Psyllid ID: psy8255

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
Protein Sequence
MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE
Secondary Structure (PSIPRED)
ccccccHHHHHHHHcccccHHHHHHccccccccccccHHHHHHcccccccccccHHHHHHcccccccccccccccccHHHHHHHHHHHHccccccccHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccHHHHHHHHHccccccccccHHHHHHHHHEEEccccccccc
Coil and Loop (DISEMBL)
mgedrdkdrerdrrrrsrsrdhkkrsrsrdrrsrsrskdkkraarsrsrsprdktksrrrkaslywdvpppgfehvspsQYKAMQAAAAAAVPVVGSTITRQARRLYvgnipfgvte
Flexible Loop (DISEMBL)
mgedrdkdrerdrrrrsrsrdhkkrsrsrdrrsrsrskdkkraarsrsrsprdktksrrrkaslywdvpppgFEHVSPSQYKAMQAAAAAAVPVVGSTItrqarrlyvgnipfgvte
Low Complexity Region (SEG)
MGEdrdkdrerdrrrrsrsrdhkkrsrsrdrrsrsrskdkkraarsrsrsprdkTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQaaaaaaVPVVGSTITRQARRLYVGNIPFGVTE
Disordered region (IsUnstruct)
***************************************************************LYWDV*************KAMQAAAAAAVPVVGSTITRQARRLYVGNIPFG***
Disordered Region (DISOPRED)
******************************************************************DVPPPGFEHVSPSQYKAMQAAAA****V*****TRQARRLYVGNIPFG***
Disordered Region (DISEMBL)
*************************************************************ASLYWDVPPPGFEHVSPSQ************PVVGSTITRQARRLYVGNIPFGVTE
Disordered Region (DISPRO)
*************************************************************ASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVT*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE
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	117	2.2.26 [Sep-21-2011]
Q24562	416	Splicing factor U2AF 50 k	yes	N/A	0.504	0.141	0.728	7e-23
P26369	475	Splicing factor U2AF 65 k	yes	N/A	0.564	0.138	0.568	5e-20
P26368	475	Splicing factor U2AF 65 k	yes	N/A	0.564	0.138	0.568	6e-20
P90727	488	Splicing factor U2AF 65 k	N/A	N/A	0.572	0.137	0.527	3e-15
P90978	496	Splicing factor U2AF 65 k	yes	N/A	0.615	0.145	0.518	1e-14

>sp|Q24562|U2AF2_DROME Splicing factor U2AF 50 kDa subunit OS=Drosophila melanogaster GN=U2af50 PE=2 SV=1

 Score =  105 bits (262), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 51/70 (72%), Positives = 54/70 (77%), Gaps = 11/70 (15%)

Query: 59  RRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTITRQARRLY 107
           RRK SLYWDVPPPGFEH++P QYKAMQA+              AVPVVGSTITRQARRLY
Sbjct: 37  RRKPSLYWDVPPPGFEHITPMQYKAMQASGQIPASVVPDTPQTAVPVVGSTITRQARRLY 96

Query: 108 VGNIPFGVTE 117
           VGNIPFGVTE
Sbjct: 97  VGNIPFGVTE 106

Necessary for the splicing of pre-mRNA. Binds to the polypyrimidine tract of introns early during spliceosome assembly.
Drosophila melanogaster (taxid: 7227)

>sp|P26369|U2AF2_MOUSE Splicing factor U2AF 65 kDa subunit OS=Mus musculus GN=U2af2 PE=1 SV=3

 Score = 96.3 bits (238), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 50/88 (56%), Positives = 56/88 (63%), Gaps = 22/88 (25%)

Query: 49  RSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-------------------A 89
           RSPR + K + RK   YWDVPPPGFEH++P QYKAMQAA                     
Sbjct: 78  RSPRHEKKKKVRK---YWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTP 134

Query: 90  AAVPVVGSTITRQARRLYVGNIPFGVTE 117
             VPVVGS +TRQARRLYVGNIPFG+TE
Sbjct: 135 TPVPVVGSQMTRQARRLYVGNIPFGITE 162

Necessary for the splicing of pre-mRNA. Induces cardiac troponin-T (TNNT2) pre-mRNA exon inclusion in muscle. Regulates the TNNT2 exon 5 inclusion through competition with MBNL1. Binds preferentially to a single-stranded structure within the polypyrimidine tract of TNNT2 intron 4 during spliceosome assembly. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Represses the splicing of MAPT/Tau exon 10.

Mus musculus (taxid: 10090)

>sp|P26368|U2AF2_HUMAN Splicing factor U2AF 65 kDa subunit OS=Homo sapiens GN=U2AF2 PE=1 SV=4

 Score = 96.3 bits (238), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 50/88 (56%), Positives = 56/88 (63%), Gaps = 22/88 (25%)

Query: 49  RSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAA------------------- 89
           RSPR + K + RK   YWDVPPPGFEH++P QYKAMQAA                     
Sbjct: 78  RSPRHEKKKKVRK---YWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTP 134

Query: 90  AAVPVVGSTITRQARRLYVGNIPFGVTE 117
             VPVVGS +TRQARRLYVGNIPFG+TE
Sbjct: 135 TPVPVVGSQMTRQARRLYVGNIPFGITE 162

Necessary for the splicing of pre-mRNA. Induces cardiac troponin-T (TNNT2) pre-mRNA exon inclusion in muscle. Regulates the TNNT2 exon 5 inclusion through competition with MBNL1. Binds preferentially to a single-stranded structure within the polypyrimidine tract of TNNT2 intron 4 during spliceosome assembly. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

>sp|P90727|U2AF2_CAEBR Splicing factor U2AF 65 kDa subunit OS=Caenorhabditis briggsae GN=uaf-1 PE=3 SV=2

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 7/74 (9%)

Query: 51  PRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAA-------AAVPVVGSTITRQA 103
           P++  K R  K   +WDVPP GFE+++P +YK MQA+ A       +AVPVVG ++T Q+
Sbjct: 115 PQEPAKPREPKKYRFWDVPPTGFENITPMEYKNMQASGAVPRGSVQSAVPVVGPSVTCQS 174

Query: 104 RRLYVGNIPFGVTE 117
           RRLYVGNIPFG  E
Sbjct: 175 RRLYVGNIPFGCNE 188

Necessary for the splicing of pre-mRNA. Binds to the polypyrimidine tract of introns early during spliceosome assembly.

Caenorhabditis briggsae (taxid: 6238)

>sp|P90978|U2AF2_CAEEL Splicing factor U2AF 65 kDa subunit OS=Caenorhabditis elegans GN=uaf-1 PE=2 SV=2

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/79 (51%), Positives = 50/79 (63%), Gaps = 7/79 (8%)

Query: 46  SRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-------AAAVPVVGST 98
           +RSR   +  K R  K   +WDVPP GFE  +P +YK MQAA         +AVPVVG +
Sbjct: 119 ARSRREPEPQKPREPKKYRFWDVPPTGFETTTPMEYKNMQAAGQVPRGSVQSAVPVVGPS 178

Query: 99  ITRQARRLYVGNIPFGVTE 117
           +T Q+RRLYVGNIPFG  E
Sbjct: 179 VTCQSRRLYVGNIPFGCNE 197

Necessary for the splicing of pre-mRNA. Binds to the polypyrimidine tract of introns early during spliceosome assembly.

