Citrus Sinensis ID: 019667

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------
Protein Sequence
MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKKEKKDDGTDHPDPEIAEANRIRASLGLKPLKL
Secondary Structure (PSIPRED)
cccEEEcccccccccccHHHHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccEEEEEHHHHHHHHHHHHccccccccccccccHHHHccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccHHcccccccccccccccccccccccccHHHHHccccccccccccccccccccccccHHHHHHHcccccccccccHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccccccccHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEHHHHHHHHHccccEEccEccccccHHHHHHcccccccccccHHHHHHHccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
meldhlggtfggnrkptpFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRltgtdidiyrYLEPLYNDYRKlrqksgdgrfILTHVDEVIDELLtkdyscdialprikkrwnletvgaleprksvleddfeeeeekeendqlddgledgayerdyhhgrsptrerdrdrrrdsyryrdrdydrdydrdrgrgrerdrgrdrdrdrdrdrdrerdrdrnryrlrddreygrerdrdreregrdrerrdrdrgrrrsrsrsrsrsrdrkrharssmsprrdrdepedvgtraepkkkkekkekkddgtdhpdpeiAEANRIRAslglkplkl
Flexible Loop (DISEMBL)
meldhlggtfggnrkpTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLrltgtdidiyrYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTkdyscdialprikkrwnletvgaleprksvleddfeeeeekeendqlddgledgayerdyhhgrsptrerdrdrrrdsyryrdrdydrdydrdrgrgrerdrgrdrdrdrdrdrdrerdrdrnryrlrddreygrerdrdreregrdrerrdrdrgrrrsrsrsrsrsrdrkrharssmsprrdrdepedvgtraepkkkkekkekkddgtdhpdpeiaeanriraslglkplkl
Low Complexity Region (SEG)
MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVLeddfeeeeekeendqlddGLEDGAYERDYHHGRSPTrerdrdrrrdsyryrdrdydrdydrdrgrgrerdrgrdrdrdrdrdrdrerdrdrnryrlrddreygrerdrdreregrdrerrdrdrgrrrsrsrsrsrsrdrKRHARSSMSPRRDRDEPEDVGTRAEPkkkkekkekkDDGTDHPDPEIAEANRIRASLGLKPLKL
Disordered region (IsUnstruct)
***************PTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGAL*******************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*ELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSV******************************************************************************************************************************************************************************************************GLKPL**
Disordered Region (DISEMBL)
MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVLE***************DDGLEDGAYERDY***************RDSYRYRDRDYDRDYDR***************************RDRNRYRLRDDRE*********************************************************************************PDPEIAEANRIRASLGLKPLKL
Disordered Region (DISPRO)
MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVL*DD*EEEE*****************************************************************************************************************************************************************************************R*SLGL*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKKEKKDDGTDHPDPEIAEANRIRASLGLKPLKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	337	2.2.26 [Sep-21-2011]
Q4FK66	312	Pre-mRNA-splicing factor	yes	no	0.406	0.439	0.649	1e-50
Q5RDD2	312	Pre-mRNA-splicing factor	yes	no	0.406	0.439	0.656	2e-50
Q8HXH6	312	Pre-mRNA-splicing factor	N/A	no	0.406	0.439	0.656	2e-50
Q8NAV1	312	Pre-mRNA-splicing factor	yes	no	0.406	0.439	0.656	2e-50
Q0P5I6	312	Pre-mRNA-splicing factor	yes	no	0.406	0.439	0.656	2e-50
Q6DHU4	313	Pre-mRNA-splicing factor	yes	no	0.406	0.437	0.642	2e-49
Q4FZQ6	312	Pre-mRNA-splicing factor	N/A	no	0.406	0.439	0.635	9e-49
Q28H87	312	Pre-mRNA-splicing factor	yes	no	0.406	0.439	0.627	1e-48
Q9UUD2	210	Pre-mRNA-splicing factor	yes	no	0.335	0.538	0.460	2e-25
F1QBY1	2876	Nipped-B-like protein B O	no	no	0.305	0.035	0.379	8e-09

>sp|Q4FK66|PR38A_MOUSE Pre-mRNA-splicing factor 38A OS=Mus musculus GN=Prpf38a PE=1 SV=1

 Score =  200 bits (509), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 89/137 (64%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELKFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T ID Y+YLEPLYNDYRK++ ++ +G F+L HVDE I ELL  +  CDI LPR++KR+ L
Sbjct: 112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFVLMHVDEFIYELLHSERVCDIILPRLQKRYVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    LEPR S LE+D 
Sbjct: 172 EEAEQLEPRVSALEEDM 188

May be required for pre-mRNA splicing.
Mus musculus (taxid: 10090)

>sp|Q5RDD2|PR38A_PONAB Pre-mRNA-splicing factor 38A OS=Pongo abelii GN=PRPF38A PE=2 SV=1

 Score =  199 bits (506), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 90/137 (65%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct: 112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    LEPR S LE+D 
Sbjct: 172 EEAEQLEPRVSALEEDM 188

May be required for pre-mRNA splicing.

Pongo abelii (taxid: 9601)

>sp|Q8HXH6|PR38A_MACFA Pre-mRNA-splicing factor 38A OS=Macaca fascicularis GN=PRPF38A PE=2 SV=1

 Score =  199 bits (506), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 90/137 (65%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct: 112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    LEPR S LE+D 
Sbjct: 172 EEAEQLEPRVSALEEDM 188

May be required for pre-mRNA splicing.

Macaca fascicularis (taxid: 9541)

>sp|Q8NAV1|PR38A_HUMAN Pre-mRNA-splicing factor 38A OS=Homo sapiens GN=PRPF38A PE=1 SV=1

 Score =  199 bits (506), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 90/137 (65%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct: 112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    LEPR S LE+D 
Sbjct: 172 EEAEQLEPRVSALEEDM 188

May be required for pre-mRNA splicing.

Homo sapiens (taxid: 9606)

>sp|Q0P5I6|PR38A_BOVIN Pre-mRNA-splicing factor 38A OS=Bos taurus GN=PRPF38A PE=2 SV=1

 Score =  199 bits (506), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 90/137 (65%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct: 112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    LEPR S LE+D 
Sbjct: 172 EEAEQLEPRVSALEEDM 188

May be required for pre-mRNA splicing.

Bos taurus (taxid: 9913)

>sp|Q6DHU4|PR38A_DANRE Pre-mRNA-splicing factor 38A OS=Danio rerio GN=prpf38a PE=2 SV=1

 Score =  196 bits (498), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 88/137 (64%), Positives = 109/137 (79%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct: 52  MELKFVGGVYGGNVKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRLLGAMYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T +D Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR  L
Sbjct: 112 TSVDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHAERMCDIILPRLQKRQVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    L+PR S LE+D 
Sbjct: 172 EEAELLDPRISALEEDL 188

May be required for pre-mRNA splicing.

Danio rerio (taxid: 7955)

>sp|Q4FZQ6|PR38A_XENLA Pre-mRNA-splicing factor 38A OS=Xenopus laevis GN=prpf38a PE=2 SV=1

 Score =  194 bits (492), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 87/137 (63%), Positives = 109/137 (79%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR LGA Y+RLTG
Sbjct: 52  MELKFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRALGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T  D Y+YLEPLYNDYRK++ ++ DG F L HVDE ID+LL ++  CD+ LPR++KR+ L
Sbjct: 112 TATDCYKYLEPLYNDYRKVKVQNRDGEFELMHVDEFIDQLLHEERVCDVILPRLQKRFVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    L+PR S LE+D 
Sbjct: 172 EETEQLDPRVSALEEDM 188

May be required for pre-mRNA splicing.

Xenopus laevis (taxid: 8355)

>sp|Q28H87|PR38A_XENTR Pre-mRNA-splicing factor 38A OS=Xenopus tropicalis GN=prpf38a PE=2 SV=1

 Score =  193 bits (491), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 86/137 (62%), Positives = 110/137 (80%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MEL ++GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR LGA Y+RLTG
Sbjct: 52  MELKYVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRTLGALYMRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           T  D Y+YLEPLYNDYRK++ ++ +G F L HVDE ID+LL ++  CD+ LPR++KR+ L
Sbjct: 112 TATDCYKYLEPLYNDYRKVKVQNRNGEFELMHVDEFIDQLLHEERVCDVILPRLQKRFVL 171

Query: 121 ETVGALEPRKSVLEDDF 137
           E    L+PR S LE+D 
Sbjct: 172 EETEQLDPRVSALEEDM 188

May be required for pre-mRNA splicing.

