SFDQVVKAVALILEK 68

                .
gi 71988874 481 L 481
Cdd:cd22437  69 L 69

third 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 third one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEEKTQRE 586
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPE 46

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
                ....*....|....*....|....*....|....*..
gi 71988874 541 RQVRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIE 577
Cdd:cd02393   4 RITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE 40

K homology RNA-binding domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874    397 ADTVLRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPpggisgltanellglmERTIMVRGPSiEAVVQAEAL 476
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE----------------ERVVEITGPP-ENVEKAAEL 63

                   ....*
gi 71988874    477 ISAKL 481
Cdd:smart00322  64 ILEIL 68

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), 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 also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. 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 first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71988874 312 PIRCVVEGKYHAVIIGPNGSTIKDIASSTRCRVDfvnLSKKERTvlGNNDRILTVHGVAEQATKAVARILDVIQSEAVK 390
Cdd:cd22491   1 PLRILVPTQFVGAIIGKEGLTIKNITKQTQSKVD---IHRKENA--GAAEKPITIHATPEGCSAACRMILEIMQKEANE 74

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71988874 313 IRCVVEGKYHAVIIGPNGSTIKDIASSTRCRVDFvnlSKKertVLGNNDRILTVHGVAEQATKA---VARIL 381
Cdd:cd22455   3 LRALVSSKEAAVIIGKGGENIARLRATTGVKAGV---SKV---VPGVHDRVLTVSGPLEGVAKAfglIARTL 68

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
                ....*....|....*....|....*....|....*.
gi 71988874 407 NQLCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPPG 442
Cdd:cd22395   8 SELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQN 43

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
                ....*....|....*....|....*....|....*....
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEE 581
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKEN 40

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71988874 401 LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKyieppggisgltanELLGLMERTIMVRGPSiEAVVQAEALI 477
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPK--------------EGEGSGERVVTITGTP-EAVEKAKELI 62

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71988874 407 NQLCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPPGgisgltanellglmERTIMVRGpSIEAVVQAEALISAKLK 482
Cdd:cd22404   9 NSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQG--------------DRRITIKG-SADATRQAAQLINALIK 69

first 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 first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71988874 407 NQLCGRLIGKAGSSIKEIMQKTGTNITVTKyieppggisgltANELL-GLMERTIMVRGpSIEAVVQAEALISAKLK 482
Cdd:cd22435  10 NYAAGSIIGKGGQTIAQLQKETGARIKLSK------------NNDFYpGTTERVCLIQG-EVEAVNAVLDFILEKIR 73

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 71988874 312 PIRCVvegkyhAVIIGPNGSTIKDIASSTRCRVDFvnlsKKERTVLGNNDRILTVHGVAEQATKAVARILDVI 384
Cdd:cd22428  12 PREAV------GLIIGRQGATIKQIQKETGARIDF----KDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74

second 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 second one.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 399 TVLRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKyieppggisgltaNELLGLMERTIMVRGpSIEAVVQAEALIS 478
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVAS-------------EMLPNSTERAVTISG-SPEAITKCVEQIC 67

                ...
gi 71988874 479 AKL 481
Cdd:cd02396  68 CVM 70

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 71988874 547 VPDSMIGALIGAKGKNIKMIIRDTGASVKIeAPEEKTQREAEEAEKK 593
Cdd:cd22447  10 IPASTRARIIGKKGANLKQIREKTGVRIDI-PPRDADAAPADEDDDT 55

third 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 third one.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPE 580
Cdd:cd22496   5 VHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE 42

first 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 first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71988874 312 PIRCVVEGKYHAVIIGPNGSTIKDIASSTRCRVDfvnLSKKERTvlGNNDRILTVHGVAEQATKAVARILDVIQSEA 388
Cdd:cd22492   1 PLRLLVPTQFVGAIIGKEGATIRNITKQTQSKID---VHRKENA--GAAEKSITILSTPEGTSAACKSILEIMHKEA 72

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 71988874 411 GRLIGKAGSSIKEIMQKTGTNITV----TKYIEPPggiSGLTANEllGLMertIMVRGPSIEAVVQAEALISAKLKKCYE 486
Cdd:cd22386  22 GKLIGPGGSNVKHIQQETGAKVQLrgkgSGFIEPA---SGREADE--PLH---LLISHPDPEGLQQAKKLCEDLLQTVHQ 93

                ....*...
gi 71988874 487 SDSQLRAQ 494
Cdd:cd22386  94 EYGEFQQQ 101

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 401 LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVtkyieppggisgltANELL-GLMERTIMVRGpSIEAVVQAEALISA 479
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQV--------------AGDLLpNSTERAVTVSG-VPDAIIQCVRQICA 68

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        30
                ....*....|....*....|....*....|....*.
gi 71988874 544 RMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAP 579
Cdd:cd22459   5 RLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDG 40

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), 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 also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. 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 third one.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIeAPEE 581
Cdd:cd22497   5 VYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKI-APAE 42

third 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 third one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKI---EAPEEKTQ 584
Cdd:cd22498   7 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIapaEGPDAKLR 51

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        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 71988874 324 VIIGPNGSTIKDIASSTRCRvdfVNLSKKERTVLGNNDRILTVHGVAEQATKAVARIL 381
Cdd:cd09031  14 AILGKGGKTLVEIQELTGAR---IQISKKGEFVPGTRNRKVTITGTPAAVQAAQYLIE 68

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        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 401 LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKyieppGGISgltanellglmERTIMVRGPsIEAVVQAEALISAK 480
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISD-----GSCP-----------ERIVTVTGT-TDAVFKAFELICRK 63

                .
gi 71988874 481 L 481
Cdd:cd22438  64 L 64

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        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 400 VLRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPPGGISgltanellgLMERTIMVRGpSIEAVVQAEALISA 479
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCAS---------PDDRVVQISG-EAQAVKKALELVSS 70

                ..
gi 71988874 480 KL 481
Cdd:cd22460  71 RL 72

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
                ....*....|....*....|....*....|....*....
gi 71988874 543 VRMWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEE 581
Cdd:cd22396   3 EEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSG 41

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 71988874 409 LCGRLIGKAGSSIKEIMQKTGTNITVTKYIEPPGGISGLTANEL 452
Cdd:cd22458  11 LCGRLIGAKGKNIKALSEKSGASIRLIPISNSSQQTIHLSGTDK 54

eighth 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 eighth one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71988874 320 KYHAVIIGPNGSTIKDIASSTRCRVDFVNlskkertvLGNNDRILTVHGVAEQATKAVARIL 381
Cdd:cd22411   9 QFHKNIIGKGGATIKKIREETNTRIDLPE--------ENSDSDVITITGKKEDVEKARERIL 62

third 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 third one.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 71988874 545 MWVPDSMIGALIGAKGKNIKMIIRDTGASVKIEAPEE 581
Cdd:cd22439   6 ITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED 42

first 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 first one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988874 325 IIGPNGSTIKDIASSTRCRvdfVNLSKKERTVLGNNDRILTVHGVAEQATKAVARILDVI 384
Cdd:cd22435  16 IIGKGGQTIAQLQKETGAR---IKLSKNNDFYPGTTERVCLIQGEVEAVNAVLDFILEKI 72

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
                ....*....|....*....|....*....|....
gi 71988874 401 LRMRAHNQLCGRLIGKAGSSIKEIMQKTGTNITV 434
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDI 35

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.