Citrus Sinensis ID: 027188

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------

MLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI

cccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEccccccHHHHHHHHccEEEEEccccccccccEEEEccccHHHHHHHHHHHHHHccccccccccccccccccccHHHccccccccccccccccccccccHHHHHcccc

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEEHHHHHHHHcccccccHHHHHHcccEEEEEccccccccccEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHcccccccccccccccccHHHHHcccc

mlnlggtpahppppprnsgappsfpdgssppavkSRLCnkynsaegckfgdkchfahgewelgrptvpsyedpramggpmhgrmggrlepppqslgaaasfgasATAKISIDAKLAGaiigkngvnsKQICRLtgaklsirdhevdpnlrnielegtFDQIKQASAMVRELIVNVgsgsghsmksnsssqsnnFKTKLCEnfakgsctfgdrchfahgsEELRKSVI

mlnlggtpahpppppRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAiigkngvnskQICRLTgaklsirdhevdpnlrnielEGTFDQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFgdrchfahgseelrksvi

MLNLGGTpahppppprnsgappsfpDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPramggpmhgrmggrLEPPPQSLgaaasfgasataKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVgsgsghsmksnsssqsnnFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSVI

************************************LCNKYNSAEGCKFGDKCHFAHGEWELG*****************************************ATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNV*********************KLCENFAKGSCTFGDRCHFA***********

**********************************************************************************RMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLT************************DQIKQASAMVRELIVNVGSGSGHSMKSNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELR****

********************************VKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS****************FKTKLCENFAKGSCTFGDRCHFAHGS********

*******************************AVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGRPTVPS*********************************ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGS***************NFKTKLCENFAKGSCTFGDRCHFAHG*********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		227	2.2.26 [Sep-21-2011]
Q7F8R0		300	Zinc finger CCCH domain-c	yes	no	0.982	0.743	0.616	2e-67
Q69XQ3		295	Zinc finger CCCH domain-c	no	no	0.942	0.725	0.568	4e-61
Q7XPK1		309	Zinc finger CCCH domain-c	no	no	0.863	0.634	0.610	9e-60
Q9FG30		240	Zinc finger CCCH domain-c	yes	no	0.832	0.787	0.526	5e-46
Q9C7C3		248	Zinc finger CCCH domain-c	no	no	0.841	0.770	0.502	1e-45
Q9LT81		386	Zinc finger CCCH domain-c	no	no	0.898	0.528	0.280	3e-06
Q84UQ3		367	Zinc finger CCCH domain-c	no	no	0.132	0.081	0.612	0.0005
P47976		325	mRNA decay factor CTH1 OS	yes	no	0.132	0.092	0.548	0.0009

>sp\|Q7F8R0\|C3H14_ORYSJ Zinc finger CCCH domain-containing protein 14 OS=Oryza sativa subsp. japonica GN=Os02g0194200 PE=2 SV=1	Back alignment and function desciption

 Score =  255 bits (652), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 143/232 (61%), Positives = 161/232 (69%), Gaps = 9/232 (3%)

Query: 1   MLNLGGTPAHPPPPPRNSGAPPSFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEW 60
           M NLGG PA  PPP R      + PDG   P VK+RLCNKYN+AEGCK+GDKCHFAHGE 
Sbjct: 70  MTNLGG-PAIAPPPGRMPMGN-AVPDGPPTPTVKTRLCNKYNTAEGCKWGDKCHFAHGER 127

Query: 61  ELGRPTVPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGAII 120
           ELG+P +     P  MG    G       P   ++   ASFGASATAKIS+DA LAG II
Sbjct: 128 ELGKPMLMDSSMPPPMGPRPTGHFAPPPMPS-PAMSTPASFGASATAKISVDASLAGGII 186

Query: 121 GKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSGSG 180
           G+ GVN+KQI R+TGAKL+IRDHE D NL+NIELEGTFDQIK ASAMVRELIV++G G+ 
Sbjct: 187 GRGGVNTKQISRVTGAKLAIRDHESDTNLKNIELEGTFDQIKNASAMVRELIVSIGGGAP 246

Query: 181 HSMK------SNSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKSV 226
              K             +NFKTKLCENF KGSCTFGDRCHFAHG  ELRKS 
Sbjct: 247 PQGKKPVGGSHRGGGPGSNFKTKLCENFTKGSCTFGDRCHFAHGENELRKSA 298

Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q69XQ3\|C3H44_ORYSJ Zinc finger CCCH domain-containing protein 44 OS=Oryza sativa subsp. japonica GN=Os06g0618100 PE=2 SV=1	Back alignment and function description

>sp\|Q7XPK1\|C3H31_ORYSJ Zinc finger CCCH domain-containing protein 31 OS=Oryza sativa subsp. japonica GN=Os04g0665700 PE=2 SV=1	Back alignment and function description