Xenopus tropicalis (taxid: 8364)

>sp|Q9UUD2|PRP38_SCHPO Pre-mRNA-splicing factor 38 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=prp38 PE=3 SV=1

 Score =  116 bits (290), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/115 (46%), Positives = 87/115 (75%), Gaps = 2/115 (1%)

Query: 3   LDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTD 62
           L+++GG +G N++PT F+CL+ K+LQI PEK+I+ +++   ++KY+R L AFY+RLT  D
Sbjct: 58  LEYIGGQYG-NQRPTEFICLLYKLLQIAPEKEIIQQYLSIPEFKYLRALAAFYVRLTWDD 116

Query: 63  IDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKR 117
           +++++ LEPL  DYRKLR ++ +    LT++DEV+D+LL  +  CDI+LP ++ R
Sbjct: 117 VEVHQTLEPLLRDYRKLRIRT-NSEIRLTYLDEVVDDLLNAEVVCDISLPPLRSR 170

Required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Implicated in the formation of stable and biologically active snRNP structures. As part of the U4/U6.U5 tri-snRNP particle, dispensible for spliceosome assembly, but required for conformational changes, which result in U4 snRNA release and the subsequent catalytic activation of the spliceosome.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|F1QBY1|NIPLB_DANRE Nipped-B-like protein B OS=Danio rerio GN=nipblb PE=2 SV=1

 Score = 61.6 bits (148), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 41/108 (37%), Positives = 80/108 (74%), Gaps = 5/108 (4%)

Query: 170 RERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRL 229
           RE+DRD+  +  R +D+D + +  R++ + +E ++G+++DRD+ R++DR++ RD++R ++
Sbjct: 802 REKDRDKEMEKAREKDQDKELEKGREKDQDKELEKGQEKDRDKVREKDRDKVRDKDRDKV 861

Query: 230 RD-DREYGRERDRDREREGRDRER---RDRDRGRRRSRSRSRSRSRDR 273
           R+ DR+  RE+DRD+ RE +DRE+   RDRD+GR + R + + ++R++
Sbjct: 862 REKDRDKVREKDRDKLRE-KDREKIRERDRDKGREKDRDKEQVKTREK 908

Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by facilitating the cohesin complex loading, and in transcription regulation.

Danio rerio (taxid: 7955)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	337
388513517	385	unknown [Medicago truncatula]	0.976	0.854	0.707	7e-82
317106643	390	JHL23J11.3 [Jatropha curcas]	0.498	0.430	0.887	9e-74
225450673	393	PREDICTED: uncharacterized protein LOC10	0.557	0.478	0.829	1e-72
296089736	326	unnamed protein product [Vitis vinifera]	0.557	0.576	0.829	2e-72
356576821	383	PREDICTED: uncharacterized protein LOC10	0.501	0.441	0.810	3e-71
147863592	235	hypothetical protein VITISV_013614 [Viti	0.545	0.782	0.826	2e-70
363808110	381	uncharacterized protein LOC100792466 [Gl	0.501	0.443	0.798	3e-69
357441821	385	Pre-mRNA-splicing factor 38A [Medicago t	0.563	0.493	0.789	9e-68
224125088	297	predicted protein [Populus trichocarpa]	0.394	0.447	0.902	1e-67
148906831	400	unknown [Picea sitchensis]	0.572	0.482	0.723	1e-66

>gi|388513517|gb|AFK44820.1| unknown [Medicago truncatula]

 Score =  310 bits (794), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 242/342 (70%), Positives = 278/342 (81%), Gaps = 13/342 (3%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGT+GGNRKPTPFMCLVMKMLQIQPEK+IV+EFIKNDDYKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTYGGNRKPTPFMCLVMKMLQIQPEKEIVIEFIKNDDYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           +D D+Y Y EPLYNDYRKLR+K  DG+F LTHVDEVIDELLT DYSCDIA+PRIKKRW L
Sbjct: 112 SDTDVYHYPEPLYNDYRKLRRKLPDGQFALTHVDEVIDELLTTDYSCDIAMPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDS 180
           E++GALEPR+S LE+DFEEEEE E+N+Q  +       E+DY+ GRSP RERDRDRRRDS
Sbjct: 172 ESLGALEPRQSALEEDFEEEEENEDNEQPAE-----EPEKDYNRGRSPARERDRDRRRDS 226

Query: 181 YRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERD 240
           +R+RDRDYDR+YDRD  R R R R RDRDRDR+++RDR+R+RDR RYRLR++++YGRER+
Sbjct: 227 HRHRDRDYDREYDRDYDRERGRGRDRDRDRDREKERDRDRERDRGRYRLREEKDYGRERE 286

Query: 241 RDREREGRDRERRDRDRGRRRSRSRSRSRSRD-----RKRHARSSMSPRRDRDEPEDVGT 295
                       R R R   RSRSRSR R        RKRHARSS+SPRRD  E    G 
Sbjct: 287 GRERERRDRDRDRGRRRSYSRSRSRSRDRKDHDGGDYRKRHARSSVSPRRDGAED---GE 343

Query: 296 RAEPKKKKEKKEKKDDGTDHPDPEIAEANRIRASLGLKPLKL 337
             + K+KKEKKE+KDDGTDHPDPEIAEANRIRASLGLKPLK+
Sbjct: 344 PKKKKEKKEKKEEKDDGTDHPDPEIAEANRIRASLGLKPLKM 385

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106643|dbj|BAJ53148.1| JHL23J11.3 [Jatropha curcas]

 Score =  283 bits (724), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 150/169 (88%), Positives = 162/169 (95%), Gaps = 1/169 (0%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           TD+D+YRYLEPLYNDYRKLRQK  DG+F LTHVDEVIDELLTKDYSCD+ALPRIKKRW L
Sbjct: 112 TDVDVYRYLEPLYNDYRKLRQKLPDGKFALTHVDEVIDELLTKDYSCDVALPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPT 169
           E++G+LEPRKSVLEDDFEEEEEKEEN+Q DDGL++G  ERDY+HGRSPT
Sbjct: 172 ESLGSLEPRKSVLEDDFEEEEEKEENEQ-DDGLDNGIDERDYYHGRSPT 219

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225450673|ref|XP_002283131.1| PREDICTED: uncharacterized protein LOC100266508 [Vitis vinifera]

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 156/188 (82%), Positives = 174/188 (92%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKN++YKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNEEYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
            D D+Y+YLEPLYNDYRKLR+K  DG + LTHVDEVIDELLTKDYSCD+ALPRIKKRW L
Sbjct: 112 IDTDVYQYLEPLYNDYRKLRRKLSDGNYSLTHVDEVIDELLTKDYSCDVALPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDS 180
           E++G LEPR+S LEDDFEEEEEKEE+DQL D L+ GA+E+DY+ GRSP RERDRDR+RDS
Sbjct: 172 ESLGTLEPRRSALEDDFEEEEEKEEDDQLMDELDVGAHEKDYYRGRSPARERDRDRKRDS 231

Query: 181 YRYRDRDY 188
           +RYRDRDY
Sbjct: 232 HRYRDRDY 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089736|emb|CBI39555.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (712), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 156/188 (82%), Positives = 174/188 (92%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKN++YKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNEEYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
            D D+Y+YLEPLYNDYRKLR+K  DG + LTHVDEVIDELLTKDYSCD+ALPRIKKRW L
Sbjct: 112 IDTDVYQYLEPLYNDYRKLRRKLSDGNYSLTHVDEVIDELLTKDYSCDVALPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDS 180
           E++G LEPR+S LEDDFEEEEEKEE+DQL D L+ GA+E+DY+ GRSP RERDRDR+RDS
Sbjct: 172 ESLGTLEPRRSALEDDFEEEEEKEEDDQLMDELDVGAHEKDYYRGRSPARERDRDRKRDS 231

Query: 181 YRYRDRDY 188
           +RYRDRDY
Sbjct: 232 HRYRDRDY 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576821|ref|XP_003556528.1| PREDICTED: uncharacterized protein LOC100794094 [Glycine max]

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 137/169 (81%), Positives = 159/169 (94%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGT+GGNRKPTPFMCLVMKMLQIQPEK+IV+EFIKN+DYKYVR+LGAFYLR+TG
Sbjct: 52  MELDHLGGTYGGNRKPTPFMCLVMKMLQIQPEKEIVIEFIKNEDYKYVRILGAFYLRITG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           +DID+YRYLEPLYNDYRKLR+K  DG+F LTHVDEVIDELLTKDYSCDIALPR+KKRW L
Sbjct: 112 SDIDVYRYLEPLYNDYRKLRRKLADGQFTLTHVDEVIDELLTKDYSCDIALPRVKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPT 169
           E++G+LEPR+S LE+DFEEEEEKE+N+Q  D +ED AYE+D++ GRSPT
Sbjct: 172 ESLGSLEPRRSALEEDFEEEEEKEDNEQPVDEIEDKAYEKDHYRGRSPT 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147863592|emb|CAN79776.1| hypothetical protein VITISV_013614 [Vitis vinifera]