Caenorhabditis elegans (taxid: 6239)

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	117
328721670	416	PREDICTED: splicing factor U2AF 50 kDa s	0.606	0.170	0.738	3e-25
193629757	446	PREDICTED: splicing factor U2AF 50 kDa s	0.606	0.159	0.738	3e-25
328721668	451	PREDICTED: splicing factor U2AF 50 kDa s	1.0	0.259	0.589	6e-25
312372039	384	hypothetical protein AND_20681 [Anophele	0.572	0.174	0.730	1e-24
347968827	446	AGAP002908-PA [Anopheles gambiae str. PE	0.572	0.150	0.730	1e-24
345480698	455	PREDICTED: splicing factor U2AF 50 kDa s	0.581	0.149	0.721	3e-24
95103124	306	U2 small nuclear ribonucleoprotein auxil	0.521	0.199	0.763	3e-24
157132061	418	splicing factor u2af large subunit [Aede	0.572	0.160	0.730	1e-23
170054347	438	splicing factor u2af large subunit [Cule	0.572	0.152	0.730	1e-23
270011684	432	hypothetical protein TcasGA2_TC005736 [T	1.0	0.270	0.538	3e-23

>gi|328721670|ref|XP_001951521.2| PREDICTED: splicing factor U2AF 50 kDa subunit-like isoform 1 [Acyrthosiphon pisum]

 Score =  119 bits (297), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/84 (73%), Positives = 65/84 (77%), Gaps = 13/84 (15%)

Query: 45  RSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVP 93
           RSRS+SP  K KSRRRK SLYWDVPPPGFEH++P QYKAMQAA              AVP
Sbjct: 32  RSRSKSP--KNKSRRRKPSLYWDVPPPGFEHIAPLQYKAMQAAGQIPANTMPDTPQTAVP 89

Query: 94  VVGSTITRQARRLYVGNIPFGVTE 117
           VVGSTITRQARRLYVGNIPFGVTE
Sbjct: 90  VVGSTITRQARRLYVGNIPFGVTE 113

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193629757|ref|XP_001950852.1| PREDICTED: splicing factor U2AF 50 kDa subunit-like [Acyrthosiphon pisum]

 Score =  118 bits (296), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/84 (73%), Positives = 65/84 (77%), Gaps = 13/84 (15%)

Query: 45  RSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVP 93
           RSRS+SP  K KSRRRK SLYWDVPPPGFEH++P QYKAMQAA              AVP
Sbjct: 48  RSRSKSP--KNKSRRRKPSLYWDVPPPGFEHIAPLQYKAMQAAGQIPANTMPDTPQTAVP 105

Query: 94  VVGSTITRQARRLYVGNIPFGVTE 117
           VVGSTITRQARRLYVGNIPFGVTE
Sbjct: 106 VVGSTITRQARRLYVGNIPFGVTE 129

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328721668|ref|XP_003247369.1| PREDICTED: splicing factor U2AF 50 kDa subunit-like isoform 2 [Acyrthosiphon pisum]

 Score =  117 bits (294), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 79/134 (58%), Positives = 91/134 (67%), Gaps = 17/134 (12%)

Query: 1   MGEDRDKDR------ERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDK 54
           MGED++++R      ERD+ R     + ++RSRSRDR    R + + R  R RSRS   K
Sbjct: 1   MGEDKERERDRGERGERDKERDKERGERRRRSRSRDRERHRRHRSRSREGRKRSRSKSPK 60

Query: 55  TKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTITRQA 103
            KSRRRK SLYWDVPPPGFEH++P QYKAMQAA              AVPVVGSTITRQA
Sbjct: 61  NKSRRRKPSLYWDVPPPGFEHIAPLQYKAMQAAGQIPANTMPDTPQTAVPVVGSTITRQA 120

Query: 104 RRLYVGNIPFGVTE 117
           RRLYVGNIPFGVTE
Sbjct: 121 RRLYVGNIPFGVTE 134

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312372039|gb|EFR20089.1| hypothetical protein AND_20681 [Anopheles darlingi]

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/78 (73%), Positives = 60/78 (76%), Gaps = 11/78 (14%)

Query: 51  PRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTI 99
           P  K +SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTI
Sbjct: 78  PYRKNRSRRRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTI 137

Query: 100 TRQARRLYVGNIPFGVTE 117
           TRQARRLYVGNIPFGVTE
Sbjct: 138 TRQARRLYVGNIPFGVTE 155

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347968827|ref|XP_311994.4| AGAP002908-PA [Anopheles gambiae str. PEST] gi|333467820|gb|EAA08228.4| AGAP002908-PA [Anopheles gambiae str. PEST]

 Score =  116 bits (291), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/78 (73%), Positives = 60/78 (76%), Gaps = 11/78 (14%)

Query: 51  PRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTI 99
           P  K +SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTI
Sbjct: 61  PYRKHRSRRRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTI 120

Query: 100 TRQARRLYVGNIPFGVTE 117
           TRQARRLYVGNIPFGVTE
Sbjct: 121 TRQARRLYVGNIPFGVTE 138

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480698|ref|XP_001604333.2| PREDICTED: splicing factor U2AF 50 kDa subunit-like [Nasonia vitripennis]

 Score =  115 bits (288), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 57/79 (72%), Positives = 60/79 (75%), Gaps = 11/79 (13%)

Query: 50  SPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGST 98
           SP+    SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGST
Sbjct: 79  SPKKSRNSRRRKLSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGST 138

Query: 99  ITRQARRLYVGNIPFGVTE 117
           ITRQARRLYVGNIPFGVTE
Sbjct: 139 ITRQARRLYVGNIPFGVTE 157

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|95103124|gb|ABF51503.1| U2 small nuclear ribonucleoprotein auxiliary factor 2 isoform 2 [Bombyx mori]

 Score =  115 bits (288), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 57/72 (79%), Gaps = 11/72 (15%)

Query: 57  SRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTITRQARR 105
           SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTITRQARR
Sbjct: 41  SRRRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTITRQARR 100

Query: 106 LYVGNIPFGVTE 117
           LYVGNIPFGVTE
Sbjct: 101 LYVGNIPFGVTE 112

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157132061|ref|XP_001662443.1| splicing factor u2af large subunit [Aedes aegypti] gi|108881728|gb|EAT45953.1| AAEL002818-PA [Aedes aegypti]

 Score =  114 bits (284), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 57/78 (73%), Positives = 60/78 (76%), Gaps = 11/78 (14%)

Query: 51  PRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTI 99
           P  K +SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTI
Sbjct: 33  PYRKGRSRRRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTI 92

Query: 100 TRQARRLYVGNIPFGVTE 117
           TRQARRLYVGNIPFGVTE
Sbjct: 93  TRQARRLYVGNIPFGVTE 110

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170054347|ref|XP_001863087.1| splicing factor u2af large subunit [Culex quinquefasciatus] gi|167874693|gb|EDS38076.1| splicing factor u2af large subunit [Culex quinquefasciatus]

 Score =  113 bits (283), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 57/78 (73%), Positives = 60/78 (76%), Gaps = 11/78 (14%)

Query: 51  PRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTI 99
           P  K +SRRRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTI
Sbjct: 53  PYRKGRSRRRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTI 112

Query: 100 TRQARRLYVGNIPFGVTE 117
           TRQARRLYVGNIPFGVTE
Sbjct: 113 TRQARRLYVGNIPFGVTE 130

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270011684|gb|EFA08132.1| hypothetical protein TcasGA2_TC005736 [Tribolium castaneum]

 Score =  112 bits (279), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 70/130 (53%), Positives = 81/130 (62%), Gaps = 13/130 (10%)

Query: 1   MGEDRD-KDRERDR-RRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSR 58
           MGE++D K+ ER+R R R      ++R        R      +   R    + R K+ SR
Sbjct: 1   MGEEKDGKNNERERSRERGDREKDRRRRSRSREHRRRSRSRSRDRRRKSRSTSRHKSHSR 60

Query: 59  RRKASLYWDVPPPGFEHVSPSQYKAMQAAA-----------AAAVPVVGSTITRQARRLY 107
           RRK SLYWDVPPPGFEH++P QYKAMQAA             AAVPVVGSTITRQARRLY
Sbjct: 61  RRKPSLYWDVPPPGFEHITPLQYKAMQAAGQIPANIVADTPQAAVPVVGSTITRQARRLY 120

Query: 108 VGNIPFGVTE 117
           VGNIPFGVTE
Sbjct: 121 VGNIPFGVTE 130

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	117
FB|FBgn0005411	416	U2af50 "U2 small nuclear ribop	0.529	0.149	0.671	9.6e-20
WB|WBGene00006697	496	uaf-1 [Caenorhabditis elegans	0.529	0.125	0.507	2e-11
FB|FBgn0034834	449	LS2 "Large Subunit 2" [Drosoph	0.538	0.140	0.434	3.1e-09
ZFIN|ZDB-GENE-040426-1881	475	u2af2b "U2 small nuclear RNA a	0.384	0.094	0.466	3e-07
UNIPROTKB|E2R0G3	471	U2AF2 "Uncharacterized protein	0.367	0.091	0.488	4.8e-07
UNIPROTKB|Q24JZ8	475	U2AF2 "Uncharacterized protein	0.367	0.090	0.488	4.9e-07
UNIPROTKB|P26368	475	U2AF2 "Splicing factor U2AF 65	0.367	0.090	0.488	4.9e-07
MGI|MGI:98886	475	U2af2 "U2 small nuclear ribonu	0.367	0.090	0.488	4.9e-07
RGD|1597319	475	LOC690372 "similar to U2 (RNU2	0.367	0.090	0.488	4.9e-07
ZFIN|ZDB-GENE-050706-131	470	u2af2a "U2 small nuclear RNA a	0.222	0.055	0.884	1e-06