>sp\|Q9FG30\|C3H52_ARATH Zinc finger CCCH domain-containing protein 52 OS=Arabidopsis thaliana GN=At5g06770 PE=2 SV=1	Back alignment and function description

>sp\|Q9C7C3\|C3H36_ARATH Zinc finger CCCH domain-containing protein 36 OS=Arabidopsis thaliana GN=At3g12130 PE=2 SV=1	Back alignment and function description

>sp\|Q9LT81\|C3H39_ARATH Zinc finger CCCH domain-containing protein 39 OS=Arabidopsis thaliana GN=At3g19360 PE=2 SV=1	Back alignment and function description

>sp\|Q84UQ3\|C3H56_ORYSJ Zinc finger CCCH domain-containing protein 56 OS=Oryza sativa subsp. japonica GN=Os08g0159800 PE=2 SV=1	Back alignment and function description

>sp\|P47976\|CTH1_YEAST mRNA decay factor CTH1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CTH1 PE=1 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		227
224057168		304	predicted protein [Populus trichocarpa]	0.982	0.733	0.734	5e-87
224076054		315	predicted protein [Populus trichocarpa]	0.942	0.679	0.713	2e-86
357445163		340	Zinc finger CCCH domain-containing prote	0.982	0.655	0.718	6e-85
225435608		301	PREDICTED: zinc finger CCCH domain-conta	0.964	0.727	0.777	1e-84
356536568		297	PREDICTED: zinc finger CCCH domain-conta	0.982	0.750	0.754	1e-84
358248424		297	uncharacterized protein LOC100818781 [Gl	0.982	0.750	0.745	1e-84
225450321		296	PREDICTED: zinc finger CCCH domain-conta	0.977	0.75	0.748	1e-82
225441425		297	PREDICTED: zinc finger CCCH domain-conta	0.938	0.717	0.693	1e-81
356504859		295	PREDICTED: zinc finger CCCH domain-conta	0.973	0.749	0.658	3e-80
356504857		295	PREDICTED: zinc finger CCCH domain-conta	0.973	0.749	0.658	6e-80

>gi\|224057168\|ref\|XP_002299153.1\| predicted protein [Populus trichocarpa] gi\|222846411\|gb\|EEE83958.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  326 bits (835), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 169/230 (73%), Positives = 188/230 (81%), Gaps = 7/230 (3%)

Query: 1   MLNLGGTPAHPPPPPRNSGAPP-SFPDGSSPPAVKSRLCNKYNSAEGCKFGDKCHFAHGE 59
           MLN+GG+PA  PP  RN G P  S+ D SSPP+VKSRLCNKYN+ EGCKFGDKCHFAHGE
Sbjct: 75  MLNVGGSPA-LPPASRNQGVPTLSYQDRSSPPSVKSRLCNKYNTVEGCKFGDKCHFAHGE 133

Query: 60  WELGRPT-VPSYEDPRAMGGPMHGRMGGRLEPPPQSLGAAASFGASATAKISIDAKLAGA 118
           WELG+ +  PSYEDPRAM GP+ GRM   +E P Q  GAAASFG+SAT KISIDA LAGA
Sbjct: 134 WELGKASAAPSYEDPRAM-GPIPGRMSRHMEHPHQGHGAAASFGSSATTKISIDASLAGA 192

Query: 119 IIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAMVRELIVNVGSG 178
           IIGKNGVNSK ICR+TGAKLSIRDHE DP  R+IELEG+FDQI QAS MVR+LI NVG  
Sbjct: 193 IIGKNGVNSKHICRVTGAKLSIRDHEADPKKRSIELEGSFDQISQASDMVRQLISNVGQA 252

Query: 179 SGHSMKS---NSSSQSNNFKTKLCENFAKGSCTFGDRCHFAHGSEELRKS 225
           SG  +K+   +SS  SNNFKTK+CENF KGSCTFGDRCHFAHG+EELRKS
Sbjct: 253 SGPPIKNQAMHSSGGSNNFKTKICENFNKGSCTFGDRCHFAHGAEELRKS 302

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224076054\|ref\|XP_002304891.1\| predicted protein [Populus trichocarpa] gi\|222842323\|gb\|EEE79870.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|357445163\|ref\|XP_003592859.1\| Zinc finger CCCH domain-containing protein [Medicago truncatula] gi\|355481907\|gb\|AES63110.1\| Zinc finger CCCH domain-containing protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|225435608\|ref\|XP_002285629.1\| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356536568\|ref\|XP_003536809.1\| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]	Back alignment and taxonomy information