 Score =  272 bits (695), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 152/184 (82%), Positives = 170/184 (92%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKN++YKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNEEYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
            D D+Y+YLEPLYNDYRKLR+K  DG + LTHVDEVIDELLTKDYSCD+ALPRIKKRW L
Sbjct: 112 IDTDVYQYLEPLYNDYRKLRRKLSDGNYSLTHVDEVIDELLTKDYSCDVALPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDS 180
           E++G LEPR+S LEDDFEEEEEKEE+DQL D L+ GA+E+DY+ GRSP RERDRDR+RDS
Sbjct: 172 ESLGTLEPRRSALEDDFEEEEEKEEDDQLMDELDAGAHEKDYYRGRSPARERDRDRKRDS 231

Query: 181 YRYR 184
           +RYR
Sbjct: 232 HRYR 235

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363808110|ref|NP_001242475.1| uncharacterized protein LOC100792466 [Glycine max] gi|255642457|gb|ACU21492.1| unknown [Glycine max]

 Score =  268 bits (684), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 135/169 (79%), Positives = 157/169 (92%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGT+GGNRKPTPFMCLVMKMLQIQPEK+I++EFIKN+DYKYVR+LGAFYLR+TG
Sbjct: 52  MELDHLGGTYGGNRKPTPFMCLVMKMLQIQPEKEIIIEFIKNEDYKYVRILGAFYLRITG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           +DID+YRYLEPL NDYRKLR+K  DG+F LTHVDEVIDELLTKDYSCDIA+PR+KKRW L
Sbjct: 112 SDIDVYRYLEPLCNDYRKLRRKLADGQFALTHVDEVIDELLTKDYSCDIAMPRVKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPT 169
           E++G+LEPR+S LE+DFEEEEEKE+NDQ  D +ED AYE+D + GRSPT
Sbjct: 172 ESLGSLEPRRSALEEDFEEEEEKEDNDQPVDEIEDRAYEKDQYRGRSPT 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441821|ref|XP_003591188.1| Pre-mRNA-splicing factor 38A [Medicago truncatula] gi|124359153|gb|ABN05680.1| PRP38 [Medicago truncatula] gi|355480236|gb|AES61439.1| Pre-mRNA-splicing factor 38A [Medicago truncatula]

 Score =  263 bits (672), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 154/195 (78%), Positives = 175/195 (89%), Gaps = 5/195 (2%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGT+GGNRKPTPFMCLVMKMLQIQPEK+IV+EFIKNDDYKYVR+LGAFYLRLTG
Sbjct: 52  MELDHLGGTYGGNRKPTPFMCLVMKMLQIQPEKEIVIEFIKNDDYKYVRILGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           +D D+Y YLEPLYNDYRKLR+K  DG+F LTHVDEVIDELLT DYSCDIA+PRIKKRW L
Sbjct: 112 SDTDVYHYLEPLYNDYRKLRRKLPDGQFALTHVDEVIDELLTTDYSCDIAMPRIKKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDS 180
           E++GALEPR+S LE+DFEEEEE E+N+Q  +       E+DY+ GRSP RERDRDRRRDS
Sbjct: 172 ESLGALEPRQSALEEDFEEEEENEDNEQPAE-----EPEKDYNRGRSPARERDRDRRRDS 226

Query: 181 YRYRDRDYDRDYDRD 195
           +R+RDRDYDR+YDRD
Sbjct: 227 HRHRDRDYDREYDRD 241

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125088|ref|XP_002319497.1| predicted protein [Populus trichocarpa] gi|222857873|gb|EEE95420.1| predicted protein [Populus trichocarpa]

 Score =  263 bits (671), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 120/133 (90%), Positives = 128/133 (96%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDHLGGT+GGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKN+DYKYVRVLGAFYLRLTG
Sbjct: 52  MELDHLGGTYGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNEDYKYVRVLGAFYLRLTG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
           TDID+YRYLEPLYNDYRKLR+K  DG+F LTH+DEVIDELLTKDYSCDIA+PRIKKRW L
Sbjct: 112 TDIDVYRYLEPLYNDYRKLRKKLTDGKFALTHMDEVIDELLTKDYSCDIAMPRIKKRWTL 171

Query: 121 ETVGALEPRKSVL 133
           ET+ ALEPRKSVL
Sbjct: 172 ETLAALEPRKSVL 184

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148906831|gb|ABR16561.1| unknown [Picea sitchensis]

 Score =  259 bits (662), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 141/195 (72%), Positives = 160/195 (82%), Gaps = 2/195 (1%)

Query: 1   MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
           MELDH GGT GGNRK TPFMCL+MKMLQIQPEK+IVVEFIKN+DYKYVR+LGA YLRL G
Sbjct: 52  MELDHFGGTHGGNRKATPFMCLMMKMLQIQPEKEIVVEFIKNEDYKYVRILGALYLRLVG 111

Query: 61  TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
              D+Y+YLEPLYNDYRKLR+K  DG F L+HVDE IDELLT DY+CD+ALPR+ KRW L
Sbjct: 112 KPTDVYQYLEPLYNDYRKLRRKLADGSFALSHVDEFIDELLTTDYACDVALPRVPKRWTL 171

Query: 121 ETVGALEPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRD-RRRD 179
           E  G LEPR+S LEDDFEEEEEKEE DQ   GL   A ++D+  GRS  RERDRD ++RD
Sbjct: 172 EASGQLEPRRSALEDDFEEEEEKEEEDQTLIGLGSLALDKDHRRGRSSPRERDRDAKKRD 231

Query: 180 SYR-YRDRDYDRDYD 193
            YR +RDR+YDRDYD
Sbjct: 232 MYRQHRDRNYDRDYD 246

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	337
TAIR|locus:2064811	355	AT2G40650 [Arabidopsis thalian	0.394	0.374	0.849	3e-77
UNIPROTKB|Q0P5I6	312	PRPF38A "Pre-mRNA-splicing fac	0.394	0.426	0.661	3.3e-47
UNIPROTKB|Q8NAV1	312	PRPF38A "Pre-mRNA-splicing fac	0.394	0.426	0.661	3.3e-47
MGI|MGI:1916962	312	Prpf38a "PRP38 pre-mRNA proces	0.394	0.426	0.654	5.3e-47
ZFIN|ZDB-GENE-040801-225	313	prpf38a "PRP38 pre-mRNA proces	0.394	0.424	0.646	8.6e-47
WB|WBGene00008380	320	prp-38 [Caenorhabditis elegans	0.394	0.415	0.578	2e-45
FB|FBgn0050342	330	Prp38 "pre-mRNA processing fac	0.394	0.403	0.639	2.8e-41
DICTYBASE|DDB_G0274361	515	prpf38a "putative U4/U6.U5 sma	0.391	0.256	0.571	3.2e-41
GENEDB_PFALCIPARUM|PF11_0336	386	PF11_0336 "hypothetical protei	0.388	0.339	0.462	1.9e-33
UNIPROTKB|Q8II38	386	PF11_0336 "Pre-mRNA splicing f	0.388	0.339	0.462	1.9e-33

TAIR|locus:2064811 AT2G40650 [Arabidopsis thaliana (taxid:3702)]

 Score = 627 (225.8 bits), Expect = 3.0e-77, Sum P(3) = 3.0e-77
 Identities = 113/133 (84%), Positives = 126/133 (94%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MELDHLGGTFGG+RKPTPF+CL++KMLQIQPEK+IVVEFIKNDDYKYVR+LGAFYLRLTG
Sbjct:    52 MELDHLGGTFGGSRKPTPFLCLILKMLQIQPEKEIVVEFIKNDDYKYVRILGAFYLRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
             TD+D+YRYLEPLYNDYRK+RQK  DG+F LTHVDEVI+ELLTKDYSCDIA+PR+KKRW L
Sbjct:   112 TDVDVYRYLEPLYNDYRKVRQKLSDGKFSLTHVDEVIEELLTKDYSCDIAMPRLKKRWTL 171