FB|FBgn0005411 U2af50 "U2 small nuclear riboprotein auxiliary factor 50" [Drosophila melanogaster (taxid:7227)]

 Score = 239 (89.2 bits), Expect = 9.6e-20, P = 9.6e-20
 Identities = 49/73 (67%), Positives = 53/73 (72%)

Query:    56 KSRRRKASLYWDVPPPGFEHVSPSQYKAMQXXXX-----------XXVPVVGSTITRQAR 104
             ++ RRK SLYWDVPPPGFEH++P QYKAMQ                 VPVVGSTITRQAR
Sbjct:    34 RNSRRKPSLYWDVPPPGFEHITPMQYKAMQASGQIPASVVPDTPQTAVPVVGSTITRQAR 93

Query:   105 RLYVGNIPFGVTE 117
             RLYVGNIPFGVTE
Sbjct:    94 RLYVGNIPFGVTE 106

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

GO:0005686 "U2 snRNP" evidence=TAS

GO:0008187 "poly-pyrimidine tract binding" evidence=NAS;IDA

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0046982 "protein heterodimerization activity" evidence=NAS

GO:0005634 "nucleus" evidence=IC;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051168 "nuclear export" evidence=IMP

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008380 "RNA splicing" evidence=IMP

GO:0003723 "RNA binding" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

WB|WBGene00006697 uaf-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 165 (63.1 bits), Expect = 2.0e-11, P = 2.0e-11
 Identities = 35/69 (50%), Positives = 41/69 (59%)

Query:    56 KSRRRKASLYWDVPPPGFEHVSPSQYKAMQXXXX-------XXVPVVGSTITRQARRLYV 108
             K R  K   +WDVPP GFE  +P +YK MQ             VPVVG ++T Q+RRLYV
Sbjct:   129 KPREPKKYRFWDVPPTGFETTTPMEYKNMQAAGQVPRGSVQSAVPVVGPSVTCQSRRLYV 188

Query:   109 GNIPFGVTE 117
             GNIPFG  E
Sbjct:   189 GNIPFGCNE 197

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

GO:0040007 "growth" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0009790 "embryo development" evidence=IMP

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0030628 "pre-mRNA 3'-splice site binding" evidence=IDA

GO:0048589 "developmental growth" evidence=IMP

GO:0010172 "embryonic body morphogenesis" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

FB|FBgn0034834 LS2 "Large Subunit 2" [Drosophila melanogaster (taxid:7227)]

 Score = 144 (55.7 bits), Expect = 3.1e-09, P = 3.1e-09
 Identities = 33/76 (43%), Positives = 44/76 (57%)

Query:    55 TKSRRR--KASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVG-----------STITR 101
             T+ +RR  +    WD+PP G+ H++P Q+KAM         ++            S ITR
Sbjct:    49 TRLQRRFSRPPSSWDIPPEGYNHLTPQQHKAMLASGQIASRILSDGVHGGESAAISMITR 108

Query:   102 QARRLYVGNIPFGVTE 117
             QARRLYVGNIPFGVT+
Sbjct:   109 QARRLYVGNIPFGVTD 124

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0005686 "U2 snRNP" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0060968 "regulation of gene silencing" evidence=IMP

GO:0033119 "negative regulation of RNA splicing" evidence=IMP

GO:0003723 "RNA binding" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-040426-1881 u2af2b "U2 small nuclear RNA auxiliary factor 2b" [Danio rerio (taxid:7955)]

 Score = 126 (49.4 bits), Expect = 3.0e-07, P = 3.0e-07
 Identities = 21/45 (46%), Positives = 29/45 (64%)

Query:    56 KSRRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             + +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    85 REKKKKIKKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 129

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

UNIPROTKB|E2R0G3 U2AF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 124 (48.7 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query:    58 RRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    84 KKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 126

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q24JZ8 U2AF2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 124 (48.7 bits), Expect = 4.9e-07, P = 4.9e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query:    58 RRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    84 KKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 126

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P26368 U2AF2 "Splicing factor U2AF 65 kDa subunit" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 4.9e-07, P = 4.9e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query:    58 RRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    84 KKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 126

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

MGI|MGI:98886 U2af2 "U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2" [Mus musculus (taxid:10090)]

 Score = 124 (48.7 bits), Expect = 4.9e-07, P = 4.9e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query:    58 RRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    84 KKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 126

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IDA

GO:0016607 "nuclear speck" evidence=TAS

GO:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISO

GO:0070742 "C2H2 zinc finger domain binding" evidence=IPI

RGD|1597319 LOC690372 "similar to U2 (RNU2) small nuclear RNA auxiliary factor 2 isoform b" [Rattus norvegicus (taxid:10116)]

 Score = 124 (48.7 bits), Expect = 4.9e-07, P = 4.9e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query:    58 RRRKASLYWDVPPPGFEHVSPSQYKAMQXXXXXXVPVVGSTIT 100
             +++K   YWDVPPPGFEH++P QYKAMQ         +  T+T
Sbjct:    84 KKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMT 126

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

ZFIN|ZDB-GENE-050706-131 u2af2a "U2 small nuclear RNA auxiliary factor 2a" [Danio rerio (taxid:7955)]

 Score = 121 (47.7 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 23/26 (88%), Positives = 25/26 (96%)

Query:    92 VPVVGSTITRQARRLYVGNIPFGVTE 117
             VPVVGS +TRQARRLYVGNIPFG+TE
Sbjct:   130 VPVVGSQMTRQARRLYVGNIPFGITE 155

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

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)
P26369	U2AF2_MOUSE	No assigned EC number	0.5681	0.5641	0.1389	yes	N/A
P26368	U2AF2_HUMAN	No assigned EC number	0.5681	0.5641	0.1389	yes	N/A
P90978	U2AF2_CAEEL	No assigned EC number	0.5189	0.6153	0.1451	yes	N/A
Q24562	U2AF2_DROME	No assigned EC number	0.7285	0.5042	0.1418	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	117
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-21
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-05
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	5e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	0.003

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

 Score = 88.4 bits (219), Expect = 1e-21
 Identities = 47/139 (33%), Positives = 58/139 (41%), Gaps = 26/139 (18%)

Query: 4   DRDKDRERDRRRRSRSRDHKKRSRSR-DRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKA 62
            RD+ R   R  RS      +RSR R  RRSRS    ++   R R RSP ++ +   +K 
Sbjct: 52  PRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

Query: 63  SLYWDVPPPGFEHVSPSQYKAMQAA------------------------AAAAVPVVGST 98
           S  WD+ PPG+E V+  Q KA Q                              V      
Sbjct: 112 S-LWDIKPPGYELVTADQAKASQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQ 170

Query: 99  ITRQARRLYVGNIPFGVTE 117
            TRQARRLYVG IP    E
Sbjct: 171 ATRQARRLYVGGIPPEFVE 189

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 24/66 (36%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 4  DRDKDRERDRRRRSRSRDHKKRSRSRDRRS--RSRSKDKKRAARSRSRSPRDKTKSRRRK 61
          DR++ R R+  RRS     + R RSR R    R R +D  R  R RSRS       R R 
Sbjct: 4  DRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRG 63

Query: 62 ASLYWD 67
             Y  
Sbjct: 64 DRSYRR 69

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.3 bits (90), Expect = 5e-05
 Identities = 12/15 (80%), Positives = 14/15 (93%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGN+P G+TE
Sbjct: 1   ARRLYVGNLPPGITE 15

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 7  KDRERDRRRRSRSRDHKKRSRSRDR-RSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
          +D E DR R       + RS  R R RSR RS+ + R  RSR RS R+ ++ R R+
Sbjct: 1  RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRR 56