>gi\|358248424\|ref\|NP_001240135.1\| uncharacterized protein LOC100818781 [Glycine max] gi\|255636715\|gb\|ACU18693.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|225450321\|ref\|XP_002273052.1\| PREDICTED: zinc finger CCCH domain-containing protein 14 [Vitis vinifera] gi\|147768909\|emb\|CAN75883.1\| hypothetical protein VITISV_024456 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225441425\|ref\|XP_002279071.1\| PREDICTED: zinc finger CCCH domain-containing protein 14-like isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356504859\|ref\|XP_003521212.1\| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]	Back alignment and taxonomy information

>gi\|356504857\|ref\|XP_003521211.1\| PREDICTED: zinc finger CCCH domain-containing protein 14-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		227
TAIR\|locus:2170169		240	AT5G06770 [Arabidopsis thalian	0.528	0.5	0.601	5.2e-41
TAIR\|locus:2099292		248	AT3G12130 [Arabidopsis thalian	0.528	0.483	0.564	2.5e-39
UNIPROTKB\|G3V2D5		176	ZFP36L1 "Zinc finger protein 3	0.132	0.170	0.548	0.00088
TAIR\|locus:2090669		386	AT3G19360 [Arabidopsis thalian	0.145	0.085	0.588	6.1e-09
UNIPROTKB\|G3V2P5		207	ZFP36L1 "Zinc finger protein 3	0.132	0.144	0.516	1.3e-08
UNIPROTKB\|Q7ZXW9		363	zfp36l2-A "Zinc finger protein	0.140	0.088	0.484	6.7e-08
UNIPROTKB\|A7MB98		338	ZFP36L1 "Uncharacterized prote	0.132	0.088	0.516	8e-08
UNIPROTKB\|E2R2W0		338	ZFP36L1 "Uncharacterized prote	0.132	0.088	0.516	8e-08
UNIPROTKB\|Q07352		338	ZFP36L1 "Zinc finger protein 3	0.132	0.088	0.516	8e-08
UNIPROTKB\|I3LB77		338	ZFP36L1 "Uncharacterized prote	0.132	0.088	0.516	8e-08

TAIR\|locus:2170169 AT5G06770 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 364 (133.2 bits), Expect = 5.2e-41, Sum P(2) = 5.2e-41
 Identities = 74/123 (60%), Positives = 89/123 (72%)

Query:   108 KISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQASAM 167
             KIS+DA LAGAIIGK G++SKQICR TGAKLSI+DHE DPNL+ IELEGTF+QI  AS M
Sbjct:   117 KISVDASLAGAIIGKGGIHSKQICRETGAKLSIKDHERDPNLKIIELEGTFEQINVASGM 176

Query:   168 VRELIV---NVXXXXXXXXXXXXXXXXXXFKTKLCENFAKGSCTFGDRCHFAHGSEELRK 224
             VRELI    +V                  +KTK+C+ ++KG+CT+GDRCHFAHG  ELR+
Sbjct:   177 VRELIGRLGSVKKPQGIGGPEGKPHPGSNYKTKICDRYSKGNCTYGDRCHFAHGESELRR 236

Query:   225 SVI 227
             S I
Sbjct:   237 SGI 239

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR\|locus:2099292 AT3G12130 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V2D5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

TAIR\|locus:2090669 AT3G19360 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V2P5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7ZXW9 zfp36l2-A "Zinc finger protein 36, C3H1 type-like 2-A" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|A7MB98 ZFP36L1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R2W0 ZFP36L1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q07352 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LB77 ZFP36L1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FG30	C3H52_ARATH	No assigned EC number	0.5265	0.8325	0.7875	yes	no
Q7F8R0	C3H14_ORYSJ	No assigned EC number	0.6163	0.9823	0.7433	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pm.C_LG_I0043	hypothetical protein (304 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		227
cd00105		64	cd00105, KH-I, K homology RNA-binding domain, type	3e-14
smart00322		68	smart00322, KH, K homology RNA-binding domain	6e-13
pfam00013		59	pfam00013, KH_1, KH domain	2e-12
cd02396		65	cd02396, PCBP_like_KH, K homology RNA-binding doma	6e-08
smart00356		27	smart00356, ZnF_C3H1, zinc finger	1e-07
pfam00642		27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	4e-07
pfam13014		42	pfam13014, KH_3, KH domain	6e-07
cd02394		62	cd02394, vigilin_like_KH, K homology RNA-binding d	1e-04
pfam00642		27	pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H t	2e-04
TIGR03665		172	TIGR03665, arCOG04150, arCOG04150 universal archae	2e-04
COG5063		351	COG5063, CTH1, CCCH-type Zn-finger protein [Genera	0.001
PRK13763		180	PRK13763, PRK13763, putative RNA-processing protei	0.003
COG1094		194	COG1094, COG1094, Predicted RNA-binding protein (c	0.004

>gnl\|CDD\|238053 cd00105, KH-I, K homology RNA-binding domain, type I	Back alignment and domain information