Query:   121 ETVGALEPRKSVL 133
             E  G LEPRKSVL
Sbjct:   172 EQNGLLEPRKSVL 184

GO:0005634 "nucleus" evidence=ISM

GO:0006396 "RNA processing" evidence=ISS

UNIPROTKB|Q0P5I6 PRPF38A "Pre-mRNA-splicing factor 38A" [Bos taurus (taxid:9913)]

 Score = 473 (171.6 bits), Expect = 3.3e-47, Sum P(2) = 3.3e-47
 Identities = 88/133 (66%), Positives = 107/133 (80%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct:    52 MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
             T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct:   112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query:   121 ETVGALEPRKSVL 133
             E    LEPR S L
Sbjct:   172 EEAEQLEPRVSAL 184

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

UNIPROTKB|Q8NAV1 PRPF38A "Pre-mRNA-splicing factor 38A" [Homo sapiens (taxid:9606)]

 Score = 473 (171.6 bits), Expect = 3.3e-47, Sum P(2) = 3.3e-47
 Identities = 88/133 (66%), Positives = 107/133 (80%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct:    52 MELRFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
             T ID Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR+ L
Sbjct:   112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKRYVL 171

Query:   121 ETVGALEPRKSVL 133
             E    LEPR S L
Sbjct:   172 EEAEQLEPRVSAL 184

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

MGI|MGI:1916962 Prpf38a "PRP38 pre-mRNA processing factor 38 (yeast) domain containing A" [Mus musculus (taxid:10090)]

 Score = 471 (170.9 bits), Expect = 5.3e-47, Sum P(2) = 5.3e-47
 Identities = 87/133 (65%), Positives = 107/133 (80%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct:    52 MELKFVGGVYGGNIKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
             T ID Y+YLEPLYNDYRK++ ++ +G F+L HVDE I ELL  +  CDI LPR++KR+ L
Sbjct:   112 TAIDCYKYLEPLYNDYRKIKSQNRNGEFVLMHVDEFIYELLHSERVCDIILPRLQKRYVL 171

Query:   121 ETVGALEPRKSVL 133
             E    LEPR S L
Sbjct:   172 EEAEQLEPRVSAL 184

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

ZFIN|ZDB-GENE-040801-225 prpf38a "PRP38 pre-mRNA processing factor 38 (yeast) domain containing A" [Danio rerio (taxid:7955)]

 Score = 467 (169.5 bits), Expect = 8.6e-47, Sum P(2) = 8.6e-47
 Identities = 86/133 (64%), Positives = 106/133 (79%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MEL  +GG +GGN KPTPF+CL +KMLQIQPEKDI+VEFIKN+D+KYVR+LGA Y+RLTG
Sbjct:    52 MELKFVGGVYGGNVKPTPFLCLTLKMLQIQPEKDIIVEFIKNEDFKYVRLLGAMYMRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
             T +D Y+YLEPLYNDYRK++ ++ +G F L HVDE IDELL  +  CDI LPR++KR  L
Sbjct:   112 TSVDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHAERMCDIILPRLQKRQVL 171

Query:   121 ETVGALEPRKSVL 133
             E    L+PR S L
Sbjct:   172 EEAELLDPRISAL 184

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

WB|WBGene00008380 prp-38 [Caenorhabditis elegans (taxid:6239)]

 Score = 416 (151.5 bits), Expect = 2.0e-45, Sum P(2) = 2.0e-45
 Identities = 77/133 (57%), Positives = 101/133 (75%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             M+L ++GG + GN KPTPF+CL +KMLQIQP+KDIV+EFI+ +++KY+R LGA YLRLT 
Sbjct:    52 MDLRYIGGIYAGNIKPTPFLCLALKMLQIQPDKDIVLEFIQQEEFKYIRALGAMYLRLTF 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
                +IY+YLEPLYND+RKLR  +  GRF   ++D+ ID LL +D  CDI LPR++KRW L
Sbjct:   112 DSTEIYKYLEPLYNDFRKLRYMNKMGRFEAIYMDDFIDNLLREDRYCDIQLPRLQKRWAL 171

Query:   121 ETVGALEPRKSVL 133
             E V  L   KS+L
Sbjct:   172 EEVDMLPSYKSLL 184

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0007126 "meiosis" evidence=IMP

GO:0045132 "meiotic chromosome segregation" evidence=IMP

FB|FBgn0050342 Prp38 "pre-mRNA processing factor 38" [Drosophila melanogaster (taxid:7227)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 85/133 (63%), Positives = 104/133 (78%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             MEL  +GG +GGN KPT F+CL +KMLQIQPEKDIVVEFIKN+++KYVR LGAFYLRLTG
Sbjct:    52 MELRFVGGVYGGNIKPTQFLCLTLKMLQIQPEKDIVVEFIKNEEFKYVRALGAFYLRLTG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
               +D Y+YLEPLY D RKLR+++  G+F + ++DE IDELL  D  CDI LPRI+KR  L
Sbjct:   112 AALDCYKYLEPLYIDNRKLRRQNRAGQFEIVYMDEYIDELLRNDRVCDIILPRIQKRSIL 171

Query:   121 ETVGALEPRKSVL 133
             E    +EP+ SVL
Sbjct:   172 EENNEIEPKVSVL 184

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0043234 "protein complex" evidence=IPI

GO:0010389 "regulation of G2/M transition of mitotic cell cycle" evidence=IMP

DICTYBASE|DDB_G0274361 prpf38a "putative U4/U6.U5 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 389 (142.0 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 76/133 (57%), Positives = 97/133 (72%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             M L+  GG FGGN++PT F+CL++KMLQIQPE DI+ EFI+N+D+KYVR+LGA YLRL G
Sbjct:    90 MALESYGGCFGGNKQPTHFLCLLLKMLQIQPEMDIIKEFIENEDFKYVRILGAIYLRLVG 149

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
               +DIY  L+PLY D+R LR+K+  G      VD+ I+ELLT +YSCDIALP I  R NL
Sbjct:   150 KPVDIYNQLDPLYKDFRALRRKTDMGS-TKVFVDQFIEELLTTNYSCDIALPHIPSRANL 208

Query:   121 ETVGALEPRKSVL 133
                  L+ R+S L
Sbjct:   209 IQQSLLKERESPL 221

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GENEDB_PFALCIPARUM|PF11_0336 PF11_0336 "hypothetical protein, conserved" [Plasmodium falciparum (taxid:5833)]

 Score = 333 (122.3 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 61/132 (46%), Positives = 92/132 (69%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             + L ++GGT+GGNRKPT F+CL++K+LQIQP+KDI+ E+IKN+D+ Y+R LG FYLRL G
Sbjct:    52 INLKYVGGTYGGNRKPTRFLCLILKLLQIQPDKDIIYEYIKNEDFVYLRALGIFYLRLIG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
               +++Y +LEP+  DYRK+R +  +G F   ++D  +D  L  +   D+  P + KR  L
Sbjct:   112 KSLEVYNHLEPILFDYRKIRMRLQNGTFEKIYMDVFVDNCLILNNFLDVDFPTLTKRQVL 171

Query:   121 ETVGALEPRKSV 132
             E    L+ RK++
Sbjct:   172 EENNLLQ-RKNL 182

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8II38 PF11_0336 "Pre-mRNA splicing factor, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 333 (122.3 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 61/132 (46%), Positives = 92/132 (69%)

Query:     1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTG 60
             + L ++GGT+GGNRKPT F+CL++K+LQIQP+KDI+ E+IKN+D+ Y+R LG FYLRL G
Sbjct:    52 INLKYVGGTYGGNRKPTRFLCLILKLLQIQPDKDIIYEYIKNEDFVYLRALGIFYLRLIG 111

Query:    61 TDIDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNL 120
               +++Y +LEP+  DYRK+R +  +G F   ++D  +D  L  +   D+  P + KR  L
Sbjct:   112 KSLEVYNHLEPILFDYRKIRMRLQNGTFEKIYMDVFVDNCLILNNFLDVDFPTLTKRQVL 171

Query:   121 ETVGALEPRKSV 132
             E    L+ RK++
Sbjct:   172 EENNLLQ-RKNL 182

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	337
pfam03371	173	pfam03371, PRP38, PRP38 family	4e-60
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-15
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-15
PRK12678	672	PRK12678, PRK12678, transcription termination fact	5e-15
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-14
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-14
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-13
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-10
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-10
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-09
PRK12678	672	PRK12678, PRK12678, transcription termination fact	9e-09
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-06
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	6e-05
pfam07420	377	pfam07420, DUF1509, Protein of unknown function (D	2e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	0.003

>gnl|CDD|217519 pfam03371, PRP38, PRP38 family

 Score =  190 bits (485), Expect = 4e-60
 Identities = 75/124 (60%), Positives = 96/124 (77%)