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 4  DRDKDRERDRRRRSRS--RDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKT 55
           R + R+R RRRR R   R  + RSRSR      R +   R+ R   R     T
Sbjct: 26 RRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPR-GDRSYRRDDRRSGRNT 78

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|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 1/57 (1%)

Query: 3  EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRR 59
          +D DK     R  +   R   K      RR     ++ +   R    SP  +T SR 
Sbjct: 21 DDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPW-RTVSRA 76

Length = 346

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	117
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.28
KOG0120|consensus	500		99.21
PF06495	182	Transformer: Fruit fly transformer protein; InterP	98.58
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	97.59
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	95.18
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	89.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	87.54
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	85.41
KOG0126|consensus	219		84.24
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	83.58
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	80.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	80.29

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

Probab=99.28  E-value=3e-12  Score=106.62  Aligned_cols=57  Identities=46%  Similarity=0.675  Sum_probs=44.2

Q ss_pred             cCCCCCCCCCCCCCCCChhHHHHHHH---hhh---------------------ccCCCCCCccccccceeEeecCCCCCC
Q psy8255          61 KASLYWDVPPPGFEHVSPSQYKAMQA---AAA---------------------AAVPVVGSTITRQARRLYVGNIPFGVT  116 (117)
Q Consensus        61 k~~s~WDv~PpG~E~vta~QaK~mq~---ag~---------------------~~~p~~~~~~SRQaRRLYVGNLP~~vt  116 (117)
                      +....||.+|++|+.+++.|++++++   ++.                     .+++++.+++++++++|||||||+++|
T Consensus       109 ~~~~~~d~~p~~~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~lyVgnLp~~~t  188 (509)
T TIGR01642       109 KKRSLWDIKPPGYELVTADQAKASQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQARRLYVGGIPPEFV  188 (509)
T ss_pred             ccccccccCCCcccccchHHHhhccccCCCCCCCCCCCCCcccccccccccCCccccccCccCCccccEEEEeCCCCCCC
Confidence            34578999999999999999997642   220                     011235678899999999999999998


Q ss_pred             C
Q psy8255         117 E  117 (117)
Q Consensus       117 E  117 (117)
                      |
T Consensus       189 ~  189 (509)
T TIGR01642       189 E  189 (509)
T ss_pred             H
Confidence            6

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

>KOG0120|consensus

Probab=99.21  E-value=6.3e-12  Score=109.89  Aligned_cols=57  Identities=51%  Similarity=0.916  Sum_probs=48.2

Q ss_pred             cCCCCCCCCCCCCCCCCh---hHHHHHHHhhh----------------ccCCCCCCccccccceeEeecCCCCCCC
Q psy8255          61 KASLYWDVPPPGFEHVSP---SQYKAMQAAAA----------------AAVPVVGSTITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        61 k~~s~WDv~PpG~E~vta---~QaK~mq~ag~----------------~~~p~~~~~~SRQaRRLYVGNLP~~vtE  117 (117)
                      +....||++|+|||.+|+   +++++|++.|+                ++.+++++++|+|+++|||||||++++|
T Consensus       114 r~~~~~~~~~~~fe~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~q~~r~~v~~~~~~~~e  189 (500)
T KOG0120|consen  114 RKRSLWDVPPEGFETITPDGAKLYKNFNATGQVPGDLSNPKKSLKLPQLPTPPMDSQATRQARRLYVGNIPFTSNE  189 (500)
T ss_pred             cchhhhcCCCCCCcccCchhhhhhhhccccCCCCCCccccccccccccCCCCccCcchhhhhhhhcccccCCccCc
Confidence            556789999999999999   77777777653                2345788999999999999999999987

>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly)

Probab=98.58  E-value=1.1e-08  Score=79.96  Aligned_cols=25  Identities=40%  Similarity=0.550  Sum_probs=19.5

Q ss_pred             hccCCCCCCCCCCCCCCCChhHHHH
Q psy8255          59 RRKASLYWDVPPPGFEHVSPSQYKA   83 (117)
Q Consensus        59 ~rk~~s~WDv~PpG~E~vta~QaK~   83 (117)
                      +++.+.+|||||+|||++++.+.+.
T Consensus       112 PkiI~~yv~VPp~gf~~~y~~~~~~  136 (182)
T PF06495_consen  112 PKIITKYVDVPPPGFEYAYGWPPPA  136 (182)
T ss_pred             CCeeeeeccCCCcccccccCCCCcc
Confidence            4445789999999999999955443

The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=97.59  E-value=4.3e-05  Score=63.32  Aligned_cols=19  Identities=21%  Similarity=0.405  Sum_probs=16.7

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      ..+..+.|||||||+.++|
T Consensus        85 ~~~~~~~l~V~nlp~~~~~  103 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARE  103 (457)
T ss_pred             cccCCcEEEEeCCCCCCCH
Confidence            4778899999999999985

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=95.18  E-value=0.029  Score=46.55  Aligned_cols=15  Identities=53%  Similarity=0.935  Sum_probs=13.5

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||||||+++||
T Consensus       186 ~~~l~v~nl~~~~te  200 (457)
T TIGR01622       186 FLKLYVGNLHFNITE  200 (457)
T ss_pred             CCEEEEcCCCCCCCH
Confidence            478999999999986

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=89.58  E-value=0.19  Score=37.04  Aligned_cols=15  Identities=20%  Similarity=0.864  Sum_probs=13.1

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||+|||++++|
T Consensus        34 ~~~lfVgnL~~~~te   48 (144)
T PLN03134         34 STKLFIGGLSWGTDD   48 (144)
T ss_pred             CCEEEEeCCCCCCCH
Confidence            448999999999986

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=87.54  E-value=0.3  Score=34.75  Aligned_cols=15  Identities=53%  Similarity=1.061  Sum_probs=13.6

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||||||+.+||
T Consensus       115 ~~~l~v~nL~~~~~~  129 (306)
T COG0724         115 NNTLFVGNLPYDVTE  129 (306)
T ss_pred             CceEEEeCCCCCCCH
Confidence            589999999999986

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

Probab=85.41  E-value=0.59  Score=39.30  Aligned_cols=17  Identities=35%  Similarity=0.798  Sum_probs=14.4

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      -..+.|||||||+.+||
T Consensus       293 ~~~~~l~v~nlp~~~~~  309 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGE  309 (509)
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            34589999999999985

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

>KOG0126|consensus

Probab=84.24  E-value=0.53  Score=38.04  Aligned_cols=14  Identities=36%  Similarity=0.973  Sum_probs=12.7

Q ss_pred             ceeEeecCCCCCCC
Q psy8255         104 RRLYVGNIPFGVTE  117 (117)
Q Consensus       104 RRLYVGNLP~~vtE  117 (117)
                      ==||||||||.+||
T Consensus        36 A~Iyiggl~~~LtE   49 (219)
T KOG0126|consen   36 AYIYIGGLPYELTE   49 (219)
T ss_pred             eEEEECCCcccccC
Confidence            37999999999998

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=83.58  E-value=0.99  Score=35.95  Aligned_cols=16  Identities=19%  Similarity=0.220  Sum_probs=13.0

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.++|
T Consensus       268 ~~~~lfV~NL~~~~~e  283 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDE  283 (352)
T ss_pred             CCcEEEEeCCCCCCCH
Confidence            3346999999999875

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=80.90  E-value=1.2  Score=40.27  Aligned_cols=16  Identities=31%  Similarity=0.623  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      +.-.|||||||++++|
T Consensus        57 ~~~~lFVgnLp~~~tE   72 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYE   72 (578)
T ss_pred             CCCEEEeCCCCCCCCH
Confidence            4468999999999986

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=80.29  E-value=0.86  Score=41.57  Aligned_cols=20  Identities=35%  Similarity=0.559  Sum_probs=16.1

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      ++.....+|||||||+.++|
T Consensus       102 ~a~~~~~rLfVGnLp~~~tE  121 (612)
T TIGR01645       102 QALAIMCRVYVGSISFELRE  121 (612)
T ss_pred             hhhcCCCEEEEcCCCCCCCH
Confidence            44456679999999999986

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	117
1jmt_B	28	X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER		5e-07