 Score = 64.5 bits (158), Expect = 3e-14
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 106 TAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIKQAS 165
           T ++ + + L G IIGK G   K+I   TGAK+ I D       R + + GT + +++A 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 166 AMV 168
            ++
Sbjct: 61  ELI 63

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 N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl\|CDD\|197652 smart00322, KH, K homology RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|215657 pfam00013, KH_1, KH domain	Back alignment and domain information

>gnl\|CDD\|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like	Back alignment and domain information

>gnl\|CDD\|214632 smart00356, ZnF_C3H1, zinc finger	Back alignment and domain information

>gnl\|CDD\|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Back alignment and domain information

>gnl\|CDD\|221895 pfam13014, KH_3, KH domain	Back alignment and domain information

>gnl\|CDD\|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like	Back alignment and domain information

>gnl\|CDD\|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Back alignment and domain information

>gnl\|CDD\|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>gnl\|CDD\|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional	Back alignment and domain information

>gnl\|CDD\|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH domains) [General function prediction only]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		227
KOG1677		332	consensus CCCH-type Zn-finger protein [General fun	99.56
cd02396		65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.38
PF00013		60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.1
cd02394		62	vigilin_like_KH K homology RNA-binding domain_vigi	99.05
KOG1676		600	consensus K-homology type RNA binding proteins [RN	99.01
cd00105		64	KH-I K homology RNA-binding domain, type I. KH bin	99.0
KOG1676		600	consensus K-homology type RNA binding proteins [RN	99.0
COG5063		351	CTH1 CCCH-type Zn-finger protein [General function	98.95
KOG2192		390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	98.88
cd02393		61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.86
PF00642		27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.77
PF00642		27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	98.74
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	98.65
smart00322		69	KH K homology RNA-binding domain.	98.64
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	98.51
KOG1677		332	consensus CCCH-type Zn-finger protein [General fun	98.48
PF13014		43	KH_3: KH domain	98.48
KOG2190		485	consensus PolyC-binding proteins alphaCP-1 and rel	98.46
COG5063		351	CTH1 CCCH-type Zn-finger protein [General function	98.44
smart00356		27	ZnF_C3H1 zinc finger.	98.4
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	98.3
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	98.23
cd02395		120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.19
smart00356		27	ZnF_C3H1 zinc finger.	98.19
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	98.17
PRK13763		180	putative RNA-processing protein; Provisional	98.11
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	98.05
PRK13763		180	putative RNA-processing protein; Provisional	97.84
KOG2190		485	consensus PolyC-binding proteins alphaCP-1 and rel	97.79
KOG1595		528	consensus CCCH-type Zn-finger protein [General fun	97.67
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.09
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.05
KOG1595		528	consensus CCCH-type Zn-finger protein [General fun	96.68
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	96.57
KOG2185		486	consensus Predicted RNA-processing protein, contai	96.47
cd02134		61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.35
KOG2192		390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	96.12
KOG0119		554	consensus Splicing factor 1/branch point binding p	96.06
PF14608		19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	95.9
COG1094		194	Predicted RNA-binding protein (contains KH domains	95.82
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	95.63
KOG2494		331	consensus C3H1-type Zn-finger protein [Transcripti	95.46
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	95.37
KOG1040		325	consensus Polyadenylation factor I complex, subuni	94.9
KOG1040		325	consensus Polyadenylation factor I complex, subuni	94.41
PF14608		19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	94.18
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	94.07
KOG2185		486	consensus Predicted RNA-processing protein, contai	94.0
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	93.95
KOG1763		343	consensus Uncharacterized conserved protein, conta	93.56
COG5176		269	MSL5 Splicing factor (branch point binding protein	93.47
COG5252		299	Uncharacterized conserved protein, contains CCCH-t	93.02
PF13184		69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	92.77
COG5152		259	Uncharacterized conserved protein, contains RING a	92.67
PRK08406		140	transcription elongation factor NusA-like protein;	92.57
KOG2494		331	consensus C3H1-type Zn-finger protein [Transcripti	91.86
PRK12328		374	nusA transcription elongation factor NusA; Provisi	91.49
COG5152		259	Uncharacterized conserved protein, contains RING a	91.12
PRK08406		140	transcription elongation factor NusA-like protein;	91.1
KOG2279		608	consensus Kinase anchor protein AKAP149, contains	90.89
COG0195		190	NusA Transcription elongation factor [Transcriptio	90.84
KOG2279		608	consensus Kinase anchor protein AKAP149, contains	90.71
TIGR01953		341	NusA transcription termination factor NusA. This m	89.56
PRK12704		520	phosphodiesterase; Provisional	89.5
TIGR01952		141	nusA_arch NusA family KH domain protein, archaeal.	89.37
PRK02821		77	hypothetical protein; Provisional	89.35
KOG1588		259	consensus RNA-binding protein Sam68 and related KH	89.13
KOG4369		2131	consensus RTK signaling protein MASK/UNC-44 [Signa	88.7
PRK00468		75	hypothetical protein; Provisional	88.62
TIGR01952		141	nusA_arch NusA family KH domain protein, archaeal.	88.61
TIGR03319		514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	88.45
PRK12327		362	nusA transcription elongation factor NusA; Provisi	88.15
COG1837		76	Predicted RNA-binding protein (contains KH domain)	87.06
PRK00106		535	hypothetical protein; Provisional	86.08
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	85.74
PRK12329		449	nusA transcription elongation factor NusA; Provisi	85.54
KOG2814		345	consensus Transcription coactivator complex, P50 c	85.49
PRK06418		166	transcription elongation factor NusA-like protein;	84.88
PRK01064		78	hypothetical protein; Provisional	84.75
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	84.6
PRK09202		470	nusA transcription elongation factor NusA; Validat	84.06
PF07650		78	KH_2: KH domain syndrome, contains KH motifs.; Int	80.81