Query: 3   LDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTD 62
           +DH+GGT+GGNR+P+PF+CL++K+LQIQP K+I+ E + N+D+KY+R LG FYLRLT   
Sbjct: 50  VDHIGGTYGGNRRPSPFLCLLLKLLQIQPSKEIIKELLNNEDFKYIRALGLFYLRLTYPP 109

Query: 63  IDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLET 122
            D+Y++LEP   DYRKLR K GDG F LTH+DE +D+LLTKD  CD  LPRI KR  LE 
Sbjct: 110 ADLYKWLEPYLQDYRKLRPKLGDGDFKLTHMDEFVDDLLTKDRVCDTILPRIPKRIILEE 169

Query: 123 VGAL 126
            G L
Sbjct: 170 DGEL 173

Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation. Length = 173

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 76.9 bits (190), Expect = 2e-15
 Identities = 40/146 (27%), Positives = 52/146 (35%), Gaps = 2/146 (1%)

Query: 127 EPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDR 186
             RK+    +    E + +  +  +  E     R              +R R   R RD 
Sbjct: 141 AARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDG 200

Query: 187 DYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDRERE 246
           D DRD    R +G  R+    RD    R R R RDR   R    +  + G     D E  
Sbjct: 201 D-DRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGD-DNREDRGDRDGDDGEGR 258

Query: 247 GRDRERRDRDRGRRRSRSRSRSRSRD 272
           G  R RR RDR RR  R       R+
Sbjct: 259 GGRRGRRFRDRDRRGRRGGDGGNERE 284

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 76.5 bits (189), Expect = 2e-15
 Identities = 46/190 (24%), Positives = 65/190 (34%), Gaps = 6/190 (3%)

Query: 139 EEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGR 198
            + E     +        A            RER    RR + R      ++     R  
Sbjct: 100 AKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARAD 159

Query: 199 GRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGR-----ERDRDREREGRDRERR 253
             ER    +RD  R R    +R  +  R       E GR     +R   RE+  R  ER 
Sbjct: 160 AAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG 219

Query: 254 DRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKK-EKKDDG 312
            RD G RR R R R R   R    R     R   D     G R    + ++++  +  DG
Sbjct: 220 RRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279

Query: 313 TDHPDPEIAE 322
            +  +PE+ E
Sbjct: 280 GNEREPELRE 289

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 75.3 bits (186), Expect = 5e-15
 Identities = 37/155 (23%), Positives = 48/155 (30%), Gaps = 18/155 (11%)

Query: 138 EEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRG 197
            E  E+   +   D  E                 R R  R D     +R      +    
Sbjct: 146 GEGGEQPATEARADAAERTE-------EEERDERRRRGDREDRQAEAERGERGRREERGR 198

Query: 198 RGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDR 257
            G +RDR   R++   R+    RD    R R R         D +RE  G         R
Sbjct: 199 DGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGR 258

Query: 258 GRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPED 292
           G RR R   R R RDR+         RR  D   +
Sbjct: 259 GGRRGR---RFRDRDRRG--------RRGGDGGNE 282

Length = 672

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 73.8 bits (181), Expect = 2e-14
 Identities = 48/153 (31%), Positives = 61/153 (39%), Gaps = 19/153 (12%)

Query: 174 RDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDR 233
           RD   D  R + R  DRD   +R R R RDR R RDR R               R R+  
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHR---------------RSRERS 45

Query: 234 EYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDV 293
                R RDR R      R  R    RRSR R R RSR  +   +     RR RD     
Sbjct: 46  YREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHR---RRLRDRSPSN 102

Query: 294 GTRAEPKKKKEKKEKKDDGTDHPDPEIAEANRI 326
             R + KK+     K   G +    + A+A+++
Sbjct: 103 QWRKDDKKRSLWDIKP-PGYELVTADQAKASQV 134

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 72.2 bits (177), Expect = 5e-14
 Identities = 40/142 (28%), Positives = 52/142 (36%), Gaps = 14/142 (9%)

Query: 200 RERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDRGR 259
           R+ +  R+R++ R RDRDR  +R R        R   R R RDR R  R+R  R+  R R
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPR-------RRSRDRSRFRDRHRRSRERSYREDSRPR 53

Query: 260 RRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAE-------PKKKKEKKEKKDDG 312
            R R  SRS    R    R S    R R        +         P  +  K +KK   
Sbjct: 54  DRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSL 113

Query: 313 TDHPDPEIAEANRIRASLGLKP 334
            D   P        +A      
Sbjct: 114 WDIKPPGYELVTADQAKASQVF 135

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 71.1 bits (174), Expect = 1e-13
 Identities = 40/116 (34%), Positives = 54/116 (46%), Gaps = 4/116 (3%)

Query: 170 RERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDR-GRDRDRDRD-RDRDRERDRDRNRY 227
            +R+R++ R   R R  +  R   RDR R R+R R  R+R    D R RDR R   R+  
Sbjct: 5   PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPR 64

Query: 228 RLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSP 283
            LR      R RDR R R  R     ++ R R R RS S    +D K+ +   + P
Sbjct: 65  SLRYSS-VRRSRDRPRRRS-RSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKP 118

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 69.9 bits (172), Expect = 4e-13
 Identities = 36/161 (22%), Positives = 47/161 (29%), Gaps = 9/161 (5%)

Query: 138 EEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRG 197
            E  E           E G          +  R  + +R     R    D   + +R   
Sbjct: 131 RERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGER 190

Query: 198 RGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRD- 256
             RE       DRDR   R++   R+    R   DR   R R   R+  G D      D 
Sbjct: 191 GRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

Query: 257 --------RGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDE 289
                    GRR  R R R R   R     +   P    D+
Sbjct: 251 DGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELREDD 291

Length = 672

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 59.9 bits (145), Expect = 5e-10
 Identities = 34/98 (34%), Positives = 42/98 (42%), Gaps = 18/98 (18%)

Query: 194 RDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERR 253
           RDR RGR R+  R  D+ R+R R R R RDR+R R        R+RD  R R GR R R 
Sbjct: 3   RDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRR--------RDRDYYRGRRGRSRSR- 53

Query: 254 DRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPE 291
                          R R  + + R      R+  EP 
Sbjct: 54  ---------SPNRYYRPRGDRSYRRDDRRSGRNTKEPL 82

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 59.9 bits (146), Expect = 6e-10
 Identities = 31/164 (18%), Positives = 48/164 (29%), Gaps = 1/164 (0%)

Query: 163 HHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDR 222
              ++      R     +               R RG    RG  R      ++     R
Sbjct: 98  AAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAR 157

Query: 223 DRNRYRLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSR-SRSRDRKRHARSSM 281
                R  ++    R R  DRE    + ER +R R   R R      R   R++  R   
Sbjct: 158 ADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREE 217

Query: 282 SPRRDRDEPEDVGTRAEPKKKKEKKEKKDDGTDHPDPEIAEANR 325
             RRD  +      R + +  +    ++D G    D       R
Sbjct: 218 RGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR 261

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 58.4 bits (142), Expect = 2e-09
 Identities = 26/181 (14%), Positives = 45/181 (24%), Gaps = 1/181 (0%)

Query: 138 EEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRG 197
                              A  +           +                         
Sbjct: 67  AATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQ 126

Query: 198 RGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDR-D 256
               R+RG    R   R      ++     R         E   +R R G   +R+   +
Sbjct: 127 ARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAE 186

Query: 257 RGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKKEKKDDGTDHP 316
           RG R  R        DR R  R     RR+     D G R   ++++++++ + D     
Sbjct: 187 RGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRED 246

Query: 317 D 317
            
Sbjct: 247 R 247

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 56.5 bits (137), Expect = 9e-09
 Identities = 35/125 (28%), Positives = 44/125 (35%), Gaps = 7/125 (5%)

Query: 127 EPRKSVLEDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDR 186
             R+   ED   E E  E   + + G +    +R     +     R+   RRD    R R
Sbjct: 172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQG--DRREERGRRDGGDRRGR 229

Query: 187 DYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDRERE 246
              RD    RG     DRG     D +    R   R R+R     DR   R  D   ERE
Sbjct: 230 RRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR-----DRRGRRGGDGGNERE 284

Query: 247 GRDRE 251
              RE
Sbjct: 285 PELRE 289

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 51.4 bits (124), Expect = 3e-07
 Identities = 26/91 (28%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 134 EDDFEEEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYD 193
            D  E+ + +EE  + D G      +R     R   R+   D  R+    RD D      
Sbjct: 206 RDRREQGDRREERGRRDGG------DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRG 259

Query: 194 RDRG-RGRERDRGRDRDRDRDRDRDRERDRD 223
             RG R R+RDR   R  D   +R+ E   D
Sbjct: 260 GRRGRRFRDRDRRGRRGGDGGNEREPELRED 290

Length = 672

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 50.3 bits (120), Expect = 7e-07
 Identities = 31/89 (34%), Positives = 40/89 (44%), Gaps = 2/89 (2%)

Query: 237 RERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTR 296
           R RDR+R R  R+  RR  D+GR RSR RSRSR R R+R  R     RR R         
Sbjct: 1   RYRDRERGRL-RNDTRR-SDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRY 58

Query: 297 AEPKKKKEKKEKKDDGTDHPDPEIAEANR 325
             P+  +  +        +    + EA R
Sbjct: 59  YRPRGDRSYRRDDRRSGRNTKEPLTEAER 87

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 48.0 bits (114), Expect = 4e-06
 Identities = 36/108 (33%), Positives = 43/108 (39%), Gaps = 17/108 (15%)

Query: 172 RDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRD 231
           R RDR R   R   R  D+  +R R R R RDR R R RDRD  R R             
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSR-RRRDRDYYRGRRG----------- 48

Query: 232 DREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARS 279
                R R R   R  R R  R   R  RRS   ++    + +R  R+
Sbjct: 49  -----RSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRT 91

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 28/95 (29%), Positives = 48/95 (50%), Gaps = 3/95 (3%)

Query: 165 GRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDR 224
              P R++DR + R + R RDR+  RD  RD    RE    R+ +R R+R + +++  + 
Sbjct: 597 EAKPERQQDRRKPRQNNR-RDRNERRD-TRDNRTRREGRENREENR-RNRRQAQQQTAET 653

Query: 225 NRYRLRDDREYGRERDRDREREGRDRERRDRDRGR 259
              +  +  E  R +D  ++   R+R+RR  D  R
Sbjct: 654 RESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKR 688

Length = 1068

>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509)

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 22/62 (35%), Positives = 24/62 (38%)

Query: 231 DDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEP 290
           +D   G      R       ERR R R R  SRSRSRSRS  R+   R        R E 
Sbjct: 304 EDSAGGSHHTMRRPPHSTSGERRGRRRNRSESRSRSRSRSGSRRYRRRRGRGVPGRRSES 363

Query: 291 ED 292
             
Sbjct: 364 RQ 365

This family consists of several uncharacterized viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 residues in length. The function of this family is unknown. Length = 377

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 42.2 bits (100), Expect = 3e-04
 Identities = 16/135 (11%), Positives = 32/135 (23%)

Query: 191 DYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDR 250
                R   R     R  ++        + +                      +   R  
Sbjct: 73  PAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRE 132

Query: 251 ERRDRDRGRRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKKEKKD 310
                 RG  R       +     R   +  +   +RDE    G R + + + E+ E+  
Sbjct: 133 RGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGR 192

Query: 311 DGTDHPDPEIAEANR 325
                 D +  +   
Sbjct: 193 REERGRDGDDRDRRD 207

Length = 672

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 30/86 (34%), Positives = 36/86 (41%), Gaps = 5/86 (5%)

Query: 159 ERDYHHGRSPTRERDRDRRRDSYRYRD---RDYDRDYDRDRGRGRERDRGRDRDRDRDRD 215
           ER      +   ++ R+R R   R RD   R  DRDY R R RGR R R  +R   R R 
Sbjct: 6   ERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGR-RGRSRSRSPNR-YYRPRG 63

Query: 216 RDRERDRDRNRYRLRDDREYGRERDR 241
               R  DR   R   +     ERD 
Sbjct: 64  DRSYRRDDRRSGRNTKEPLTEAERDD 89

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 31/91 (34%), Positives = 34/91 (37%), Gaps = 4/91 (4%)

Query: 160 RDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRE 219
           RD   GR     R  D+ R+  R R R   RD  R R R R+  RGR             
Sbjct: 3   RDRERGRLRNDTRRSDKGRE--RSRRRSRSRDRSR-RRRDRDYYRGRRGRSRSRSPNRYY 59

Query: 220 RDRDRNRYRLRDDREYGRERDRDREREGRDR 250
           R R    YR RDDR  GR          RD 
Sbjct: 60  RPRGDRSYR-RDDRRSGRNTKEPLTEAERDD 89

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 6/96 (6%)

Query: 168 PTRERDRDRRRDSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRY 227
           P  E   +R++D  R + R  +R   RDR   R+    R R   R+   +  R+R + + 
Sbjct: 594 PKAEAKPERQQD--RRKPRQNNR---RDRNERRDTRDNRTRREGRENREENRRNRRQAQQ 648

Query: 228 RLRDDREYGRERDRDREREGRDRERRDR-DRGRRRS 262
           +  + RE  +    ++ R   ++++  R +R RRR+
Sbjct: 649 QTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRN 684

Length = 1068

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 32/114 (28%), Positives = 41/114 (35%), Gaps = 21/114 (18%)

Query: 139 EEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRR------------RDSYRYRDR 186
           +EE   E ++      D + ER     R  +R RDR RR            RD  RY  R
Sbjct: 2   DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR 61

Query: 187 DYD--------RDYDRDRGRGRERDRG-RDRDRDRDRDRDRERDRDRNRYRLRD 231
                      R  DR R R R      + R R RDR    +  +D  +  L D
Sbjct: 62  SPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 25/56 (44%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 220 RDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKR 275
             R R R+R R  R   R   R R R    R RR R R RRR R R R R R RK+
Sbjct: 6   WRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRR-RRRRRRRKRKK 60

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 28/192 (14%), Positives = 66/192 (34%), Gaps = 4/192 (2%)

Query: 139 EEEEKEENDQLDDGLEDGAYERDYHHGRSPTRERDRDRRRDSYRYRDRDYDRDYDRDRGR 198
            +E K E+ + ++  ++   E        P  E    + ++  + +    +++ ++++  
Sbjct: 95  AKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKV 154

Query: 199 GRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGRDRERRDRDRG 258
              RDR  ++ R+R R + R +   + +   +       E+ R   RE    +  + D  
Sbjct: 155 EEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVN 214

Query: 259 RRRSRSRSRSRSRDRKRHARSSMSPRRDRDEPEDVGTRAEPKKKKEKKEKKDDGTDHPDP 318
             R +     + R+           R+  +       R+    KK          +  + 
Sbjct: 215 EEREKEEDDGKDRETTTSPMEEDESRQSSEISR----RSSSSLKKPDPSPSMASPETRES 270

Query: 319 EIAEANRIRASL 330
                 R R SL
Sbjct: 271 SKRTETRPRTSL 282

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 39.3 bits (91), Expect = 0.002
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 228 RLRDDREYGRERDRDREREGRDRERRDRDRGRRRSRSRSRSRSRDRKRHARSS 280
           +L   RE   E+ + RE E + RE R+R++ + + R R R R  +R   A SS
Sbjct: 576 KLAKKREEAVEKAK-REAEQKAREEREREKEKEKEREREREREAERAAKASSS 627

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 38.1 bits (88), Expect = 0.003
 Identities = 37/102 (36%), Positives = 44/102 (43%), Gaps = 2/102 (1%)

Query: 179 DSYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRE 238
           DS     RD  RD  +        D  R+RDR R   R R+    R     R  R   R 
Sbjct: 4   DSSSRSPRDTRRDSRKKEKIPYFADEVRERDRVR-NLRQRKTQSTRPTTSHRGRRTRSRS 62

Query: 239 RDRDREREGRDRERRDRDRGRRRSRSRSRSRS-RDRKRHARS 279
           R +  ER    R  R R R R RS SR RS S  +R+R +RS
Sbjct: 63  RSQSAERNSCQRRHRSRSRSRNRSDSRHRSTSSTERRRRSRS 104

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	337
KOG2889	204	consensus Predicted PRP38-like splicing factor [Fu	100.0
PF03371	172	PRP38: PRP38 family; InterPro: IPR005037 Members o	100.0
KOG2888	453	consensus Putative RNA binding protein [General fu	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.14
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.82
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	96.78
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	96.65
PF12871	97	PRP38_assoc: Pre-mRNA-splicing factor 38-associate	96.15
KOG3263	196	consensus Nucleic acid binding protein [General fu	95.57
KOG2217	705	consensus U4/U6.U5 snRNP associated protein [RNA p	95.26
KOG2888	453	consensus Putative RNA binding protein [General fu	94.61
KOG4368	757	consensus Predicted RNA binding protein, contains	81.49

>KOG2889 consensus Predicted PRP38-like splicing factor [Function unknown]

Probab=100.00  E-value=4.7e-47  Score=337.58  Aligned_cols=148  Identities=64%  Similarity=1.090  Sum_probs=143.2

Q ss_pred             CcccccCCccCCCCCCCchhHHHHHHhccCCCHHHHHHHhcCCCcceeeecccchhhhccchHHHHHHhhhhhhhhhhhh
Q 019667            1 MELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLR   80 (337)
Q Consensus         1 ~~l~~iGg~~g~~~~Ps~f~CLL~KLlqi~P~~~iv~~~L~~~d~KYlRaLg~lYlRltg~p~ely~~lEp~l~DyrKlr   80 (337)
                      |+|.||||.||||.+||||+||.+|||||+|+++|+.+||.+.+||||+|||||||||||...++|+||+|||+||+||+
T Consensus        52 m~l~~lgg~yGgn~kpt~fKOG~lkmLqiqpeK~i~~efi~~~~fkY~ralgafYlRLt~~~~~~y~ylepl~nDyRKir  131 (204)
T KOG2889|consen   52 MELLYLGGKYGGNSKPTPFLCLDLKMLQIQPEKEIGSEFIMNHDFKYVRALGAFYLRLTGTDVDVYKYLEPLLNDYRKIR  131 (204)
T ss_pred             HHHHHHHHHhcCCCCCccHHHHHHHHcCCCCCcccchHHHhccchHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhh
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCCCceeeeeHHHHHHHHHhccccccccCCCcccchhHhHhccCCCccccchhhhhHHHhhhhhhc
Q 019667           81 QKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKSVLEDDFEEEEEKEENDQ  148 (337)
Q Consensus        81 ~~~~dg~~~~~~~defvd~LL~~~~~~~i~LPRip~R~~lE~~~~LepR~s~Le~~~Ee~eeeeEee~  148 (337)
                      +.+.+|++++||||+|||+||++.+||+|+|||+.+|++||+++.|+|++|.|+++++++++.++++.
T Consensus       132 ~~~~~g~~~l~ylDe~iDdLL~~~r~cdI~Lprl~kr~~le~~~~lep~~s~ld~d~~~~e~~~~~e~  199 (204)
T KOG2889|consen  132 VVNGQGNRTLMYLDEVIDDLLNKSRICDIHLPRLDKRWQLEELDLLEPRKSSLDEDDDDEESSEEEEE  199 (204)
T ss_pred             hhcCCCceeeeeHHHHHHHHhhhcceeccccchhhhhhhhhhhccccccccccccchhhhhhhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999887766663

>PF03371 PRP38: PRP38 family; InterPro: IPR005037 Members of this family are related to the pre mRNA splicing factor PRP38 from yeast [], therefore all the members of this family could be involved in splicing

Probab=100.00  E-value=4.1e-44  Score=320.74  Aligned_cols=124  Identities=48%  Similarity=0.917  Sum_probs=120.0

Q ss_pred             cccccCCccCCCCCCCchhHHHHHHhccCCCHHHHHHHhcCCCcceeeecccchhhhccchHHHHHHhhhhhhhhhhhhh
Q 019667            2 ELDHLGGTFGGNRKPTPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQ   81 (337)
Q Consensus         2 ~l~~iGg~~g~~~~Ps~f~CLL~KLlqi~P~~~iv~~~L~~~d~KYlRaLg~lYlRltg~p~ely~~lEp~l~DyrKlr~   81 (337)
                      .|+|||||+||+++||+|||||||||||+|+++||.+||++.+||||||||||||||+++|.++|+||+|||+||+||++
T Consensus        49 ~v~~ig~~~~g~~~Ps~f~CLL~KLl~l~pt~~~v~~~l~~~d~kYiralg~lYlR~~~~p~~~~~~lep~l~D~rkl~~  128 (172)
T PF03371_consen   49 IVRYIGPWYGGNRRPSPFFCLLYKLLQLRPTKEQVKELLNNDDFKYIRALGFLYLRYVGPPEELYKWLEPYLNDYRKLRV  128 (172)
T ss_pred             HhhhhhcccCCCCCCchHHHHHHHHHhcccCHHHHHHHHcCCCccHHHHHHHHHheeeCCHHHHHHHHHHHhccceeeee
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCceeeeeHHHHHHHHHhccccccccCCCcccchhHhHhccC
Q 019667           82 KSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGAL  126 (337)
Q Consensus        82 ~~~dg~~~~~~~defvd~LL~~~~~~~i~LPRip~R~~lE~~~~L  126 (337)
                      +..+|. ++|||||||++||++++||||+|||||++.++|+.++|
T Consensus       129 ~~~~~~-~~~~~de~vd~LL~~~~~~~~~LPrlp~r~~~e~~~~~  172 (172)
T PF03371_consen  129 RNDGGD-KITHMDEFVDDLLTKDRYCGTILPRLPKRIVLEIDDEL  172 (172)
T ss_pred             ecCCCc-eeEEHHHHHHHHhhhCcEecccCCCCCchHHHHhhccC
Confidence            988664 89999999999999999999999999999999998876

This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation [].

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=100.00  E-value=4.2e-40  Score=316.02  Aligned_cols=128  Identities=23%  Similarity=0.447  Sum_probs=116.5

Q ss_pred             cccccCCccCCC-------------CCC------CchhHHHHHHhccCCCHHHHHHHhcCCCcceeeecccchhhhccch
Q 019667            2 ELDHLGGTFGGN-------------RKP------TPFMCLVMKMLQIQPEKDIVVEFIKNDDYKYVRVLGAFYLRLTGTD   62 (337)
Q Consensus         2 ~l~~iGg~~g~~-------------~~P------s~f~CLL~KLlqi~P~~~iv~~~L~~~d~KYlRaLg~lYlRltg~p   62 (337)
                      .|+||.||.+|+             +-|      |++||||||||+|++|.+||++||+|.+++|||||||||||||.+|
T Consensus        92 qVkHvEPWekGsrkt~gqtgmCggvRGvgaggivSTAyCLLYklftlklTrKQ~~gllnhtdSpYIRalGFmYiRYtqpp  171 (453)
T KOG2888|consen   92 QVKHVEPWEKGSRKTQGQTGMCGGVRGVGAGGIVSTAYCLLYKLFTLKLTRKQLIGLLNHTDSPYIRALGFMYIRYTQPP  171 (453)
T ss_pred             HHhccCchhcCCccccccccccccccccCcCcchhhHHHHHHHHHHHHhHHHHHHHHhhcCCchhhhhheeeEEeecCCh
Confidence            467777775444             445      9999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhhhhhhhhhhhccCCCceeeeeHHHHHHHHHhccccccccCCCcccchhHhHhccCCCccc
Q 019667           63 IDIYRYLEPLYNDYRKLRQKSGDGRFILTHVDEVIDELLTKDYSCDIALPRIKKRWNLETVGALEPRKS  131 (337)
Q Consensus        63 ~ely~~lEp~l~DyrKlr~~~~dg~~~~~~~defvd~LL~~~~~~~i~LPRip~R~~lE~~~~LepR~s  131 (337)
                      .+||.||||||+|.+.|.++...|  .+|||+++|..|||+..||+|.|||||++++..+...|+.++.
T Consensus       172 ~dLw~WyEpyldDdeeidpkaggG--~vmTiGqmvr~~l~kLdwf~TLFPRIPVPvqkqId~~ie~r~r  238 (453)
T KOG2888|consen  172 ADLWDWYEPYLDDDEEIDPKAGGG--DVMTIGQMVRTFLTKLDWFSTLFPRIPVPVQKQIDEKIEERKR  238 (453)
T ss_pred             hHHHHHhhhhccchhhcCCcCCCC--ceeeHHHHHHHHHhhhhHHhccCCCCCchHHHHHHHHHHhccc
Confidence            999999999999999999987655  6999999999999999999999999999999998888776654

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.14  E-value=0.0006  Score=69.21  Aligned_cols=9  Identities=22%  Similarity=0.231  Sum_probs=3.9

Q ss_pred             CChhHHHHH
Q 019667          316 PDPEIAEAN  324 (337)
Q Consensus       316 ~d~~~~~~~  324 (337)
                      .++.-++++
T Consensus       124 ~~~~~~~~~  132 (509)
T TIGR01642       124 VTADQAKAS  132 (509)
T ss_pred             cchHHHhhc
Confidence            344444444

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.82  E-value=0.00057  Score=68.72  Aligned_cols=6  Identities=17%  Similarity=0.468  Sum_probs=2.5

Q ss_pred             HHHhcC
Q 019667           37 VEFIKN   42 (337)
Q Consensus        37 ~~~L~~   42 (337)
                      .++|+|
T Consensus        68 aQhLtn   73 (479)
T KOG4676|consen   68 AQHLTN   73 (479)
T ss_pred             Hhhhcc
Confidence            344443

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=96.78  E-value=0.0013  Score=66.74  Aligned_cols=11  Identities=27%  Similarity=0.416  Sum_probs=4.4

Q ss_pred             hhHHHHHHHHH
Q 019667          318 PEIAEANRIRA  328 (337)
Q Consensus       318 ~~~~~~~~~~~  328 (337)
                      ..+..++...+
T Consensus       121 ~~~~~~~~~~~  131 (509)
T TIGR01642       121 YELVTADQAKA  131 (509)
T ss_pred             ccccchHHHhh
Confidence            33444444433

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=96.65  E-value=0.0017  Score=63.36  Aligned_cols=71  Identities=24%  Similarity=0.285  Sum_probs=57.8

Q ss_pred             CCCCCCchhHHHHHHhccCCCHHHHH-HHhcCCCcceeeecccchhhhccchHHHHHHhhhhhhhhhhhhhccCCC
Q 019667           12 GNRKPTPFMCLVMKMLQIQPEKDIVV-EFIKNDDYKYVRVLGAFYLRLTGTDIDIYRYLEPLYNDYRKLRQKSGDG   86 (337)
Q Consensus        12 ~~~~Ps~f~CLL~KLlqi~P~~~iv~-~~L~~~d~KYlRaLg~lYlRltg~p~ely~~lEp~l~DyrKlr~~~~dg   86 (337)
                      .|.+-.||.+||+-.|.++.+..-|. +|..++.+|-|++|-..   +|++|. .|+|++.-..-..+..++.++|
T Consensus        94 p~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~---vTgksk-GYAFIeye~erdm~~AYK~adG  165 (335)
T KOG0113|consen   94 PNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDK---VTGKSK-GYAFIEYEHERDMKAAYKDADG  165 (335)
T ss_pred             CcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeec---ccCCcc-ceEEEEeccHHHHHHHHHhccC
Confidence            44556899899999999999998887 78899999999999887   889886 8999986655556666666665

>PF12871 PRP38_assoc: Pre-mRNA-splicing factor 38-associated hydrophilic C-term; InterPro: IPR024767 This entry represents a hydrophilic domain found mainly at the C terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins

Probab=96.15  E-value=0.0052  Score=50.65  Aligned_cols=22  Identities=45%  Similarity=0.717  Sum_probs=16.4

Q ss_pred             CccccchhhhhHHHhhhhhhcc
Q 019667          128 PRKSVLEDDFEEEEEKEENDQL  149 (337)
Q Consensus       128 pR~s~Le~~~Ee~eeeeEee~~  149 (337)
                      |++++|+.+|++....+|+.+.
T Consensus         1 p~~s~l~~d~~~~~~~~Ee~~~   22 (97)
T PF12871_consen    1 PRVSALEEDLDDEESGEEETAR   22 (97)
T ss_pred             Cccccccccccccccccccccc
Confidence            6789999999887766655444

The function of the domain is not known.

>KOG3263 consensus Nucleic acid binding protein [General function prediction only]

Probab=95.57  E-value=0.013  Score=53.30  Aligned_cols=14  Identities=21%  Similarity=0.209  Sum_probs=10.4

Q ss_pred             CCCChhHHHHHHHH
Q 019667          314 DHPDPEIAEANRIR  327 (337)
Q Consensus       314 ~~~d~~~~~~~~~~  327 (337)
                      .+..+|++||-+|=
T Consensus       137 eg~eeEeiEMmk~M  150 (196)
T KOG3263|consen  137 EGKEEEEIEMMKIM  150 (196)
T ss_pred             cCCCHHHHHHHHHh
Confidence            45688999887763

>KOG2217 consensus U4/U6

Probab=95.26  E-value=0.014  Score=62.14  Aligned_cols=21  Identities=52%  Similarity=0.841  Sum_probs=18.6

Q ss_pred             CChhHHHHHHHHHhcCCCCCC
Q 019667          316 PDPEIAEANRIRASLGLKPLK  336 (337)
Q Consensus       316 ~d~~~~~~~~~~~~~~~~~~~  336 (337)
                      .--.|-|-|+|||+||||||-
T Consensus        51 dslSIeETNklRakLGlkPle   71 (705)
T KOG2217|consen   51 DSLSIEETNKLRAKLGLKPLE   71 (705)
T ss_pred             cccchhHhHHHHHhcCCCccc
Confidence            356899999999999999983

U5 snRNP associated protein [RNA processing and modification]

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=94.61  E-value=0.024  Score=56.41  Aligned_cols=18  Identities=17%  Similarity=0.119  Sum_probs=10.4

Q ss_pred             eHHHHHHHHHhccccccc
Q 019667           92 HVDEVIDELLTKDYSCDI  109 (337)
Q Consensus        92 ~~defvd~LL~~~~~~~i  109 (337)
                      ++=.|.+..|.++.-+++
T Consensus       173 dLw~WyEpyldDdeeidp  190 (453)
T KOG2888|consen  173 DLWDWYEPYLDDDEEIDP  190 (453)
T ss_pred             HHHHHhhhhccchhhcCC
Confidence            344566666766665554

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=81.49  E-value=1.3  Score=47.27  Aligned_cols=9  Identities=22%  Similarity=0.139  Sum_probs=3.6

Q ss_pred             HHhcccccc
Q 019667          100 LLTKDYSCD  108 (337)
Q Consensus       100 LL~~~~~~~  108 (337)
                      ++..--||+
T Consensus       511 ~iPn~py~d  519 (757)
T KOG4368|consen  511 LIPNVPYFD  519 (757)
T ss_pred             cCCCCcccc
Confidence            333334444

---

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	Length	Definition	E-value
Query	337
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	6e-07
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-06

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 49.8 bits (119), Expect = 6e-07
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 1/92 (1%)

Query: 180 SYRYRDRDYDRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRER 239
           S R+ D+         +     RD       ++  D D + +      +  ++R   R+ 
Sbjct: 488 SRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDY 547

Query: 240 DRDREREGRDRERRDRDRGRRRSRSRSRSRSR 271
           D +  R   +  RR   R   ++   SR+ + 
Sbjct: 548 DDEPFRRSNN-NRRSFSRSNDKNNYSSRNSNI 578

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 47.9 bits (114), Expect = 2e-06
 Identities = 15/87 (17%), Positives = 22/87 (25%)

Query: 189 DRDYDRDRGRGRERDRGRDRDRDRDRDRDRERDRDRNRYRLRDDREYGRERDRDREREGR 248
            R +    G  R        +      RD                   +  +   +    
Sbjct: 488 SRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDY 547

Query: 249 DRERRDRDRGRRRSRSRSRSRSRDRKR 275
           D E   R    RRS SRS  ++    R
Sbjct: 548 DDEPFRRSNNNRRSFSRSNDKNNYSSR 574

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	337
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.89
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.71
3plv_C	21	66 kDa U4/U6.U5 small nuclear ribonucleoprotein C;	97.34

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=97.89  E-value=8e-06  Score=81.34  Aligned_cols=13  Identities=23%  Similarity=0.248  Sum_probs=8.4

Q ss_pred             cchHHHHHHhhhh
Q 019667           60 GTDIDIYRYLEPL   72 (337)
Q Consensus        60 g~p~ely~~lEp~   72 (337)
                      .+..+|..+|.+|
T Consensus       114 ~te~~L~~~F~~~  126 (437)
T 3pgw_S          114 TTESKLRREFEVY  126 (437)
T ss_pred             CCHHHHHHHHHHc
Confidence            3456677777764

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=97.71  E-value=2.3e-05  Score=78.02  Aligned_cols=14  Identities=14%  Similarity=0.188  Sum_probs=8.6

Q ss_pred             HHHhhhhhhhhhhh
Q 019667           66 YRYLEPLYNDYRKL   79 (337)
Q Consensus        66 y~~lEp~l~DyrKl   79 (337)
                      ...|..++..|-.|
T Consensus       116 e~~L~~~F~~~G~I  129 (437)
T 3pgw_S          116 ESKLRREFEVYGPI  129 (437)
T ss_pred             HHHHHHHHHHcCCe
Confidence            55666666666544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00