>pdb|1JMT|B Chain B, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER Length = 28

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 19/27 (70%), Positives = 23/27 (85%)
Query: 59 RRKASLYWDVPPPGFEHVSPSQYKAMQ 85
          ++K   YWDVPPPGFEH++P QYKAMQ
Sbjct: 1  KKKVRKYWDVPPPGFEHITPMQYKAMQ 27

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	117
1jmt_B	28	Splicing factor U2AF 65 kDa subunit; RRM, RNA spli	6e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-04

>1jmt_B Splicing factor U2AF 65 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} Length = 28

 Score = 49.8 bits (118), Expect = 6e-10
 Identities = 20/28 (71%), Positives = 24/28 (85%)

Query: 59 RRKASLYWDVPPPGFEHVSPSQYKAMQA 86
          ++K   YWDVPPPGFEH++P QYKAMQA
Sbjct: 1  KKKVRKYWDVPPPGFEHITPMQYKAMQA 28

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 40.5 bits (95), Expect = 7e-06
 Identities = 14/17 (82%), Positives = 15/17 (88%)

Query: 101 RQARRLYVGNIPFGVTE 117
             ARRLYVGNIPFG+TE
Sbjct: 4   GSARRLYVGNIPFGITE 20

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 14/16 (87%), Positives = 15/16 (93%)

Query: 102 QARRLYVGNIPFGVTE 117
            ARRLYVGNIPFG+TE
Sbjct: 3   MARRLYVGNIPFGITE 18

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	117
1jmt_B	28	Splicing factor U2AF 65 kDa subunit; RRM, RNA spli	99.47
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	95.41
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	94.99
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	94.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	94.82
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	94.78
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	94.72
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	94.45
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	94.37
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	94.09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	93.96
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	93.94
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	93.88
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	93.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	93.78
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	93.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	93.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	93.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	93.62
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	93.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	93.59
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	93.51
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	93.48
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	93.45
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	93.36
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	93.27
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	93.25
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	93.23
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	93.18
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	93.13
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	92.93
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	92.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	92.59
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	92.56
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	92.32
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	92.28
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	92.15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	91.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	91.73
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	91.63
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	91.43
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	90.57
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	90.53
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	89.95
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	89.76
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	89.51
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	89.37
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	88.9
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	88.24
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	88.09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	87.99
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	87.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	87.49
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	86.78
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	85.59
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	85.52
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	85.11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	84.46
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	84.33
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	83.7
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	83.1
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	81.77
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	81.64
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	80.81
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	80.44

>1jmt_B Splicing factor U2AF 65 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens}

Probab=99.47  E-value=8.1e-15  Score=83.22  Aligned_cols=27  Identities=74%  Similarity=1.431  Sum_probs=21.6

Q ss_pred             ccCCCCCCCCCCCCCCCChhHHHHHHH
Q psy8255          60 RKASLYWDVPPPGFEHVSPSQYKAMQA   86 (117)
Q Consensus        60 rk~~s~WDv~PpG~E~vta~QaK~mq~   86 (117)
                      ++++++|||||||||+|||+|||+||+
T Consensus         2 r~p~~~WDvpP~GyE~vtp~qykamq~   28 (28)
T 1jmt_B            2 KKVRKYWDVPPPGFEHITPMQYKAMQA   28 (28)
T ss_dssp             ----CCBTCCCTTCTTSCHHHHHHTCC
T ss_pred             CCcccccCCCCCCccccCHHHHhhccC
Confidence            466779999999999999999999874

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=95.41  E-value=0.0051  Score=40.59  Aligned_cols=16  Identities=31%  Similarity=0.480  Sum_probs=13.3

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      |.-.|||||||+++||
T Consensus        18 ~gt~lfV~nLp~~~te   33 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQ   33 (99)
T ss_dssp             CCSEEEEESCCTTCCH
T ss_pred             CCCEEEEeCCCCCCCH
Confidence            3347999999999986

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=94.99  E-value=0.011  Score=38.94  Aligned_cols=19  Identities=11%  Similarity=0.270  Sum_probs=15.3

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      ..-..+.|||+|||+.++|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~   39 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGD   39 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCH
T ss_pred             CCCCCcEEEEeCCCCCCCH
Confidence            3445679999999999985

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=94.83  E-value=0.012  Score=38.48  Aligned_cols=21  Identities=19%  Similarity=0.159  Sum_probs=16.7

Q ss_pred             CccccccceeEeecCCCCCCC
Q psy8255          97 STITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        97 ~~~SRQaRRLYVGNLP~~vtE  117 (117)
                      ++.+-..+.|||||||+.+||
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~   40 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQE   40 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCH
T ss_pred             CCCCCCCCEEEEeCCCCCCCH
Confidence            344556789999999999885

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.82  E-value=0.013  Score=37.74  Aligned_cols=18  Identities=33%  Similarity=0.525  Sum_probs=14.8

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||||||+.++|
T Consensus        16 ~~~~~~l~V~nL~~~~t~   33 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARV   33 (97)
T ss_dssp             SCCCCEEEEECCCTTCCH
T ss_pred             CCCCCEEEEeCCCCcCcH
Confidence            345679999999999985

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.78  E-value=0.013  Score=38.89  Aligned_cols=24  Identities=33%  Similarity=0.535  Sum_probs=17.9

Q ss_pred             CCCCccccccceeEeecCCCCCCC
Q psy8255          94 VVGSTITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        94 ~~~~~~SRQaRRLYVGNLP~~vtE  117 (117)
                      .+.+......+.|||||||++++|
T Consensus        20 S~~~~~~~~~~~l~V~nLp~~~te   43 (109)
T 2err_A           20 HMNTENKSQPKRLHVSNIPFRFRD   43 (109)
T ss_dssp             --CCSCTTCCCEEEEESCCTTCCH
T ss_pred             CCCccCCCCCCEEEEECCCCcCCH
Confidence            344455667889999999999885

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=94.72  E-value=0.013  Score=37.91  Aligned_cols=20  Identities=20%  Similarity=0.179  Sum_probs=15.9

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      +.+...+.|||||||+.++|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~   37 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATE   37 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCH
T ss_pred             CCCCCCCEEEEeCCCCCCCH
Confidence            33455679999999999885

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=94.45  E-value=0.0079  Score=40.88  Aligned_cols=18  Identities=39%  Similarity=0.438  Sum_probs=15.2

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+.++|
T Consensus        39 ~~~~~~l~V~nLp~~~~~   56 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDE   56 (139)
T ss_dssp             TTTTSEEEEESCSTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            445689999999999986

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=94.37  E-value=0.017  Score=40.55  Aligned_cols=18  Identities=22%  Similarity=0.482  Sum_probs=15.2

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||||||+.+||
T Consensus        39 ~~~~~~lfVgnLp~~~te   56 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTK   56 (126)
T ss_dssp             SSSCCEEEEECCCTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            446678999999999986

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=94.16  E-value=0.038  Score=38.11  Aligned_cols=20  Identities=20%  Similarity=0.263  Sum_probs=16.6

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      ...-..+.|||||||+.+||
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSC
T ss_pred             cCCCCCCEEEEeCCCCCCCH
Confidence            44456789999999999986

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.09  E-value=0.013  Score=38.53  Aligned_cols=18  Identities=17%  Similarity=0.348  Sum_probs=15.2

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+.++|
T Consensus        22 ~~~~~~l~V~nlp~~~t~   39 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRP   39 (114)
T ss_dssp             HHHHTEEEEESCCTTCCH
T ss_pred             cCCCCEEEEeCCCCCCCH
Confidence            456789999999999985

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.96  E-value=0.026  Score=36.99  Aligned_cols=17  Identities=29%  Similarity=0.782  Sum_probs=14.2

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      -....|||||||+.++|
T Consensus        23 ~~~~~l~V~nlp~~~t~   39 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDE   39 (114)
T ss_dssp             CCTTEEEEESCCTTCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            35578999999999885

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.94  E-value=0.025  Score=37.03  Aligned_cols=16  Identities=38%  Similarity=0.509  Sum_probs=13.6

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||||||+.+||
T Consensus        24 ~~~~l~V~nLp~~~t~   39 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTE   39 (115)
T ss_dssp             CCSEEEEECCCTTCCH
T ss_pred             CCCEEEEeCCCCCCCH
Confidence            3469999999999985