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

Probab=99.56  E-value=1.7e-15  Score=137.11  Aligned_cols=41  Identities=37%  Similarity=0.794  Sum_probs=37.4

Q ss_pred             CCCCCCCCCcccccccccCCCCCCC-CCCCccCCCCcccCCC
Q 027188           25 PDGSSPPAVKSRLCNKYNSAEGCKF-GDKCHFAHGEWELGRP   65 (227)
Q Consensus        25 p~~~~~~~yKT~lC~~f~~~g~C~y-G~~C~FAHg~~ELr~p   65 (227)
                      .....+..|||.||..|..++.|.| |++|+|||+.+|||.+
T Consensus       122 ~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~  163 (332)
T KOG1677|consen  122 RGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLP  163 (332)
T ss_pred             ccccCcccccCCcceeeecCccccccCchhhhcCCccccccc
Confidence            4466788999999999999999999 9999999999999964

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like	Back alignment and domain information

>PF00013 KH_1: KH domain syndrome, contains KH motifs	Back alignment and domain information

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like	Back alignment and domain information

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]	Back alignment and domain information

>cd00105 KH-I K homology RNA-binding domain, type I	Back alignment and domain information

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]	Back alignment and domain information

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)	Back alignment and domain information

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>smart00322 KH K homology RNA-binding domain	Back alignment and domain information

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF13014 KH_3: KH domain	Back alignment and domain information

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]	Back alignment and domain information

>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>smart00356 ZnF_C3H1 zinc finger	Back alignment and domain information

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)	Back alignment and domain information

>smart00356 ZnF_C3H1 zinc finger	Back alignment and domain information

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]	Back alignment and domain information

>PRK13763 putative RNA-processing protein; Provisional	Back alignment and domain information

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>PRK13763 putative RNA-processing protein; Provisional	Back alignment and domain information

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	Back alignment and domain information

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]	Back alignment and domain information

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)	Back alignment and domain information

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	Back alignment and domain information

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]	Back alignment and domain information

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]	Back alignment and domain information

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]	Back alignment and domain information

>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]	Back alignment and domain information

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	Back alignment and domain information

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	Back alignment and domain information

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]	Back alignment and domain information

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]	Back alignment and domain information

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]	Back alignment and domain information

>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A	Back alignment and domain information

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>PRK08406 transcription elongation factor NusA-like protein; Validated	Back alignment and domain information

>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]	Back alignment and domain information

>PRK12328 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>PRK08406 transcription elongation factor NusA-like protein; Validated	Back alignment and domain information

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]	Back alignment and domain information

>COG0195 NusA Transcription elongation factor [Transcription]	Back alignment and domain information

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]	Back alignment and domain information

>TIGR01953 NusA transcription termination factor NusA	Back alignment and domain information

>PRK12704 phosphodiesterase; Provisional	Back alignment and domain information

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal	Back alignment and domain information

>PRK02821 hypothetical protein; Provisional	Back alignment and domain information

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]	Back alignment and domain information

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]	Back alignment and domain information

>PRK00468 hypothetical protein; Provisional	Back alignment and domain information

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal	Back alignment and domain information

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF	Back alignment and domain information

>PRK12327 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]	Back alignment and domain information

>PRK00106 hypothetical protein; Provisional	Back alignment and domain information

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK12329 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]	Back alignment and domain information

>PRK06418 transcription elongation factor NusA-like protein; Validated	Back alignment and domain information

>PRK01064 hypothetical protein; Provisional	Back alignment and domain information

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK09202 nusA transcription elongation factor NusA; Validated	Back alignment and domain information

>PF07650 KH_2: KH domain syndrome, contains KH motifs	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		227
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-22
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-21
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	5e-19
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	4e-18
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	3e-17
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-17
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-16
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	3e-15
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	3e-14
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	7e-14
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-13
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	4e-12
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	9e-11
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-12
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-10
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	1e-11
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	7e-11
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	1e-11
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	2e-11
1we8_A		104	Tudor and KH domain containing protein; structural	2e-11
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-11
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-10
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-10
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	5e-10
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	9e-10
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	5e-09
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	9e-08
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	2e-07
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	5e-07
2d9m_A		69	Zinc finger CCCH-type domain containing protein 7A	1e-08
2d9m_A		69	Zinc finger CCCH-type domain containing protein 7A	2e-04
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	3e-08
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	3e-08
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	1e-07
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-07
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-04
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-06
1tua_A		191	Hypothetical protein APE0754; structural genomics,	5e-06
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2d9n_A		77	Cleavage and polyadenylation specificity factor, 3	1e-04
2cqe_A		98	KIAA1064 protein; CCCH zinc-finger, structural gen	2e-04
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	3e-04
2ctf_A		102	Vigilin; K homology type I domain, RNA-binding, ce	5e-04
2rhk_C		72	Cleavage and polyadenylation specificity factor su	5e-04

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82	Back alignment and structure

 Score = 86.6 bits (215), Expect = 1e-22
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 99  ASFGASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTF 158
            + G   T +++I   LAG+IIGK G   KQI   +GA + I +       R I + GT 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 159 DQIKQASAMVRELI 172
           DQI+ A  +++  +
Sbjct: 61  DQIQNAQYLLQNSV 74

PyMOL of 1zzk

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89	Back alignment and structure

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106	Back alignment and structure

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107	Back alignment and structure

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85	Back alignment and structure

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82	Back alignment and structure

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76	Back alignment and structure

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92	Back alignment and structure

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94	Back alignment and structure

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76	Back alignment and structure

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163	Back alignment and structure

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178	Back alignment and structure

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73	Back alignment and structure

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94	Back alignment and structure

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A Length = 77	Back alignment and structure

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69	Back alignment and structure

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69	Back alignment and structure

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95	Back alignment and structure

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83	Back alignment and structure

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97	Back alignment and structure

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104	Back alignment and structure

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144	Back alignment and structure

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144	Back alignment and structure

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219	Back alignment and structure

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191	Back alignment and structure

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95	Back alignment and structure

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77	Back alignment and structure

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1 Length = 98	Back alignment and structure

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376	Back alignment and structure

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 102	Back alignment and structure

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens} Length = 72	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		227
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	99.73
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.46
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	99.44
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.44
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.41
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	99.41
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	99.39
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	99.38
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	99.34
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.34
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	99.34
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.32
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	99.32
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	99.31
1we8_A		104	Tudor and KH domain containing protein; structural	99.23
2d9m_A		69	Zinc finger CCCH-type domain containing protein 7A	99.22
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	99.12
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	99.11
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	99.09
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	99.09
2d9m_A		69	Zinc finger CCCH-type domain containing protein 7A	99.08
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.08
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	99.07
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	99.06
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	99.05
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	99.04
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	99.03
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.03
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.02
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	99.0
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	98.97
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	98.97
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	98.94
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	98.9
2cqe_A		98	KIAA1064 protein; CCCH zinc-finger, structural gen	98.87
2d9n_A		77	Cleavage and polyadenylation specificity factor, 3	98.69
2cpq_A		91	FragIle X mental retardation syndrome related prot	98.59
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	98.58
2yqr_A		119	KIAA0907 protein; structure genomics, KH domain, s	98.48
2ctf_A		102	Vigilin; K homology type I domain, RNA-binding, ce	98.43
3d2q_A		70	Muscleblind-like protein 1; tandem zinc finger dom	98.41
2rhk_C		72	Cleavage and polyadenylation specificity factor su	98.33
2e5s_A		98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	98.28
1k1g_A		131	SF1-BO isoform; splicing, branch point sequence, p	98.24
2d9n_A		77	Cleavage and polyadenylation specificity factor, 3	98.16
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.08
2cqe_A		98	KIAA1064 protein; CCCH zinc-finger, structural gen	97.89
2rhk_C		72	Cleavage and polyadenylation specificity factor su	97.87
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	97.85
2bl5_A		140	MGC83862 protein, quaking protein; STAR proteins,	97.82
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	97.82
1tua_A		191	Hypothetical protein APE0754; structural genomics,	97.69
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	97.62
1tua_A		191	Hypothetical protein APE0754; structural genomics,	97.58
3d2n_A		83	Muscleblind-like protein 1; tandem zinc finger dom	97.39
3n89_A		376	Defective in GERM LINE development protein 3, ISO;	97.33
3v69_A		140	Protein filia; RNA-binding, embryogenesis, KH doma	97.24
3u1k_A		630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.24
3d2q_A		70	Muscleblind-like protein 1; tandem zinc finger dom	97.2
2e5s_A		98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	96.86
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	96.83
2rpp_A		89	Muscleblind-like protein 2; zinc finger domain, C3	96.57
3d2n_A		83	Muscleblind-like protein 1; tandem zinc finger dom	96.45
2fc6_A		50	Nuclear, target of EGR1, member 1; structure genom	96.02
2rpp_A		89	Muscleblind-like protein 2; zinc finger domain, C3	95.9
2fc6_A		50	Nuclear, target of EGR1, member 1; structure genom	95.29
3cdi_A		723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.1
1e3p_A		757	Guanosine pentaphosphate synthetase; polyribonucle	93.4
3u1l_A		240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	93.34
2cxc_A		144	NUSA; transcription termination, RNA binding prote	89.02
2asb_A		251	Transcription elongation protein NUSA; protein-RNA	88.3
2cxc_A		144	NUSA; transcription termination, RNA binding prote	88.0
1k0r_A		366	NUSA; two component arrangement, S1 domain, two K-	85.98
1hh2_P		344	NUSA, N utilization substance protein A; transcrip	83.96