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=93.88  E-value=0.018  Score=39.48  Aligned_cols=16  Identities=25%  Similarity=0.403  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ...+|||||||++++|
T Consensus        27 ~~~~l~VgnLp~~~te   42 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSW   42 (111)
T ss_dssp             CCEEEEEECSSCCCCH
T ss_pred             CCCEEEEECCCCCCCH
Confidence            4569999999999985

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=93.82  E-value=0.031  Score=36.82  Aligned_cols=18  Identities=17%  Similarity=0.372  Sum_probs=15.1

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||++++|
T Consensus        37 ~~~~~~l~V~nlp~~~t~   54 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTD   54 (118)
T ss_dssp             CCCSEEEEEECSCTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            445689999999999885

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=93.78  E-value=0.027  Score=36.20  Aligned_cols=16  Identities=44%  Similarity=0.704  Sum_probs=13.6

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||||||+.++|
T Consensus        26 ~~~~l~V~nlp~~~~~   41 (101)
T 2la4_A           26 RVTTAYIGNIPHFATE   41 (101)
T ss_dssp             SCCEEEEESCCTTCCH
T ss_pred             CCCEEEEcCCCcccCH
Confidence            3469999999999885

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.72  E-value=0.021  Score=39.93  Aligned_cols=16  Identities=31%  Similarity=0.586  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ..+.|||||||+.+||
T Consensus        30 ps~~LfVgNLp~~vte   45 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTE   45 (119)
T ss_dssp             CCSEEEEESCCTTCCH
T ss_pred             CCCEEEEeCCCCCCCH
Confidence            3568999999999986

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=93.70  E-value=0.024  Score=40.07  Aligned_cols=20  Identities=20%  Similarity=0.160  Sum_probs=15.3

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      +.+.....|||||||+.++|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~   86 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQE   86 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCH
T ss_pred             CCCCCCCEEEEeCCCCCCCH
Confidence            33455679999999999885

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=93.66  E-value=0.025  Score=37.54  Aligned_cols=18  Identities=44%  Similarity=0.818  Sum_probs=14.9

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      .-..+.|||||||++++|
T Consensus        23 ~~~~~~l~V~nLp~~~te   40 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITE   40 (108)
T ss_dssp             CSSCEEEEEECCCSSCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            345679999999999885

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=93.62  E-value=0.023  Score=38.84  Aligned_cols=15  Identities=20%  Similarity=0.215  Sum_probs=13.2

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      .+.|||+|||+++||
T Consensus        21 s~~l~V~NLp~~~te   35 (100)
T 3r27_A           21 SPVVHIRGLIDGVVE   35 (100)
T ss_dssp             CSEEEEESCCTTCCH
T ss_pred             CcEEEEeCCCCCCCH
Confidence            468999999999986

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.60  E-value=0.031  Score=37.56  Aligned_cols=15  Identities=20%  Similarity=0.518  Sum_probs=13.1

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||||||+.+||
T Consensus        25 ~~~l~V~nLp~~~te   39 (124)
T 1wel_A           25 GFCVYLKGLPFEAEN   39 (124)
T ss_dssp             CCEEEEECCCTTCCH
T ss_pred             CcEEEEeCCCCCCCH
Confidence            358999999999985

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=93.59  E-value=0.026  Score=36.51  Aligned_cols=17  Identities=35%  Similarity=0.735  Sum_probs=14.2

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .....|||+|||+.++|
T Consensus        27 ~~~~~l~V~nlp~~~t~   43 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSD   43 (107)
T ss_dssp             CCSEEEEEESCCTTCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            34578999999999985

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.51  E-value=0.024  Score=37.40  Aligned_cols=18  Identities=39%  Similarity=0.796  Sum_probs=15.0

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+.++|
T Consensus        24 ~~~~~~l~V~nLp~~~te   41 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTE   41 (116)
T ss_dssp             HHHHTEEEEECCTTCCCH
T ss_pred             cCCCCEEEEeCCCCCCCH
Confidence            445679999999999985

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=93.48  E-value=0.032  Score=37.39  Aligned_cols=19  Identities=32%  Similarity=0.485  Sum_probs=15.8

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      .....+.|||||||+.++|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~   77 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDD   77 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCH
T ss_pred             CCCCCcEEEEEeCCCCCCH
Confidence            3456789999999999885

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=93.45  E-value=0.028  Score=36.50  Aligned_cols=18  Identities=33%  Similarity=0.864  Sum_probs=14.8

Q ss_pred             ccccceeEeecCCC-CCCC
Q psy8255         100 TRQARRLYVGNIPF-GVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~-~vtE  117 (117)
                      ..-...|||||||+ +++|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~   37 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSK   37 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCH
T ss_pred             CCCCCEEEEeCCCcccCCH
Confidence            44567999999999 8875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=93.36  E-value=0.028  Score=37.41  Aligned_cols=19  Identities=32%  Similarity=0.455  Sum_probs=15.2

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      ..-....|||||||++++|
T Consensus        27 ~~~~~~~l~V~nLp~~~t~   45 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQE   45 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCH
T ss_pred             CCCCCCEEEEECCCCCCCH
Confidence            3456689999999999985

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=93.27  E-value=0.037  Score=38.57  Aligned_cols=15  Identities=20%  Similarity=0.255  Sum_probs=13.0

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||||||+.++|
T Consensus        29 ~~~LfV~nL~~~~~e   43 (127)
T 2a3j_A           29 SQVVLITNINPEVPK   43 (127)
T ss_dssp             CSEEEEESCCTTSCH
T ss_pred             CCEEEEeCCCCCCCH
Confidence            568999999999875

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.25  E-value=0.029  Score=36.67  Aligned_cols=16  Identities=31%  Similarity=0.636  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ..+.|||||||++++|
T Consensus        24 ~~~~l~V~nl~~~~t~   39 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTD   39 (109)
T ss_dssp             SCCEEEEECCSSCCCH
T ss_pred             CCcEEEEeCCCCCCCH
Confidence            4579999999999885

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=93.23  E-value=0.038  Score=39.02  Aligned_cols=20  Identities=5%  Similarity=0.122  Sum_probs=16.2

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      ........|||||||+.+||
T Consensus        39 ~~~~~~~~lfVgnLp~~~te   58 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSV   58 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCH
T ss_pred             CCCCCCCEEEEeCCCCCCCH
Confidence            33456789999999999986

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=93.18  E-value=0.027  Score=37.34  Aligned_cols=18  Identities=11%  Similarity=0.517  Sum_probs=12.9

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+.++|
T Consensus        22 ~~~~~~lfV~nLp~~~te   39 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQ   39 (109)
T ss_dssp             ----CCEEEESCCTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            445679999999999985

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=93.13  E-value=0.025  Score=38.70  Aligned_cols=18  Identities=33%  Similarity=0.434  Sum_probs=14.6

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||||||+.+||
T Consensus        42 ~~~~~~l~V~nLp~~~te   59 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQE   59 (143)
T ss_dssp             CSCCSEEEEEEECTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            344578999999999985

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=92.93  E-value=0.046  Score=37.84  Aligned_cols=16  Identities=19%  Similarity=0.459  Sum_probs=13.7

Q ss_pred             ccceeEeecCCCC-CCC
Q psy8255         102 QARRLYVGNIPFG-VTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~-vtE  117 (117)
                      -.+.|||||||++ ++|
T Consensus        24 p~~~l~V~NLp~~~~te   40 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSD   40 (112)
T ss_dssp             CCCEEEEESCCCSSCCS
T ss_pred             CCCEEEEeCCCCccCCH
Confidence            3568999999997 886

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=92.78  E-value=0.035  Score=39.66  Aligned_cols=16  Identities=25%  Similarity=0.551  Sum_probs=13.0

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||||||+.+||
T Consensus        54 ~~~~lfVgnLp~~~te   69 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTD   69 (156)
T ss_dssp             --CEEEEECCCTTCCH
T ss_pred             CCCEEEEeCCCCCCCH
Confidence            4579999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=92.59  E-value=0.037  Score=38.27  Aligned_cols=21  Identities=14%  Similarity=0.196  Sum_probs=16.7

Q ss_pred             CccccccceeEeecCCCCCCC
Q psy8255          97 STITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        97 ~~~SRQaRRLYVGNLP~~vtE  117 (117)
                      +......+.|||||||+.+||
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te   61 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSP   61 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCH
Confidence            344566789999999999875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=92.56  E-value=0.028  Score=37.35  Aligned_cols=17  Identities=41%  Similarity=0.815  Sum_probs=14.5

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      ...+.|||||||+++||
T Consensus        34 ~~~~~l~V~nlp~~~t~   50 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTA   50 (124)
T ss_dssp             HHHTEEEEEEECTTCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            45679999999999985

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=92.32  E-value=0.038  Score=39.24  Aligned_cols=18  Identities=17%  Similarity=0.397  Sum_probs=14.3

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||+|||+.+||
T Consensus        43 ~~~~~~lfV~nLp~~~te   60 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATE   60 (139)
T ss_dssp             --CCCCEECCSCCTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            456679999999999986

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=92.28  E-value=0.056  Score=36.08  Aligned_cols=18  Identities=33%  Similarity=0.702  Sum_probs=14.9

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||||||+.++|
T Consensus        32 ~~~~~~l~V~nlp~~~t~   49 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSD   49 (124)
T ss_dssp             CSSCEEEEEESCCSSCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            345679999999999885

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=92.15  E-value=0.048  Score=35.66  Aligned_cols=15  Identities=27%  Similarity=0.656  Sum_probs=13.0

Q ss_pred             cceeEeecCCCC-CCC
Q psy8255         103 ARRLYVGNIPFG-VTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~-vtE  117 (117)
                      .+.|||||||+. ++|
T Consensus        27 ~~~l~V~nl~~~~~t~   42 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKK   42 (110)
T ss_dssp             SSEEEECSCCCSSCCH
T ss_pred             CcEEEEeCCCcccCCH
Confidence            469999999999 875

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=91.84  E-value=0.068  Score=37.04  Aligned_cols=17  Identities=47%  Similarity=0.800  Sum_probs=14.5

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      ...+.|||+|||+.+||
T Consensus        37 ~~~~~l~V~nlp~~~t~   53 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTE   53 (156)
T ss_dssp             TTCCEEEEESCCTTCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            45679999999999985

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=91.73  E-value=0.084  Score=36.34  Aligned_cols=18  Identities=17%  Similarity=0.289  Sum_probs=15.1

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      .-....|||||||+.++|
T Consensus        67 ~~~~~~l~v~nl~~~~~~   84 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSP   84 (158)
T ss_dssp             CCBCCEEEEESCCTTCCH
T ss_pred             CCCCCEEEEeCCCCCCCH
Confidence            345789999999999985

>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=91.63  E-value=0.14  Score=42.45  Aligned_cols=17  Identities=24%  Similarity=0.520  Sum_probs=14.3

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      -....|||||||+.|||
T Consensus       100 ~~~~~lfV~nL~~~~te  116 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTE  116 (437)
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            34578999999999986

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=91.43  E-value=0.063  Score=37.85  Aligned_cols=18  Identities=33%  Similarity=0.556  Sum_probs=15.2

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+++||
T Consensus        25 ~~~~~~l~V~nLp~~~t~   42 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGE   42 (216)
T ss_dssp             HHHHTEEEEECCCTTCCH
T ss_pred             cCcCCEEEEECCCCCCCH
Confidence            445679999999999985

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=90.57  E-value=0.065  Score=36.84  Aligned_cols=17  Identities=24%  Similarity=0.016  Sum_probs=14.2

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      -..+.|||+|||+.++|
T Consensus        44 ~~~~~l~V~nLp~~~te   60 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTE   60 (129)
T ss_dssp             CCSSCBCEETCTTSCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            34578999999999985

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=90.53  E-value=0.062  Score=40.20  Aligned_cols=20  Identities=25%  Similarity=0.366  Sum_probs=13.1

Q ss_pred             ccccccceeEeecCCCCCCC
Q psy8255          98 TITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        98 ~~SRQaRRLYVGNLP~~vtE  117 (117)
                      ...+..+.|||||||+++||
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~   55 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQ   55 (292)
T ss_dssp             ------CEEEEEEECTTCCH
T ss_pred             ccCCCCCEEEEeCCCCCCCH
Confidence            44677889999999999985

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=89.95  E-value=0.059  Score=35.91  Aligned_cols=17  Identities=24%  Similarity=0.427  Sum_probs=0.0

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .+...|||+|||+++||
T Consensus        95 ~~~~~lyv~Nl~~~~T~  111 (115)
T 4f25_A           95 KEFTNVYIKNFGPGSTR  111 (115)
T ss_dssp             -----------------
T ss_pred             CCCCceEeCCCCCCccc
Confidence            34457999999999986

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=89.76  E-value=0.11  Score=39.22  Aligned_cols=16  Identities=31%  Similarity=0.644  Sum_probs=12.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||||||+.+||
T Consensus        67 ~~~~lfVgnL~~~~te   82 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTD   82 (229)
T ss_dssp             --CEEEEESCCTTCCH
T ss_pred             CccEEEEeCCCCCCCH
Confidence            4568999999999986

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=89.51  E-value=0.12  Score=38.32  Aligned_cols=15  Identities=33%  Similarity=0.372  Sum_probs=12.9

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      --.|||||||+.+||
T Consensus        46 vl~l~VgNL~~~vte   60 (164)
T 1sjr_A           46 VLRIIVENLFYPVTL   60 (164)
T ss_dssp             EEEEEECSCCSCCCH
T ss_pred             eEEEEEeCcCCCCCH
Confidence            457999999999986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=89.37  E-value=0.12  Score=36.88  Aligned_cols=14  Identities=36%  Similarity=0.396  Sum_probs=12.4

Q ss_pred             ceeEeecCCCCCCC
Q psy8255         104 RRLYVGNIPFGVTE  117 (117)
Q Consensus       104 RRLYVGNLP~~vtE  117 (117)
                      -+||||||++.+||
T Consensus        29 L~I~V~NL~~~vte   42 (130)
T 3zzy_A           29 LRIIVENLFYPVTL   42 (130)
T ss_dssp             EEEEEESCCSCCCH
T ss_pred             EEEEECCCCCCCCH
Confidence            48999999999986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=88.90  E-value=0.17  Score=36.69  Aligned_cols=17  Identities=35%  Similarity=0.743  Sum_probs=14.2

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .....|||+|||++++|
T Consensus        86 ~~~~~l~V~nLp~~~te  102 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSD  102 (177)
T ss_dssp             TTCEEEEEECCCSCCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            34569999999999985

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=88.24  E-value=0.19  Score=36.76  Aligned_cols=16  Identities=31%  Similarity=0.223  Sum_probs=13.7

Q ss_pred             ccceeEeecCCC-CCCC
Q psy8255         102 QARRLYVGNIPF-GVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~-~vtE  117 (117)
                      ....|||||||+ .++|
T Consensus        33 ~~~~l~V~nLp~~~~te   49 (229)
T 2adc_A           33 GNSVLLVSNLNPERVTP   49 (229)
T ss_dssp             CCSEEEEESCCTTTCCH
T ss_pred             CCCEEEEeCCCcccCCH
Confidence            457999999999 8875

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=88.09  E-value=0.22  Score=34.05  Aligned_cols=19  Identities=42%  Similarity=0.630  Sum_probs=15.8

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      .......|||+|||+.+||
T Consensus        95 ~~~~~~~l~v~nlp~~~t~  113 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITE  113 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCH
T ss_pred             ccccCCEEEEeCCCCCCCH
Confidence            3456789999999999875

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=87.99  E-value=0.14  Score=37.45  Aligned_cols=18  Identities=22%  Similarity=0.409  Sum_probs=15.2

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ....+.|||||||+.+||
T Consensus       106 ~~~~~~l~V~nLp~~~t~  123 (193)
T 2voo_A          106 DVKNRSVYIKGFPTDATL  123 (193)
T ss_dssp             HHHHTEEEEECCCTTCCH
T ss_pred             ccccCEEEecCCCCcCCH
Confidence            456789999999999875

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=87.94  E-value=0.17  Score=35.47  Aligned_cols=14  Identities=21%  Similarity=0.142  Sum_probs=12.4