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A	Back alignment and structure

Probab=99.73  E-value=1.3e-18  Score=126.67  Aligned_cols=36  Identities=39%  Similarity=0.875  Sum_probs=32.4

Q ss_pred             CCCCCcccccccccCCCCCCCCCCCccCCCCcccCC
Q 027188           29 SPPAVKSRLCNKYNSAEGCKFGDKCHFAHGEWELGR   64 (227)
Q Consensus        29 ~~~~yKT~lC~~f~~~g~C~yG~~C~FAHg~~ELr~   64 (227)
                      ++++|||+||++|..+|.|+||++|+|+|+..||+.
T Consensus         6 ~~~~~kt~~C~~f~~~G~C~~G~~C~f~H~~~e~~~   41 (77)
T 1m9o_A            6 TSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQ   41 (77)
T ss_dssp             CSSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGG
T ss_pred             CCCCccchhCHHhhhCCCcCCCCCccCCCCChhhcc
Confidence            357999999999988899999999999999888763

PyMOL of 1m9o

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A	Back alignment and structure

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}	Back alignment and structure

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A	Back alignment and structure

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A	Back alignment and structure

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*	Back alignment and structure

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A	Back alignment and structure

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}	Back alignment and structure

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}	Back alignment and structure

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*	Back alignment and structure

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1	Back alignment and structure

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A	Back alignment and structure

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}	Back alignment and structure

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B	Back alignment and structure

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1	Back alignment and structure

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}	Back alignment and structure

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}	Back alignment and structure

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1	Back alignment and structure

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B	Back alignment and structure

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A	Back alignment and structure

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}	Back alignment and structure

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}	Back alignment and structure

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}	Back alignment and structure

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}	Back alignment and structure

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A	Back alignment and structure

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A	Back alignment and structure

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}	Back alignment and structure

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}	Back alignment and structure

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1	Back alignment and structure

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}	Back alignment and structure

>2fc6_A Nuclear, target of EGR1, member 1; structure genomics, ZF-CCCH domain, member 1(nuclear), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.66.1.1	Back alignment and structure

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A	Back alignment and structure

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A	Back alignment and structure

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A	Back alignment and structure

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A	Back alignment and structure

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A	Back alignment and structure

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A	Back alignment and structure

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1	Back alignment and structure

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		227
d1x4na1		79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-16
d1zzka1		75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-15
d1wvna1		70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	7e-15
d1j4wa1		74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-15
d2ctla1		84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-14
d2ctea1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-14
d1dtja_		74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-14
d2axya1		71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-14
d1m9oa_		40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	1e-13
d1m9oa_		40	g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475	8e-10
d1rgoa1		36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	4e-13
d1rgoa1		36	g.66.1.1 (A:151-186) Butyrate response factor 2 (T	2e-09
d1viga_		71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-13
d2ctma1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-13
d1j4wa2		71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-12
d1x4ma1		81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-12
d2ctka1		91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-12
d1we8a_		104	d.51.1.1 (A:) Tudor and KH domain containing prote	5e-11
d1rgoa2		34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	7e-11
d1rgoa2		34	g.66.1.1 (A:187-220) Butyrate response factor 2 (T	5e-10
d2ctja1		82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-10
d1tuaa2		104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	2e-07
d2ba0a3		84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-07
d1tuaa1		84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-07
d2cpqa1		78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-05
d2ctfa1		90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-05
d1e3ha4		54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-05
d2je6i3		69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-04
d2z0sa2		87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	7e-04

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.2 bits (172), Expect = 1e-16
 Identities = 15/70 (21%), Positives = 33/70 (47%)