Q ss_pred             ceeEeecCCCCCCC
Q psy8255         104 RRLYVGNIPFGVTE  117 (117)
Q Consensus       104 RRLYVGNLP~~vtE  117 (117)
                      -.|||||||+.+||
T Consensus        26 l~l~V~NL~~~vt~   39 (124)
T 2e5i_A           26 LLLSIQNPLYPITV   39 (124)
T ss_dssp             EEEEEESCCSCCCH
T ss_pred             EEEEEcCcCCCCCH
Confidence            38999999999985

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=87.49  E-value=0.19  Score=34.77  Aligned_cols=16  Identities=25%  Similarity=0.561  Sum_probs=13.7

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.+||
T Consensus       103 ~~~~l~V~nLp~~~t~  118 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEE  118 (196)
T ss_dssp             CCSEEEEECCTTTCCH
T ss_pred             CcceEEEeCCCCCCCH
Confidence            3478999999999885

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=86.78  E-value=0.24  Score=33.38  Aligned_cols=16  Identities=38%  Similarity=0.657  Sum_probs=14.0

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.+||
T Consensus        94 ~~~~l~v~nl~~~~t~  109 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTE  109 (175)
T ss_dssp             GGSEEEEESCCTTCCH
T ss_pred             CCCeEEEcCCCCcCCH
Confidence            5678999999999885

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=85.59  E-value=0.27  Score=33.28  Aligned_cols=16  Identities=25%  Similarity=0.671  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.++|
T Consensus        93 ~~~~l~v~nlp~~~t~  108 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLND  108 (172)
T ss_dssp             TTTCEEEECCCTTCCH
T ss_pred             CCCEEEEEcCCCcCCH
Confidence            4689999999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=85.52  E-value=0.41  Score=33.11  Aligned_cols=17  Identities=24%  Similarity=0.649  Sum_probs=14.5

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .....|||+|||+.++|
T Consensus       112 ~~~~~l~v~nl~~~~~~  128 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLND  128 (198)
T ss_dssp             CCCCEEEEECCCTTCCH
T ss_pred             CCCCEEEEeCCCCCCCH
Confidence            45689999999999875

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=85.11  E-value=0.21  Score=33.67  Aligned_cols=17  Identities=24%  Similarity=0.456  Sum_probs=14.1

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .....|||+|||+.+||
T Consensus        85 ~~~~~l~V~nlp~~~t~  101 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRP  101 (167)
T ss_dssp             HHCEEEEEEEECTTCCH
T ss_pred             cCCCeEEECCCCCCCCH
Confidence            34668999999999875

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=84.46  E-value=0.25  Score=36.30  Aligned_cols=15  Identities=40%  Similarity=0.388  Sum_probs=12.8

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||+|||+.+||
T Consensus       123 ~~~l~v~NLp~~~t~  137 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTE  137 (205)
T ss_dssp             CSEEEEEEECTTCCH
T ss_pred             cceEEEeCCCCCCCH
Confidence            356999999999985

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=84.33  E-value=0.44  Score=31.70  Aligned_cols=18  Identities=22%  Similarity=0.549  Sum_probs=14.7

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||+|||+.+||
T Consensus        84 ~~~~~~l~v~nl~~~~t~  101 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDD  101 (166)
T ss_dssp             CTTCEEEEEESCCTTCCH
T ss_pred             CCCCceEEECCCCCCCCH
Confidence            445678999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=83.70  E-value=0.38  Score=34.71  Aligned_cols=16  Identities=6%  Similarity=0.320  Sum_probs=13.6

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.+||
T Consensus       102 ~~~~l~v~nl~~~~t~  117 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDN  117 (213)
T ss_dssp             CTTEEEEESCCTTCCH
T ss_pred             ccccceECCcccccHH
Confidence            4568999999999885

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=83.10  E-value=0.66  Score=30.84  Aligned_cols=18  Identities=28%  Similarity=0.516  Sum_probs=14.6

Q ss_pred             ccccceeEeecCCCCCCC
Q psy8255         100 TRQARRLYVGNIPFGVTE  117 (117)
Q Consensus       100 SRQaRRLYVGNLP~~vtE  117 (117)
                      ......|||+|||+.++|
T Consensus        85 ~~~~~~l~v~nl~~~~t~  102 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQ  102 (167)
T ss_dssp             GGTTCEEEEESCCTTCCH
T ss_pred             cCCCCcEEECCCCCcCCH
Confidence            345678999999999875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=81.77  E-value=0.5  Score=33.12  Aligned_cols=16  Identities=19%  Similarity=0.488  Sum_probs=13.7

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.++|
T Consensus       124 ~~~~l~v~nlp~~~t~  139 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSD  139 (216)
T ss_dssp             TSCEEEEECCCTTCCH
T ss_pred             CCcEEEEeCCCCcCCH
Confidence            4479999999999875

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=81.64  E-value=0.52  Score=35.07  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.0

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||||||+.++|
T Consensus       116 ~~~~l~v~nlp~~~t~  131 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQ  131 (292)
T ss_dssp             CSCEEEEECCCTTCCH
T ss_pred             CCCEEEEECCCCCCCH
Confidence            5679999999999875

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=80.81  E-value=0.6  Score=31.30  Aligned_cols=17  Identities=35%  Similarity=0.612  Sum_probs=14.2

Q ss_pred             cccceeEeecCCCCCCC
Q psy8255         101 RQARRLYVGNIPFGVTE  117 (117)
Q Consensus       101 RQaRRLYVGNLP~~vtE  117 (117)
                      .....|||+|||+.++|
T Consensus        87 ~~~~~l~v~nl~~~~t~  103 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITD  103 (168)
T ss_dssp             TTTCEEEEESCCTTCCH
T ss_pred             CCCCCEEEeCCCCCCCH
Confidence            45678999999999875

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=80.44  E-value=0.58  Score=34.63  Aligned_cols=16  Identities=25%  Similarity=0.441  Sum_probs=13.8

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ....|||+|||+.+||
T Consensus       206 ~~~~l~v~nl~~~~~~  221 (282)
T 3pgw_A          206 PNHILFLTNLPEETNE  221 (282)
T ss_pred             CCCEEEEeCCCCcCCH
Confidence            4578999999999885

---

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

ID	Length	Definition	Probability
Query	117
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	94.16
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	93.92
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	88.01

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=94.16  E-value=0.007  Score=40.31  Aligned_cols=16  Identities=44%  Similarity=0.497  Sum_probs=13.5

Q ss_pred             ccceeEeecCCCCCCC
Q psy8255         102 QARRLYVGNIPFGVTE  117 (117)
Q Consensus       102 QaRRLYVGNLP~~vtE  117 (117)
                      ..+.|||||||+++||
T Consensus        41 ~~~~l~V~nLp~~~te   56 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDE   56 (139)
T ss_dssp             TTSEEEEESCSTTCCH
T ss_pred             CCCEEEEeCCCCCCCH
Confidence            3457999999999986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.92  E-value=0.009  Score=38.00  Aligned_cols=15  Identities=33%  Similarity=0.645  Sum_probs=13.0

Q ss_pred             cceeEeecCCCCCCC
Q psy8255         103 ARRLYVGNIPFGVTE  117 (117)
Q Consensus       103 aRRLYVGNLP~~vtE  117 (117)
                      ...|||||||++++|
T Consensus        18 ~~~l~v~nL~~~~te   32 (96)
T d1x4ga1          18 NCTVYCGGIASGLTD   32 (96)
T ss_dssp             CCEEEEECCSSCCCH
T ss_pred             CCEEEEcCCCCCCCH
Confidence            457999999999986

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.01  E-value=0.1  Score=34.85  Aligned_cols=19  Identities=21%  Similarity=0.415  Sum_probs=15.4

Q ss_pred             cccccceeEeecCCCCCCC
Q psy8255          99 ITRQARRLYVGNIPFGVTE  117 (117)
Q Consensus        99 ~SRQaRRLYVGNLP~~vtE  117 (117)
                      .....+.|||||||+.+||
T Consensus        93 ~~~~~~~i~V~~lp~~~te  111 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEE  111 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCH
T ss_pred             cccccceeEEccCCCcCCH
Confidence            3456678999999999985