Query: 103 ASATAKISIDAKLAGAIIGKNGVNSKQICRLTGAKLSIRDHEVDPNLRNIELEGTFDQIK 162
           +  T +  +   + G IIG+ G    +I + +G K+ I         R+  L GT + ++
Sbjct: 6   SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQ 65

Query: 163 QASAMVRELI 172
            A  ++ +++
Sbjct: 66  SAKRLLDQIV 75

PyMOL of d1x4na1

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75	Back information, alignment and structure

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70	Back information, alignment and structure

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74	Back information, alignment and structure

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84	Back information, alignment and structure

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81	Back information, alignment and structure

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74	Back information, alignment and structure

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40	Back information, alignment and structure

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]} Length = 40	Back information, alignment and structure

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36	Back information, alignment and structure

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 36	Back information, alignment and structure

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81	Back information, alignment and structure

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81	Back information, alignment and structure

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91	Back information, alignment and structure

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104	Back information, alignment and structure

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34	Back information, alignment and structure

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]} Length = 34	Back information, alignment and structure

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104	Back information, alignment and structure

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84	Back information, alignment and structure

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84	Back information, alignment and structure

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78	Back information, alignment and structure

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54	Back information, alignment and structure

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69	Back information, alignment and structure

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		227
d1m9oa_		40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.59
d1m9oa_		40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	99.59
d1rgoa1		36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.58
d1j4wa1		74	Far upstream binding element, FBP {Human (Homo sap	99.54
d1wvna1		70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.53
d1rgoa1		36	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.53
d1zzka1		75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1rgoa2		34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.51
d1j4wa2		71	Far upstream binding element, FBP {Human (Homo sap	99.45
d1rgoa2		34	Butyrate response factor 2 (Tis11D) {Human (Homo s	99.44
d1dtja_		74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.44
d1x4na1		79	Far upstream binding element, FBP {Mouse (Mus musc	99.42
d2axya1		71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.41
d1x4ma1		81	Far upstream binding element, FBP {Mouse (Mus musc	99.39
d1we8a_		104	Tudor and KH domain containing protein, Tdrkh {Mou	99.37
d2ctla1		84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d2ctea1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.21
d2ctma1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.11
d2ctja1		82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d2ctka1		91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.07
d1viga_		71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.01
d2cpqa1		78	Fragile X mental retardation syndrome related prot	99.01
d2ba0a3		84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.9
d1tuaa1		84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.82
d2ctfa1		90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.67
d1e3ha4		54	Polynucleotide phosphorylase/guanosine pentaphosph	98.45
d2je6i3		69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.37
d1tuaa2		104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.3
d2z0sa2		87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.16
d1k1ga_		122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.67
d2cqea2		29	Zinc finger CCCH domain-containing protein C19orf7	97.62
d2bl5a1		134	Quaking protein A (Xqua) {African clawed frog (Xen	96.82
d2cqea2		29	Zinc finger CCCH domain-containing protein C19orf7	95.89
d2asba3		67	Transcription factor NusA, C-terminal domains {Myc	95.71
d1hh2p3		68	Transcription factor NusA, C-terminal domains {The	95.63
d2cqea1		56	Zinc finger CCCH domain-containing protein C19orf7	93.05
d2cqea1		56	Zinc finger CCCH domain-containing protein C19orf7	93.0
d2fc6a1		37	Target of EGR1 protein 1, TOE1 {Human (Homo sapien	85.21
d1egaa2		113	GTPase Era C-terminal domain {Escherichia coli [Ta	81.52

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

class: Small proteins
fold: CCCH zinc finger
superfamily: CCCH zinc finger
family: CCCH zinc finger
domain: Tristetraproline (ttp, tis11, nup475)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.9e-16  Score=103.24  Aligned_cols=37  Identities=43%  Similarity=1.030  Sum_probs=33.9

Q ss_pred             CCCccccccccccc-cccCCCCCCCcccCCccccccCC
Q 027188          190 QSNNFKTKLCENFA-KGSCTFGDRCHFAHGSEELRKSV  226 (227)
Q Consensus       190 ~~~~~KTklC~~f~-~G~C~~G~~C~FAHg~~ELr~~~  226 (227)
                      ...+|||+||++|. .|.|+||++|+||||++|||++.
T Consensus         3 ~~~~yKT~lC~~~~~~g~C~~G~~C~FAHg~~ELr~~n   40 (40)
T d1m9oa_           3 TSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQAN   40 (40)
T ss_dssp             CSSCCCSCCCSGGGGTSCCTTTTTCSSCSSSCCGGGTC
T ss_pred             CCCccccccChhhhcCCcCCCCCCCCCCCCHHHhcCCC
Confidence            45899999999998 69999999999999999999873

PyMOL of d1m9oa_

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}	Back information, alignment and structure

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}	Back information, alignment and structure

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fc6a1 g.66.1.1 (A:8-44) Target of EGR1 protein 1, TOE1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure