RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3068
(152 letters)
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 111 bits (280), Expect = 1e-32
Identities = 53/116 (45%), Positives = 66/116 (56%), Gaps = 1/116 (0%)
Query: 31 DRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK-N 89
GG R H VHMRGLP++ E DI +FFSP+ PV V I +
Sbjct: 23 SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD 82
Query: 90 GRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGSGFSRSEL 145
GR +GEADV FATHE+A+ AMSKDR N++HRYIELFLNS++ S +
Sbjct: 83 GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGM 138
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 109 bits (274), Expect = 3e-32
Identities = 34/89 (38%), Positives = 51/89 (57%), Gaps = 1/89 (1%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK-NGRPSGEADVYFATHED 105
+ SSG HTV +RG PF V EK++++F +P+ PV + I +G +G V F+ E+
Sbjct: 3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEE 62
Query: 106 AMQAMSKDRTNIRHRYIELFLNSSSPRGG 134
QA+ +R + RYIE+F S P G
Sbjct: 63 VKQALKCNREYMGGRYIEVFREKSGPSSG 91
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 109 bits (273), Expect = 6e-32
Identities = 50/93 (53%), Positives = 65/93 (69%), Gaps = 1/93 (1%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVYFATHED 105
+ H VHMRGLP+R E DI +FFSP+ P+ V I +GR +GEADV FATHED
Sbjct: 8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHED 67
Query: 106 AMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGS 138
A+ AM+KD+ N++HRY+ELFLNS++ G G S
Sbjct: 68 AVAAMAKDKANMQHRYVELFLNSTAGTSGSGPS 100
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 96.0 bits (239), Expect = 9e-27
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 41 PGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVY 99
G P V + G+PF E D+ DFF + V + GR +G V
Sbjct: 3 SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVK 62
Query: 100 FATHEDAMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGSGFS 141
F + +D +A+ ++R + RY+E+ + GG S
Sbjct: 63 FLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITS 104
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 95.1 bits (237), Expect = 1e-26
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 4/89 (4%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINYK-NGRPSGEADVYFATHED 105
S PG + ++ +PF V+ +I+DFF V+P V + Y G P+GEA V F + ++
Sbjct: 10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 106 AMQAMSK-DRTNIRHRYIELFLNSSSPRG 133
A A+ + I R ++L L S G
Sbjct: 70 ATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98
>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
Length = 126
Score = 92.2 bits (229), Expect = 4e-25
Identities = 35/98 (35%), Positives = 50/98 (51%), Gaps = 3/98 (3%)
Query: 34 GGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI---NYKNG 90
G + R N + V +RGLPF +++IV FFS + V I G
Sbjct: 22 ASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG 81
Query: 91 RPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNS 128
+ +GEA V FA+ E A +A+ K + I HRYIE+F +S
Sbjct: 82 KITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSS 119
>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
Length = 124
Score = 91.8 bits (228), Expect = 5e-25
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 3/95 (3%)
Query: 37 AGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINY-KNGRPS 93
P R + S V+++GLPF K ++DFF +V + I Y NG+ +
Sbjct: 8 KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67
Query: 94 GEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNS 128
GE V F D A+ + + + +R+I++ +
Sbjct: 68 GEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT 102
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 91.0 bits (226), Expect = 6e-25
Identities = 35/95 (36%), Positives = 50/95 (52%), Gaps = 3/95 (3%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI---NYKNGRPSGEADVYFATH 103
N V +RGLPF ++++IV FFS + V + GR +GEA V FA+
Sbjct: 8 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67
Query: 104 EDAMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGS 138
E A +A+ K + I HRYIE+F +S + G S
Sbjct: 68 EIAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPS 102
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 91.5 bits (227), Expect = 8e-25
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 6/103 (5%)
Query: 34 GGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDIN------Y 87
G +G + S V MRGLPF +++V FF P+ Y
Sbjct: 3 SGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY 62
Query: 88 KNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSS 130
+GRP+G+A V FA E A A+ K + + RYIELF ++++
Sbjct: 63 PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 89.7 bits (223), Expect = 2e-24
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINYK-NGRPSGEADVYFATH 103
+ S PG + ++ +PF V+ +I+DFF V+P V + Y G P+GEA V F +
Sbjct: 8 SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 104 EDAMQAMSK-DRTNIRHRYIELFLNSS 129
++A A+ + I R ++L SS
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLSGPSS 94
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 87.5 bits (217), Expect = 2e-23
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 3/88 (3%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINY-KNGRPSGEADVYFATH 103
H+ +PF + + D++ F V V + NG+ G+A V F
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 104 EDAMQAMSKDRTNIRHRYIELFLNSSSP 131
+DA ++ R + R + + +
Sbjct: 68 DDARKSERLHRKKLNGREAFVHVVTLED 95
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 85.3 bits (211), Expect = 1e-22
Identities = 18/88 (20%), Positives = 42/88 (47%), Gaps = 5/88 (5%)
Query: 48 ESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVD-----INYKNGRPSGEADVYFAT 102
E + +GLP+ +D+++FFS + + ++G+ G+A + +
Sbjct: 5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMES 64
Query: 103 HEDAMQAMSKDRTNIRHRYIELFLNSSS 130
+D +A+ K R + RY+E++ ++
Sbjct: 65 EQDVQKALEKHRMYMGQRYVEVYEINNE 92
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 81.9 bits (202), Expect = 3e-21
Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVDIN---YKNGRP 92
G + G + V +RGLP+ + +D+ +F S + ++ + GR
Sbjct: 1 GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60
Query: 93 SGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNS 128
SGEA V + +D A+ KDR ++ HRYIE+F +
Sbjct: 61 SGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSH 96
>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
Length = 136
Score = 78.5 bits (193), Expect = 1e-19
Identities = 32/105 (30%), Positives = 47/105 (44%), Gaps = 7/105 (6%)
Query: 31 DRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPV----VPVYVDIN 86
GG R G V +RGLP+ + +D+ +F S V
Sbjct: 23 SMTGGQQMGRGSMM--LGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFI 80
Query: 87 Y-KNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSS 130
Y + GR SGEA V + +D A+ KDR ++ HRYIE+F + +
Sbjct: 81 YTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRT 125
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 53.3 bits (128), Expect = 9e-10
Identities = 29/114 (25%), Positives = 50/114 (43%), Gaps = 14/114 (12%)
Query: 13 GANRFGGGRGCFNNDRWND--RPGGFAGPRP-GDRWVNE---------SSGPGHHTVHMR 60
NR GG R RP ++ P+P D+W ++ + +
Sbjct: 35 RVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVS 94
Query: 61 GLPFRVNEKDIVDFFSPVVPV-YVDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
L F V++ DI + F+ + ++Y ++GR G ADV+F DA++AM +
Sbjct: 95 NLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 50.8 bits (122), Expect = 3e-09
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 11/90 (12%)
Query: 34 GGFAGPRPGDRWVNE---------SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YV 83
GG R D+W ++ + + L F V++ DI + F+ +
Sbjct: 6 GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65
Query: 84 DINY-KNGRPSGEADVYFATHEDAMQAMSK 112
++Y ++GR G ADV+F DA++AM +
Sbjct: 66 AVDYDRSGRSLGTADVHFERRADALKAMKQ 95
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 49.4 bits (118), Expect = 8e-09
Identities = 14/108 (12%), Positives = 33/108 (30%), Gaps = 4/108 (3%)
Query: 25 NNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVD 84
+ + PR + + M+ LP + +D+ D
Sbjct: 2 GSSHHHHHHSSGLVPRGSHM---SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF 58
Query: 85 INYKNGRPSGEADVYFATHEDAMQAMSK-DRTNIRHRYIELFLNSSSP 131
+ G + F + E ++A+ + + R I + + + P
Sbjct: 59 SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP 106
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 47.2 bits (112), Expect = 5e-08
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 3/77 (3%)
Query: 40 RPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVY 99
R + SG +H+R LP V E +++ P V N + +A +
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV---TNLLMLKGKNQAFIE 58
Query: 100 FATHEDAMQAMSKDRTN 116
T E A ++ +
Sbjct: 59 MNTEEAANTMVNYYTSV 75
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 46.3 bits (110), Expect = 1e-07
Identities = 11/71 (15%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV-YVDI-NYKNGRPSGEADVYFATHEDAMQAMSKD 113
+V+++G P DI ++ V + + + G V F + E A + +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 114 RTNIRHRYIEL 124
+ + +
Sbjct: 73 GQKYKETDLLI 83
>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
Length = 107
Score = 46.5 bits (111), Expect = 1e-07
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 14/91 (15%)
Query: 24 FNNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-Y 82
+ +D ++ GG AG G + + L F V++ DI + F+ +
Sbjct: 11 WQHDLFDSGFGGGAGVETG------------GKLLVSNLDFGVSDADIQELFAEFGTLKK 58
Query: 83 VDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
++Y ++GR G ADV+F DA++AM +
Sbjct: 59 AAVHYDRSGRSLGTADVHFERKADALKAMKQ 89
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 45.5 bits (108), Expect = 3e-07
Identities = 22/109 (20%), Positives = 34/109 (31%), Gaps = 25/109 (22%)
Query: 51 GPGH-HTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDA 106
G V L V E + D V V + ++ + + G A V F + A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 107 MQAMSK----------------DRTNIRHRYIELFLNSSS-----PRGG 134
+ + + R +Y EL +N S P GG
Sbjct: 62 KETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPTGG 110
>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
Length = 205
Score = 46.2 bits (109), Expect = 6e-07
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 3/64 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
+ +H P V E++ + P V + S + + + DA++
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 109 AMSK 112
+
Sbjct: 181 TLGF 184
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 44.2 bits (105), Expect = 6e-07
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDA 106
N + T+ + L + E+ + + F + V +NG+ G A + FA+ EDA
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKV-PQNQNGKSKGYAFIEFASFEDA 66
Query: 107 MQAMSK-DRTNIRHRYIELFLNSSSPRG 133
+A++ ++ I R I L PRG
Sbjct: 67 KEALNSCNKREIEGRAIR--LELQGPRG 92
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 44.1 bits (105), Expect = 6e-07
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAM 107
S G + +R LPF K + D F+ V Y DI +NG+ G V F + E A
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAE 62
Query: 108 QAMSK 112
+A
Sbjct: 63 RACRM 67
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 44.2 bits (105), Expect = 8e-07
Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 7/103 (6%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSG 94
G S+ H + + GLPF ++++ + V + + + + G+P G
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRL-VTNRAGKPKG 59
Query: 95 EADVYFATHEDAMQAMSK-DRTNIRHRYIELFLNSSSPRGGVG 136
A V + A QA+ K D I+ I+ + S+ G
Sbjct: 60 LAYVEYENESQASQAVMKMDGMTIKENIIK--VAISNSGPSSG 100
>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
Length = 292
Score = 46.1 bits (110), Expect = 8e-07
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAMQAM 110
TV ++ LP N+ + +F P+ VD+ + A + FA ++ A+ A+
Sbjct: 39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI 98
Query: 111 SKD 113
+K
Sbjct: 99 TKT 101
Score = 40.0 bits (94), Expect = 1e-04
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI---NYKNGRPSGEADVYFATHEDAMQAMS 111
T+ M P +++I D + V + I + + A + + EDA +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 112 K 112
K
Sbjct: 178 K 178
Score = 38.4 bits (90), Expect = 4e-04
Identities = 12/74 (16%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 56 TVHMRGLPFRV-NEKDIVDFFSP---VVPVYVDINYK-NGRPSGEADVYFATHEDAMQAM 110
+ +R L + +E + + F + + + K + + A + F + A +A+
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271
Query: 111 SKDRTNIRHRYIEL 124
+R+ + +R I +
Sbjct: 272 QMNRSLLGNREISV 285
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 43.2 bits (102), Expect = 1e-06
Identities = 19/93 (20%), Positives = 30/93 (32%), Gaps = 9/93 (9%)
Query: 38 GPRP---GDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSG 94
G + + + P VH+RGL V E D+V+ P+
Sbjct: 2 GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPI---SYVVVMPKKR 58
Query: 95 EADVYFATHEDAMQAMSKDRTN---IRHRYIEL 124
+A V F A A++ N I +
Sbjct: 59 QALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 43.4 bits (103), Expect = 1e-06
Identities = 15/89 (16%), Positives = 34/89 (38%), Gaps = 5/89 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK---NGRPSGEADVYFATHEDAMQAMSK 112
T + LP+ V E+ I +FF + V + + R G F + + A+S
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76
Query: 113 DRTNIRHRYIELFLNSSSPRGGVGGSGFS 141
+ ++ ++ + ++ + S
Sbjct: 77 NEESLGNK--RIRVDVADQAQDKDSGPSS 103
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 43.0 bits (102), Expect = 2e-06
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 5/98 (5%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK---NGRPSG 94
G + +T + LP+ V E+ I +FF + V + + R G
Sbjct: 3 GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKG 62
Query: 95 EADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSSPR 132
F + + A+S + ++ +R + ++ +
Sbjct: 63 FGYAEFEDLDSLLSALSLNEESLGNR--RIRVDVADQA 98
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 44.0 bits (104), Expect = 2e-06
Identities = 19/101 (18%), Positives = 31/101 (30%), Gaps = 4/101 (3%)
Query: 26 NDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVY 82
+ + G G G ++ + L +R + + F V VY
Sbjct: 19 SHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY 78
Query: 83 VDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTNIRHRYI 122
+ + G A V F DA AM D + R +
Sbjct: 79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 43.1 bits (102), Expect = 2e-06
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINY-KNGRPSGEADVYFATHEDA 106
+G TV + L ++V K + + FS V DI K+G+ G V F +A
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
Query: 107 MQAMSK 112
+QA+S
Sbjct: 70 VQAISM 75
>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
Length = 115
Score = 43.0 bits (102), Expect = 3e-06
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATH 103
+ + G + ++++ L RV E+D+V F+ + GR G+A + F
Sbjct: 18 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77
Query: 104 EDAMQAM 110
E A QA+
Sbjct: 78 EIAWQAL 84
>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
Length = 129
Score = 43.2 bits (102), Expect = 3e-06
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 3/91 (3%)
Query: 25 NNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPV 81
GG R N ++ + + + GL E+D+ + FS P+ V
Sbjct: 17 RGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV 76
Query: 82 YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + ++ R G A VYF +DA +A +
Sbjct: 77 SIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
>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
Length = 175
Score = 43.7 bits (104), Expect = 3e-06
Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 10/91 (10%)
Query: 24 FNNDRWNDRP--GGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV 81
+ R T+ + L F + E ++ + F + +
Sbjct: 73 LTGLKVFGNEIKLEKPKGRD------SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI 126
Query: 82 YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ ++G+ G A + F + DA + + +
Sbjct: 127 RLV--SQDGKSKGIAYIEFKSEADAEKNLEE 155
Score = 43.4 bits (103), Expect = 3e-06
Identities = 15/104 (14%), Positives = 29/104 (27%), Gaps = 6/104 (5%)
Query: 42 GDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADV 98
G V S + + L + ++ S + V ++ + G V
Sbjct: 1 GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYV 59
Query: 99 YFATHEDAMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGSGFSR 142
F + ED +A+ + E+ L R
Sbjct: 60 DFESAEDLEKALELTGLKVFGN--EIKLEKPKGRDSKKVRAART 101
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 42.5 bits (100), Expect = 3e-06
Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 8/83 (9%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDIN-YKNGRPSGEADVY----FATH 103
S G+ + + G+P ++I++ + V +D+ Y + + + + +H
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 104 EDAMQA---MSKDRTNIRHRYIE 123
A A + R + I
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIA 85
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 42.3 bits (100), Expect = 3e-06
Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 11/69 (15%)
Query: 53 GHH------TVHMRGLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFA 101
GHH T+ +R + I+ SP V + + + + + G A V +
Sbjct: 2 GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 102 THEDAMQAM 110
+ DA Q +
Sbjct: 62 SAMDASQLL 70
>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
Length = 119
Score = 42.6 bits (100), Expect = 4e-06
Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 5/81 (6%)
Query: 38 GPRPGDRWVNESSGPGHH--TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGE 95
G P + +S G +H+R LP V E +++ P V N + +
Sbjct: 13 GLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKV---TNLLMLKGKNQ 69
Query: 96 ADVYFATHEDAMQAMSKDRTN 116
A + T E A ++ +
Sbjct: 70 AFIEMNTEEAANTMVNYYTSV 90
>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
Length = 193
Score = 43.7 bits (102), Expect = 5e-06
Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 2/82 (2%)
Query: 45 WVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDI-NYKNGRPSGEADVYFAT 102
+ + +V+++G P DI ++ V + + + G V F +
Sbjct: 100 TDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 159
Query: 103 HEDAMQAMSKDRTNIRHRYIEL 124
E A + + + + +
Sbjct: 160 IESAKKFVETPGQKYKETDLLI 181
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 41.5 bits (98), Expect = 7e-06
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SKDR 114
T+ + L F + E ++ + F + + + ++G+ G A + F + DA + + K
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 115 TNIRHRYIELFLNSSSPRGGVGG 137
I R + L + +GG G
Sbjct: 76 AEIDGR--SVSLYYTGEKGGTRG 96
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 41.6 bits (98), Expect = 8e-06
Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAMQAMSK- 112
+++R LP+++ +++ D F P+ + + G A V + DA A+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG-NTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 113 DRTNIRHRYI 122
N+ +RY+
Sbjct: 68 SGFNVSNRYL 77
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 41.3 bits (97), Expect = 1e-05
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 3/61 (4%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
VH+RGL V E D+V+ + +A V F + A + ++
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTI---CYVMMMPFKRQALVEFENIDSAKECVTFAAD 73
Query: 116 N 116
Sbjct: 74 V 74
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 41.0 bits (96), Expect = 1e-05
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
+H+R LP V E +++ P V N + +A + AT E A+ ++
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKV---TNILMLKGKNQAFLELATEEAAITMVNYYSA 73
Query: 116 N---IRHRYI 122
+R++ I
Sbjct: 74 VTPHLRNQPI 83
>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
Length = 156
Score = 41.7 bits (98), Expect = 1e-05
Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 4/106 (3%)
Query: 40 RPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEA 96
GD E T+++ L F E+ I + FS + + + ++ G
Sbjct: 25 FRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84
Query: 97 DVYFATHEDAMQAMSK-DRTNIRHRYIELFLNSSSPRGGVGGSGFS 141
V + + DA AM + T + R I ++ G G G S
Sbjct: 85 FVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRS 130
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 40.5 bits (95), Expect = 1e-05
Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 5/84 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DR 114
+ ++ LP N +++ D Y + R A V E A A+ +
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYDLKYCYV----DRNKRTAFVTLLNGEQAQNAIQMFHQ 62
Query: 115 TNIRHRYIELFLNSSSPRGGVGGS 138
+ R + + + L + G S
Sbjct: 63 YSFRGKDLIVQLQPTDALLCSGPS 86
>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
Length = 165
Score = 41.7 bits (98), Expect = 1e-05
Identities = 19/115 (16%), Positives = 39/115 (33%), Gaps = 8/115 (6%)
Query: 3 DANTTTTTTTGANRFGGGRGCFNNDRWNDRPGGFAGPRPGDRWVNESSGPGH----HTVH 58
D + + GRG F +D + GP +
Sbjct: 18 DGDQGIVRLKEKAKHRKGRG-FGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILF 76
Query: 59 MRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ + E +I + F + ++++++ + G G A V + TH+ A+ A
Sbjct: 77 VTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 40.5 bits (95), Expect = 1e-05
Identities = 8/69 (11%), Positives = 26/69 (37%), Gaps = 1/69 (1%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DR 114
+ +R +P + + + V + +V +++ + A QA+ K +
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76
Query: 115 TNIRHRYIE 123
+ + ++
Sbjct: 77 FQLENFTLK 85
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 40.7 bits (96), Expect = 2e-05
Identities = 19/85 (22%), Positives = 29/85 (34%), Gaps = 10/85 (11%)
Query: 60 RGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRT 115
L +R + + F V VY+ P G A V F DA A + D
Sbjct: 19 DNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGA 78
Query: 116 NIRHRYIELFL------NSSSPRGG 134
+ R + + + + S P G
Sbjct: 79 ELDGRELRVQVARYGRRDLSGPSSG 103
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 40.6 bits (95), Expect = 2e-05
Identities = 29/117 (24%), Positives = 37/117 (31%), Gaps = 19/117 (16%)
Query: 32 RPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNG 90
P G GP + V + GLP + +D+ D Y D+
Sbjct: 3 APRGRYGPPSRR---------SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-- 51
Query: 91 RPSGEADVYFATHEDAMQAMSK-DRTNIRHRYIEL---FLNSSSPRGGVGGSGFSRS 143
G V F ED A+ K D T R E + PR G SRS
Sbjct: 52 ---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRS 105
>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}
Length = 143
Score = 41.0 bits (96), Expect = 2e-05
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP-------VVPVYVDINY-KNGRPSGEADV 98
+ G + ++++ L V EKD+ F + DI K GR G+A +
Sbjct: 38 SYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFI 97
Query: 99 YFATHEDAMQAMSK 112
+ A +A+ +
Sbjct: 98 GLPNEKAAAKALKE 111
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 40.2 bits (94), Expect = 3e-05
Identities = 25/99 (25%), Positives = 33/99 (33%), Gaps = 10/99 (10%)
Query: 50 SGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQ 108
S + V + GLP + +D+ D V Y D+ G V F ED
Sbjct: 11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTY 65
Query: 109 AMSK-DRTNIRHRYIEL---FLNSSSPRGGVGGSGFSRS 143
A+ K D T R E + PR G S
Sbjct: 66 AVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSG 104
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 39.5 bits (93), Expect = 4e-05
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 4/95 (4%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
+ T+ ++GL E+ + + F V + + + G G V F + EDA
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 109 AMSK-DRTNIRHRYIELFLNSSSPRGGVGGSGFSR 142
A + I ++ L+ + P+ G GGSG S
Sbjct: 70 AKEAMEDGEIDGN--KVTLDWAKPK-GEGGSGPSS 101
>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 = 40.8 bits (96), Expect = 4e-05
Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 10/97 (10%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP--------VVPVYVDINYKNGRPSGEADVYFATHEDAM 107
+++ +PF + E+ ++DFF+ P + + + A + F + ++
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 108 QAMSKDRTNIRHRYIELFLNSSSPRGGVGGSGFSRSE 144
QAM+ D + + L + + G + S
Sbjct: 66 QAMAFDGIIFQGQ--SLKIRRPHDYQPLPGMSENPSV 100
Score = 38.1 bits (89), Expect = 3e-04
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 4/87 (4%)
Query: 30 NDRPGGFAGPRPGDRWVNESSGP-GHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDI 85
PG P V + P H + + GLP +N+ + + + + +
Sbjct: 89 QPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148
Query: 86 NYKNGRPSGEADVYFATHEDAMQAMSK 112
+ G G A + QA++
Sbjct: 149 DSATGLSKGYAFCEYVDINVTDQAIAG 175
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 39.8 bits (93), Expect = 6e-05
Identities = 20/112 (17%), Positives = 35/112 (31%), Gaps = 4/112 (3%)
Query: 15 NRFGGGRGCFNNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDF 74
++ G ++D F + G ++ + L +R + +
Sbjct: 31 KQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRV 90
Query: 75 FS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTNIRHRYI 122
F V VY+ + G A V F DA AM D + R +
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 38.8 bits (91), Expect = 7e-05
Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKD 113
T ++ LPF + DI F + V + + + G V F + +A++ D
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD 76
Query: 114 RTNIRHRYIELFLNSSSPR---GGVGGSG 139
+ R L ++ + R SG
Sbjct: 77 GALLGDR--SLRVDIAEGRKQDKSGPSSG 103
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 38.7 bits (91), Expect = 8e-05
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 60 RGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
R L + +E+D+ FS P+ ++ I+ +P G A V F E A++A +
Sbjct: 14 RNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 38.9 bits (91), Expect = 8e-05
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
TV +R L F E+ + + + V V ++ G A F T E A + ++
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
>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
Length = 172
Score = 39.5 bits (93), Expect = 9e-05
Identities = 12/76 (15%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVY--------VDINYKNGRPSGEADVYFATHEDAM 107
+++ +PF + E+ ++DFF+ + + + + + A + F + ++
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 108 QAMSKDRTNIRHRYIE 123
QAM+ D + + ++
Sbjct: 66 QAMAFDGIIFQGQSLK 81
Score = 33.7 bits (78), Expect = 0.010
Identities = 9/74 (12%), Positives = 22/74 (29%), Gaps = 7/74 (9%)
Query: 46 VNESSGPGHHTVHMR----GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADV 98
+ + GLP +N+ + + + + + + G G A
Sbjct: 82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141
Query: 99 YFATHEDAMQAMSK 112
+ QA++
Sbjct: 142 EYVDINVTDQAIAG 155
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 38.3 bits (89), Expect = 9e-05
Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 3/77 (3%)
Query: 35 GFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSG 94
G +G E + V++ LP D+ + V + + ++ R
Sbjct: 1 GSSGSSGPGSPPGEGAPLAA-DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR--R 57
Query: 95 EADVYFATHEDAMQAMS 111
A +++ A QA+S
Sbjct: 58 RAFLHYPDSAAAQQAVS 74
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 38.4 bits (90), Expect = 1e-04
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATH 103
+ES G + + L + +E+D++ F P + V + +G G A V F++H
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSH 66
Query: 104 EDAMQAMSK 112
+A A+
Sbjct: 67 TEAQAAIHA 75
>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
Length = 114
Score = 38.5 bits (90), Expect = 1e-04
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 5/81 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
TV L R+ +D+ DFFS V V + + + R G A V F + A+
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86
Query: 113 DRTNIRHRYIELFLNSSSPRG 133
+ I + +S
Sbjct: 87 TGQRLLGVPII--VQASQAEK 105
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 38.0 bits (89), Expect = 1e-04
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 49 SSGP-GHHTVHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNGRPSGEADVYFATHEDA 106
SSG G + +++ L V D+ F +P+ + SG A V + A
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV----LLKSGYAFVDYPDQNWA 57
Query: 107 MQAMSK 112
++A+
Sbjct: 58 IRAIET 63
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 38.5 bits (90), Expect = 1e-04
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 31 DRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINY 87
G + P E +V++ + + +D+ FS + + + +
Sbjct: 13 MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK 72
Query: 88 KNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYI 122
+G P G A + FA A++ D T R R I
Sbjct: 73 FSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTI 107
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 38.1 bits (89), Expect = 2e-04
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKN-GRPSGEADVYFATHEDAMQAM 110
+ +R +PF+ N+++I + FS + V + G G V F T +DA +A
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>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
Length = 150
Score = 38.7 bits (90), Expect = 2e-04
Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 5/98 (5%)
Query: 16 RFGGGRGCFNNDRWNDRPGGFAGPRPGDRWVNESS---GPGHHTVHMRGLPFRVNEKDIV 72
++ G ++D F + P V++ L N+ ++
Sbjct: 32 QYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELE 91
Query: 73 DFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
F P+ + P G A V F DA A+
Sbjct: 92 RAFGYYGPL-RSVWVAR-NPPGFAFVEFEDPRDAADAV 127
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 38.3 bits (89), Expect = 2e-04
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIV----DFFSPVVPVYVDINY-KNGRPSGEADVYFA 101
V + + V ++ + S + +DI + SG+A + FA
Sbjct: 22 TPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI-LDIVVDLSDDNSGKAYIVFA 80
Query: 102 THEDAMQAM 110
T E A +
Sbjct: 81 TQESAQAFV 89
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 37.2 bits (87), Expect = 2e-04
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATH 103
N ++ + + + GL E+D+ + FS P+ V + + ++ R G A VYF
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 104 EDAMQAMSK 112
+DA +A +
Sbjct: 68 DDAKEAKER 76
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 37.3 bits (87), Expect = 3e-04
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 46 VNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHED 105
+E + +++R L +E+ I F+ + P V+ + + A V+F+ ED
Sbjct: 7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE---RVKKIRDYAFVHFSNRED 63
Query: 106 AMQAMSK-DRTNIRHRYIELFL------NSSSPRGG 134
A++AM + + IE+ L +SS P G
Sbjct: 64 AVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>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
Length = 168
Score = 37.9 bits (89), Expect = 3e-04
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
+ + + LP + ++++ F P+ + +YK G G A V F + D+ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 110 MSK-DRTNIRHRYIELFLNSSSPRG 133
+ + +R++ L ++ + P G
Sbjct: 62 IKVLNGITVRNK--RLKVSYARPGG 84
Score = 34.9 bits (81), Expect = 0.004
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
+++ LP + + + F +V + + GRP G A V + E+A +
Sbjct: 87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 109 AMSK 112
A+S
Sbjct: 147 AISA 150
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 37.8 bits (88), Expect = 3e-04
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATH 103
+ S +++ GL V++K + F P + + + ++Y+ + G A V F
Sbjct: 56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 115
Query: 104 EDAMQAMS 111
EDA A+
Sbjct: 116 EDAAAAID 123
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 36.9 bits (86), Expect = 4e-04
Identities = 14/91 (15%), Positives = 27/91 (29%), Gaps = 4/91 (4%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFS--PVVPVYVDINYKNGRPSGEADVYFATHEDA 106
S + + L + ++ S ++ + G V F + ED
Sbjct: 12 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 71
Query: 107 MQAMSKDRTNIRHRYIELFLNSSSPRGGVGG 137
+A+ + E+ L R G G
Sbjct: 72 EKALELTGLKVFGN--EIKLEKPKGRDGTRG 100
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 36.8 bits (86), Expect = 4e-04
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTN 116
L E D+ + F P + +Y+ + G+ G A + F EDA +A++
Sbjct: 22 NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG 81
Query: 117 IRHRYIELFLNSSSPRGGVGGSG 139
H L + + P G S
Sbjct: 82 YDHL--ILNVEWAKPSTNSGPSS 102
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 36.5 bits (85), Expect = 4e-04
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 11/80 (13%)
Query: 35 GFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGR 91
G +G P TV + L RV E+ + + F P+ V + + G+
Sbjct: 4 GSSGMFPAQE-------EADRTVFVGNLEARVREEILYELFLQAGPLTKVTI-CKDREGK 55
Query: 92 PSGEADVYFATHEDAMQAMS 111
P V F E A++
Sbjct: 56 PKSFGFVCFKHPESVSYAIA 75
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 36.5 bits (85), Expect = 4e-04
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 20/87 (22%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS-------------PVVPVYVD 84
G ++++ T+ ++GL V + + D+F P++ +Y D
Sbjct: 2 GHHHHHHSHSDNN-----TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTD 56
Query: 85 INYKNGRPSGEADVYFATHEDAMQAMS 111
+ G+ GEA V F A A+
Sbjct: 57 --RETGKLKGEATVSFDDPPSAKAAID 81
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 37.6 bits (87), Expect = 5e-04
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 39 PRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADV 98
+PG + P T+H+ +P V+E+D+ FS V + A +
Sbjct: 106 KKPGSKNFQNIFPPSA-TLHLSNIPPSVSEEDLKVLFSS-NGGVVKGFKFFQKDRKMALI 163
Query: 99 YFATHEDAMQAMSK 112
+ E+A+QA+
Sbjct: 164 QMGSVEEAVQALID 177
>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
Length = 229
Score = 37.7 bits (87), Expect = 5e-04
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 39 PRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADV 98
+PG + P T+H+ +P V+E+D+ FS V + A +
Sbjct: 137 KKPGSKNFQNIFPPSA-TLHLSNIPPSVSEEDLKVLFSS-NGGVVKGFKFFQKDRKMALI 194
Query: 99 YFATHEDAMQAMSK 112
+ E+A+QA+
Sbjct: 195 QMGSVEEAVQALID 208
>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*
Length = 110
Score = 36.5 bits (85), Expect = 6e-04
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ E +I + F + ++++++ + G G A V + TH+ A+ A
Sbjct: 33 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 36.1 bits (84), Expect = 7e-04
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
TV++ GL +V+E + + F PVV ++ + G+ G V F + EDA A+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 35.6 bits (83), Expect = 8e-04
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
GL V++K + F P + + + ++Y+ + G A V F EDA A+
Sbjct: 14 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 36.2 bits (84), Expect = 8e-04
Identities = 23/105 (21%), Positives = 37/105 (35%), Gaps = 20/105 (19%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS-------------PVVPVYVDINYKNGRPSGEADVYFAT 102
T+ ++GL V + + D+F P++ +Y D G+ GEA V F
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE--TGKLKGEATVSFDD 66
Query: 103 HEDAMQAMSK-DRTNIRHRYIEL----FLNSSSPRGGVGGSGFSR 142
A A+ D I++ + GG G G
Sbjct: 67 PPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEH 111
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 37.3 bits (87), Expect = 9e-04
Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 4/66 (6%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDA 106
E + +RGLP V +++ D S Y + + G A V E A
Sbjct: 15 TERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV----DKYKGTAFVTLLNGEQA 70
Query: 107 MQAMSK 112
A++
Sbjct: 71 EAAINA 76
Score = 36.9 bits (86), Expect = 0.001
Identities = 10/74 (13%), Positives = 28/74 (37%), Gaps = 3/74 (4%)
Query: 42 GDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADV 98
+R ++ P + + LP + ++ + P + ++ + + G+ G
Sbjct: 83 RERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFA 142
Query: 99 YFATHEDAMQAMSK 112
+ + A +A S
Sbjct: 143 EYMKKDSAARAKSD 156
Score = 32.6 bits (75), Expect = 0.029
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 9/64 (14%)
Query: 54 HHTVHMRGLPFRVNEKDIV-DFFSPV-----VPVYVDINYKNGRPSGEADVYFATHEDAM 107
+ + LP N+ D + S V + ++G+ G A + + T E A
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG---QDGQLKGFAVLEYETAEMAE 240
Query: 108 QAMS 111
+A
Sbjct: 241 EAQQ 244
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 35.7 bits (83), Expect = 0.001
Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 50 SGPGHHTVHMRGLPFRVNEKD----IVDFFSPVVPVYVDIN-YKNGRPSGEADVYFATHE 104
+HT+++ L ++ + + + FS + +DI ++ + G+A V F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQI-LDILVSRSLKMRGQAFVIFKEVS 62
Query: 105 DAMQAM 110
A A+
Sbjct: 63 SATNAL 68
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 35.8 bits (83), Expect = 0.001
Identities = 27/108 (25%), Positives = 40/108 (37%), Gaps = 5/108 (4%)
Query: 35 GFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKN-GRPS 93
G +G G + +G +++ LP + KDI D F + DI+ KN
Sbjct: 4 GSSGMSGGGV-IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI-RDIDLKNRRGGP 61
Query: 94 GEADVYFATHEDAMQAMSK-DRTNIRHRYIEL-FLNSSSPRGGVGGSG 139
A V F DA A+ D + + + F S G SG
Sbjct: 62 PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 35.4 bits (81), Expect = 0.001
Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 56 TVHMRGLPFRVNEKD----IVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
V + + +R++ K+ + + F+ V + +A V +DA+ A++
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70
Query: 112 K-DRTNIRHRYIELFLNSSSPRGGVG 136
R I + I + L + + G
Sbjct: 71 SLHRYKIGSKKILVSLATGASGPSSG 96
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 35.7 bits (83), Expect = 0.001
Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 13/90 (14%)
Query: 25 NNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPV 81
+ D R + W + + G+ E+DI D F+ + +
Sbjct: 4 DYDSVEQDGDEPGPQRSVEGW----------ILFVTGVHEEATEEDIHDKFAEYGEIKNI 53
Query: 82 YVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+++++ + G G V + T+++A AM
Sbjct: 54 HLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 35.8 bits (83), Expect = 0.001
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 16/93 (17%)
Query: 61 GLPFRVNEKDIVDFFS-------------PVVPVYVDINYKNGRPSGEADVYFATHEDAM 107
GL V D+ DFF P++ +Y+D + G+P G+A V + A
Sbjct: 22 GLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLD--KETGKPKGDATVSYEDPPTAK 79
Query: 108 QAMSK-DRTNIRHRYIELFLNSSSPRGGVGGSG 139
A+ D + + +++ L P G S
Sbjct: 80 AAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 35.4 bits (82), Expect = 0.001
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 46 VNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHED 105
+ S+ P T ++ +P E D++ F + +D + + G + + THE
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFI-LDFKHYPEK--GCCFIKYDTHEQ 75
Query: 106 AMQAMSK 112
A +
Sbjct: 76 AAVCIVA 82
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 34.8 bits (81), Expect = 0.001
Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
++++ + + +++ F V V + + +G P G A + F+ E +++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 113 DRTNIRHRYI 122
D + R R I
Sbjct: 68 DESLFRGRQI 77
>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
Length = 167
Score = 36.0 bits (84), Expect = 0.001
Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 54 HHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ + LP + +++ F + + + G+ G V + +DA +A+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Score = 34.9 bits (81), Expect = 0.004
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
GLP + +K++ FS ++ + ++ G G + F +A +A+
Sbjct: 95 GLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 34.9 bits (81), Expect = 0.001
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
LPF + D+ FS VV V + + + G A + F + A
Sbjct: 23 NLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 35.4 bits (82), Expect = 0.001
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+P ++EKD+ F + + V + G G A + + E A++A S
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 36.0 bits (84), Expect = 0.002
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+++ L + E + +F P+ + + + KN + A V + DA A+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKI-MIDKNNKNVNYAFVEYHQSHDANIAL 58
Score = 34.4 bits (80), Expect = 0.005
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
+ + L V+++ + + F + +V + + G G V F + +DA A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 110 MSK 112
M
Sbjct: 146 MDS 148
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 35.0 bits (81), Expect = 0.002
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFS----PVVPVYVDINYKNGRPSGEADVYFATHE 104
S ++ M L ++E I F+ V+ V + N G P+G V FA
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 105 DAMQAMSK 112
A + + K
Sbjct: 64 TAEKCLHK 71
>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
Length = 167
Score = 36.0 bits (84), Expect = 0.002
Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
G+ V K+ +FFS ++ + ++ G+ G V + + + + +
Sbjct: 94 GIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDF 153
Query: 118 RHRYIEL 124
+ R IE+
Sbjct: 154 KDRKIEI 160
Score = 32.1 bits (74), Expect = 0.039
Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 14/95 (14%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL + E ++ ++F V + + + GR G + F + + K + +
Sbjct: 10 GLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV-KTQHIL 68
Query: 118 RHRYIELFLNSSSPRGG--------VGGSGFSRSE 144
+ I+ + PR VGG G
Sbjct: 69 DGKVID--PKRAIPRDEQDKTGKIFVGGIGPDVRP 101
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 35.4 bits (82), Expect = 0.002
Identities = 22/124 (17%), Positives = 47/124 (37%), Gaps = 15/124 (12%)
Query: 25 NNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPV 81
+ D R + W + + G+ E+DI D F+ + +
Sbjct: 3 DYDSVEQDGDEPGPQRSVEGW----------ILFVTGVHEEATEEDIHDKFAEYGEIKNI 52
Query: 82 YVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTNIRHRYIEL-FLNSSSPRGGVGGSG 139
+++++ + G G V + T+++A AM + ++ + I + + P G G
Sbjct: 53 HLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGG 112
Query: 140 FSRS 143
RS
Sbjct: 113 RRRS 116
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 36.2 bits (84), Expect = 0.002
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L V+ + + FS V V + GR +G+ V FA A +A+ +
Sbjct: 103 NLSPVVSNELLEQAFSQFGPVEKAVV-VVDDRGRATGKGFVEFAAKPPARKALER 156
Score = 31.2 bits (71), Expect = 0.086
Identities = 13/77 (16%), Positives = 27/77 (35%), Gaps = 4/77 (5%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDA 106
E + + + LP + E+D F ++ R G + + A
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEP-SEVFINRDR--GFGFIRLESRTLA 71
Query: 107 MQAMSK-DRTNIRHRYI 122
A ++ D T ++ R +
Sbjct: 72 EIAKAELDGTILKSRPL 88
>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
Length = 196
Score = 35.7 bits (83), Expect = 0.002
Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 5/86 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL F ++ + F + V + R G V +AT E+ AM+ +
Sbjct: 20 GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKV 79
Query: 118 RHRYIELFLNSSSPRGGVGGSGFSRS 143
R +E + R G +
Sbjct: 80 DGRVVE--PKRAVSREDSQRPGAHLT 103
Score = 34.6 bits (80), Expect = 0.005
Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
G+ E + D+F + + + + +G+ G A V F H+ + + + +
Sbjct: 111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTV 170
Query: 118 RHRYIEL 124
E+
Sbjct: 171 NGHNCEV 177
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 34.5 bits (80), Expect = 0.002
Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 6/92 (6%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
SSG +H+ + +++ F PV ++ + A V+ EDA++
Sbjct: 5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPV-IECDIVKDY----AFVHMERAEDAVE 59
Query: 109 AMSK-DRTNIRHRYIELFLNSSSPRGGVGGSG 139
A+ D T + + + + L++S R G S
Sbjct: 60 AIRGLDNTEFQGKRMHVQLSTSRLRTASGPSS 91
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 34.5 bits (80), Expect = 0.002
Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 6/95 (6%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHED 105
E + + + LP + E+++ F V I+ + G + T
Sbjct: 8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH----KDKGFGFIRLETRTL 63
Query: 106 AMQAMSK-DRTNIRHRYIELFLNSSSPRGGVGGSG 139
A A + D +R + + + S G S
Sbjct: 64 AEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98
>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 = 34.3 bits (79), Expect = 0.003
Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 8/70 (11%)
Query: 61 GLPFRVNEKDIVDFFSPVVPVYVDI--------NYKNGRPSGEADVYFATHEDAMQAMSK 112
+PF + E+ ++DFF+ + + + + A + F + ++ QAM+
Sbjct: 13 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 72
Query: 113 DRTNIRHRYI 122
D + + +
Sbjct: 73 DGIIFQGQSL 82
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 34.5 bits (80), Expect = 0.003
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
G+ R++E +I FF+ V V + I + G G V F D + +
Sbjct: 16 GIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 69
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 35.4 bits (82), Expect = 0.003
Identities = 8/78 (10%), Positives = 25/78 (32%), Gaps = 3/78 (3%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSG 94
G + +++ + +++ DI F + + + G+ G
Sbjct: 109 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168
Query: 95 EADVYFATHEDAMQAMSK 112
+ + + + A+S
Sbjct: 169 YGFIEYEKAQSSQDAVSS 186
Score = 34.2 bits (79), Expect = 0.007
Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 5/82 (6%)
Query: 34 GGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNG 90
G G + + + V++ + + + E I F+ P+ + + +
Sbjct: 10 GQQMGRGSAAQ--RQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTM 67
Query: 91 RPSGEADVYFATHEDAMQAMSK 112
+ G A V + E A A+ +
Sbjct: 68 KHKGFAFVEYEVPEAAQLALEQ 89
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 35.3 bits (82), Expect = 0.003
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
++++ L V E + + FS P++ + V + R G A V F DA +
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 109 AM 110
A+
Sbjct: 73 AL 74
Score = 30.3 bits (69), Expect = 0.19
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 9/65 (13%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFATHEDAM 107
G + ++ L ++ K + D FS V D G V+F T E A
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENGSKGYGFVHFETQEAAE 157
Query: 108 QAMSK 112
+A+ K
Sbjct: 158 RAIEK 162
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 34.1 bits (79), Expect = 0.003
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
GL V++K + F P + + + ++Y+ + G A V F EDA A+
Sbjct: 19 GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 33.9 bits (78), Expect = 0.004
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 62 LPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V +K + FS VV + I+ G+ G V + DA + +
Sbjct: 20 AKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 34.1 bits (78), Expect = 0.004
Identities = 10/68 (14%), Positives = 21/68 (30%), Gaps = 4/68 (5%)
Query: 46 VNESSGPGHHTVHMRG-LPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHE 104
+ S V G L V+ ++ V + +P + + T E
Sbjct: 18 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD-ALLMPPNKPY--SFARYRTTE 74
Query: 105 DAMQAMSK 112
++ +A
Sbjct: 75 ESKRAYVT 82
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 34.0 bits (78), Expect = 0.004
Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 4/73 (5%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + LP +I + FS + + G A V F +A +A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSL-GRVLLPEGG--ITAIVEFLEPLEARKAFRH 65
Query: 113 -DRTNIRHRYIEL 124
+ H + L
Sbjct: 66 LAYSKFHHVPLYL 78
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 33.8 bits (78), Expect = 0.005
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+P+ E+ + D FS PVV + + + G+P G + E A+ AM
Sbjct: 15 NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 33.4 bits (77), Expect = 0.006
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 1/77 (1%)
Query: 37 AGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGE 95
+G P +N + +H+ +PFR + D+ F + V+I + G
Sbjct: 12 SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 71
Query: 96 ADVYFATHEDAMQAMSK 112
V F DA +A K
Sbjct: 72 GFVTFENSADADRAREK 88
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 33.3 bits (77), Expect = 0.006
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDIN-YKNGRPSGEADVYFATHEDAM 107
VH+ L V + I++ FS + + + + G A V F ++A
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 108 QAMS 111
+A+
Sbjct: 62 KALK 65
>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
Length = 109
Score = 33.5 bits (77), Expect = 0.007
Identities = 26/107 (24%), Positives = 46/107 (42%), Gaps = 6/107 (5%)
Query: 35 GFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSG 94
G + VN+SS P + TV+ G+ + ++ + FSP + ++I + G
Sbjct: 7 GNTKQLRFEDVVNQSS-PKNCTVYCGGIASGLTDQLMRQTFSPFGQI-MEIRVFPEK--G 62
Query: 95 EADVYFATHEDAMQAMSK-DRTNIRHRYIELFL-NSSSPRGGVGGSG 139
+ V F+THE A A+ + T I ++ + S SG
Sbjct: 63 YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSSG 109
>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
Length = 175
Score = 34.1 bits (79), Expect = 0.007
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 54 HHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ + + + E DI FS + + +G G A V F T A A+
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAI 153
Query: 111 SK 112
Sbjct: 154 KA 155
Score = 32.6 bits (75), Expect = 0.022
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYV--DINYKNGRPSGEADVYFATHEDAM 107
+ + +P +EKD+ + F V + V D + + G V F T + A+
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 108 QAMSK 112
+A +
Sbjct: 62 EAQNA 66
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 33.3 bits (77), Expect = 0.007
Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 5/84 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
G+P E ++ ++F V V + + + RP G + F + QA++ +I
Sbjct: 17 GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDI 76
Query: 118 RHRYIELFLNSSSPRGGVGGSGFS 141
+ +E + + PR S
Sbjct: 77 MGKKVE--VKRAEPRDSKSSGPSS 98
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 33.4 bits (77), Expect = 0.008
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHED 105
N S +H+ +PFR + D+ F + V+I + G V F D
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 67
Query: 106 AMQAMSK 112
A +A K
Sbjct: 68 ADRAREK 74
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 33.4 bits (77), Expect = 0.008
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 7/75 (9%)
Query: 39 PRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEAD 97
PR + + + +R P V E ++ + F P P+ V I +G A
Sbjct: 16 PRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI------LNGFAF 69
Query: 98 VYFATHEDAMQAMSK 112
V F E A +A+ +
Sbjct: 70 VEFEEAESAAKAIEE 84
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 33.0 bits (76), Expect = 0.009
Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 3/87 (3%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRT 115
V++ L + ++ FS P+ + P G A V F DA A+ D
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPL-RTVWIAR-NPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 116 NIRHRYIELFLNSSSPRGGVGGSGFSR 142
I + + L++ PR +R
Sbjct: 61 VICGSRVRVELSTGMPRRSRFDRPPAR 87
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 33.7 bits (77), Expect = 0.009
Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 5/80 (6%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRP 92
P + V++ + ++ ++ VV + N NG+
Sbjct: 39 NKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQS 98
Query: 93 SGEADVYFATHEDAMQAMSK 112
G A+V A+ + +
Sbjct: 99 KGYAEVVVASENSVHKLLEL 118
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 33.0 bits (76), Expect = 0.009
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 61 GLPFRVNEKDIVDFFSPVVPVYVDINY----KNGRPSGEADVYFATHEDAMQAM 110
+P+ E+ I+D S V PV +++ + GR G A + F E + A+
Sbjct: 9 SIPYDQTEEQILDLCSNVGPV-INLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.4 bits (78), Expect = 0.011
Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 22/95 (23%)
Query: 64 FRVNEKDIVDFFSPVVPVYVDINYK---------NGRPSGEADVYFATHE---DAMQAMS 111
++++V F V + INYK +PS +Y + + Q +
Sbjct: 71 LLSKQEEMVQKF---VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127
Query: 112 KDRTNIRHRYIEL--FLNSSSPRGGV-----GGSG 139
K + Y++L L P V GSG
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG 162
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 32.2 bits (74), Expect = 0.014
Identities = 12/92 (13%), Positives = 33/92 (35%), Gaps = 6/92 (6%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
S + + + +++ F V ++ + A V+ DA
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRV-IECDVVKDY----AFVHMEKEADAKA 58
Query: 109 AMSK-DRTNIRHRYIELFLNSSSPRGGVGGSG 139
A+++ + ++ + I + L++ + SG
Sbjct: 59 AIAQLNGKEVKGKRINVELSTKGQKKSGPSSG 90
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 32.3 bits (74), Expect = 0.015
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 10/79 (12%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGE-ADVYFATHE 104
S G +V + G P V+ + ++F PV V +D + G A V
Sbjct: 3 SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD------KDKGVFAIVEMGDVG 56
Query: 105 DAMQAMSKDRTNIRHRYIE 123
+S+ + ++ +
Sbjct: 57 AREAVLSQSQHSLGGHRLR 75
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 32.2 bits (74), Expect = 0.016
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 54 HHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
T+++ L V E I+ FS P + + + P V F H DA A+
Sbjct: 15 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEFYEHRDAAAAL 72
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 32.3 bits (74), Expect = 0.019
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L F + E + F P + + + ++ + GR G + F+ E A +A+ +
Sbjct: 33 SLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 32.3 bits (74), Expect = 0.019
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
GL NEK + F P+ V + I + + G A + F DA A
Sbjct: 14 GLNRETNEKMLKAVFGKHGPISEVLL-IKDRTSKSRGFAFITFENPADAKNAAK 66
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 31.8 bits (73), Expect = 0.019
Identities = 8/58 (13%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + GL + + F + I++ G + + + + A A +K
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSI-RTIDHVKGDSFAY--IQYESLDAAQAACAK 72
>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
Length = 282
Score = 33.3 bits (75), Expect = 0.020
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 55 HTVHMRGLPFRVNEKD----IVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
HT+++ L ++ + + + FS + + ++ + G+A V F A A+
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Score = 28.3 bits (62), Expect = 0.84
Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 2/72 (2%)
Query: 39 PRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADV 98
P S P +H + + LP NE + F+ P + ++ GR A V
Sbjct: 192 PGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQF-PGFKEVRLVPGRH-DIAFV 249
Query: 99 YFATHEDAMQAM 110
F A A
Sbjct: 250 EFDNEVQAGAAR 261
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 31.3 bits (72), Expect = 0.023
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 60 RGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRT 115
RGL ++D+V P +V ++ + G V F + A +A++ +
Sbjct: 11 RGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS 70
Query: 116 NIRHRYIELFLNSSSPRGG 134
++ + S P G
Sbjct: 71 GVQAQ----MAKQSGPSSG 85
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 31.3 bits (72), Expect = 0.025
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL E+ I ++F V + + ++ K + G + F E + M K N+
Sbjct: 6 GLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNV 65
Query: 118 RHRYIE 123
E
Sbjct: 66 GLSKCE 71
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 31.8 bits (73), Expect = 0.027
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
GL F NE+ + FS + V V + + R G V F +DA AM
Sbjct: 19 GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 31.4 bits (72), Expect = 0.029
Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 6/85 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTN 116
L F + E + F P + + + + GR G + F+ E A +A+ + +
Sbjct: 12 SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE 71
Query: 117 IRHRYIELFLNSSSPRGGVGGSGFS 141
+ R + + + R G S
Sbjct: 72 LAGRPMR--VGHVTERLDGGSGPSS 94
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 31.4 bits (72), Expect = 0.031
Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 5/57 (8%)
Query: 61 GLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L + ++D+ + ++ + N NG+ G A V + + + M
Sbjct: 8 NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 64
>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*
Length = 437
Score = 32.5 bits (73), Expect = 0.040
Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 4/84 (4%)
Query: 48 ESSGPGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHE 104
+ G T+ + + + E + F P+ +++ + ++G+P G A + +
Sbjct: 96 NAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER 155
Query: 105 DAMQAMSK-DRTNIRHRYIELFLN 127
D A D I R + + +
Sbjct: 156 DMHSAYKHADGKKIDGRRVLVDVE 179
>2wsd_A Spore coat protein A; oxidoreductase, multi-copper oxidase,
sporulation, COTA- LAC copper centre; 1.60A {Bacillus
subtilis} PDB: 1gsk_A 1hkp_A 1hkz_A 1hl0_A 1hl1_A
1of0_A* 1ogr_A 1uvw_A* 1w6l_A 1w6w_A 1w8e_A 2bhf_A
2x87_A 2x88_A* 4a67_A 4akq_A 4a68_A* 4akp_A* 4a66_A
4ako_A
Length = 513
Score = 32.4 bits (73), Expect = 0.049
Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 4/88 (4%)
Query: 7 TTTTTTGANRFGGGRGCFNNDRWNDRPGGFAGPRPGD--RWVNESSGPGHHTVHMRGLPF 64
T + +G NN RW+D P+ G W + G H +H+ + F
Sbjct: 371 TLKLAGTQDEYGRPVLLLNNKRWHDPV--TETPKVGTTEIWSIINPTRGTHPIHLHLVSF 428
Query: 65 RVNEKDIVDFFSPVVPVYVDINYKNGRP 92
RV ++ D + P
Sbjct: 429 RVLDRRPFDIARYQESGELSYTGPAVPP 456
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 30.5 bits (69), Expect = 0.067
Identities = 9/66 (13%), Positives = 22/66 (33%), Gaps = 11/66 (16%)
Query: 56 TVHMRGLP------FRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDA 106
+ + +P + I FS + + +G+ G + +A+ A
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 74
Query: 107 MQAMSK 112
+ A+
Sbjct: 75 VDAVKN 80
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 30.1 bits (68), Expect = 0.068
Identities = 9/64 (14%), Positives = 22/64 (34%), Gaps = 7/64 (10%)
Query: 56 TVHMRGLP------FRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQ 108
+ + +P + I FS + ++G+ G + +A+ A+
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62
Query: 109 AMSK 112
A+
Sbjct: 63 AVKN 66
>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
Length = 229
Score = 31.6 bits (71), Expect = 0.079
Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 5/57 (8%)
Query: 61 GLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L + ++D+ + ++ + N NG+ G A V + + + M
Sbjct: 75 NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 131
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 30.2 bits (69), Expect = 0.080
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 4/65 (6%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSPVVPVY----VDINYKNGRPSGEADVYFATHEDAM 107
G + + L ++EK + D FS + + + G G A + FA+ + +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 108 QAMSK 112
A+
Sbjct: 63 AAIEA 67
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 30.7 bits (69), Expect = 0.084
Identities = 12/69 (17%), Positives = 21/69 (30%), Gaps = 5/69 (7%)
Query: 61 GLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
GLP ++E +I F V + + P G A + F +
Sbjct: 15 GLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE 74
Query: 116 NIRHRYIEL 124
Y+ +
Sbjct: 75 EDGKLYLCV 83
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 29.9 bits (68), Expect = 0.088
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
T+++ GL + E D+ + F + + + + A + FAT + A A K
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV----QRQQCAFIQFATRQAAEVAAEK 67
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 29.9 bits (68), Expect = 0.11
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAM 107
S + +R L V E+ + FS + V A ++F + A+
Sbjct: 6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK------LKDYAFIHFDERDGAV 59
Query: 108 QAMSK 112
+AM +
Sbjct: 60 KAMEE 64
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 29.1 bits (66), Expect = 0.22
Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 5/62 (8%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
S G + + LP E++I F V ++ + V+ A
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKV-LECDIIKNY----GFVHIEDKTAAED 57
Query: 109 AM 110
A+
Sbjct: 58 AI 59
>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
Length = 114
Score = 29.1 bits (66), Expect = 0.27
Identities = 8/55 (14%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
LP ++E+++ + P V+ + + +G G + E +
Sbjct: 32 NLPLSMDEQELENMLKPFGQVISTRI-LRDSSGTSRGVGFARMESTEKCEAVIGH 85
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 29.1 bits (65), Expect = 0.31
Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 54 HHTVHMRGLPFRVNEKDIV---DFFSP---VVPVYVDINYKNG---RPSGEADVYFATHE 104
+ V + GL R+ + +++ ++F + V ++ + PS A V + E
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 105 DAMQAMSK-DRTNIRHRYI 122
DA++A+ + + R +
Sbjct: 75 DALRAIQCVNNVVVDGRTL 93
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 28.2 bits (64), Expect = 0.32
Identities = 11/66 (16%), Positives = 22/66 (33%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL +D+ +F V + + R G V F + + + I
Sbjct: 6 GLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEI 65
Query: 118 RHRYIE 123
++ +E
Sbjct: 66 NNKMVE 71
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 27.8 bits (63), Expect = 0.49
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
L V+++ + + F + +V + + G G V F + +DA AM
Sbjct: 8 DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
>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
Length = 115
Score = 28.1 bits (63), Expect = 0.56
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 62 LPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
LP ++D++ F P VV V I+ + V + A A+
Sbjct: 33 LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 28.1 bits (63), Expect = 0.58
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
H V + L + +DI F+P + V + G+ G V F DA
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 109 AMS 111
A+
Sbjct: 73 AIQ 75
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 28.2 bits (63), Expect = 0.62
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+P V+E + F + V + + + + G V F + A QA++
Sbjct: 49 YIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 28.2 bits (63), Expect = 0.71
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 33 PGGFAGPRPGDRWVNESSGPGHH-TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGR 91
G GP E P T+++ G + + FSP + +D++ R
Sbjct: 17 RGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNI-IDLSMDPPR 73
Query: 92 PSGEADVYFATHEDAMQAM 110
A V + E A QA+
Sbjct: 74 --NCAFVTYEKMESADQAV 90
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 27.1 bits (61), Expect = 0.90
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L + + + + FS V V + + + +P G V E +A++K
Sbjct: 8 NLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
>2g23_A PHS, phenoxazinone synthase; copper, metalloprotein, laccase,
multicopper oxidase, hexamer; 2.30A {Streptomyces
antibioticus} PDB: 3gyr_A
Length = 612
Score = 28.4 bits (62), Expect = 1.0
Identities = 16/125 (12%), Positives = 29/125 (23%), Gaps = 4/125 (3%)
Query: 1 MYDANTTTTTTTGANRFGGGRGCFNNDRWNDRPGGFAGPRPGD--RWVNESSGPGHHTVH 58
D G + G G +W + P H +H
Sbjct: 438 PADVQVPAEGVIQVTGADGRTKTYRRTAATFNDGLGFTIGEGTHEQWTFLNLSPILHPMH 497
Query: 59 MRGLPFRVNEKDIVD--FFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
+ F+V +D D F + + H+D Q
Sbjct: 498 IHLADFQVLGRDAYDASGFDLALGGTRTPVRLDPDTPVPLAPNELGHKDVFQVPGPQGLR 557
Query: 117 IRHRY 121
+ ++
Sbjct: 558 VMGKF 562
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 27.3 bits (61), Expect = 1.0
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 3/53 (5%)
Query: 62 LPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
LP + D+ F P V+ V I+ + V F + A A+
Sbjct: 48 LPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 27.2 bits (61), Expect = 1.1
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
GLP++ E+D+ ++FS V+ V V + K G G V F +E ++ MS+
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 26.7 bits (60), Expect = 1.1
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
L + I F+P + V + G+ G V F DA A+
Sbjct: 13 DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 28.1 bits (62), Expect = 1.3
Identities = 31/204 (15%), Positives = 52/204 (25%), Gaps = 95/204 (46%)
Query: 13 GANRFGGGRGCFNN-----DRWNDRPGGFAGPRPGDRWVNESSG----------PGHHTV 57
G+ G G + D W +R D ++ G P + T+
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVW-NR---------ADNHFKDTYGFSILDIVINNPVNLTI 1674
Query: 58 H---MRGLPFRVN-----EKDIVDFFSPVVPVYVDINYK------NGRPSGE-------- 95
H +G R N + IVD ++ +IN G
Sbjct: 1675 HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS-EKGLLSATQFTQ 1733
Query: 96 ---------------------ADVYFATH-----------------EDAMQAMSKDRTNI 117
AD FA H E ++ +
Sbjct: 1734 PALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEV-------V 1786
Query: 118 RHRYIELFLNSSSPRGGVGGSGFS 141
+R + + + PR +G S +
Sbjct: 1787 FYR--GMTMQVAVPRDELGRSNYG 1808
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 26.8 bits (60), Expect = 1.5
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 11/69 (15%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSP-----VVPVYVDINYKNGRPSGEADVYFATH 103
G G+ + ++ L ++ K + D FS V D G V+F T
Sbjct: 2 PLGSGN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENGSKGYGFVHFETQ 55
Query: 104 EDAMQAMSK 112
E A +A+ K
Sbjct: 56 EAAERAIEK 64
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 26.3 bits (59), Expect = 1.7
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL ++ ++ + ++F V V + R G V F + +++ R +
Sbjct: 7 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 66
Query: 118 RHRYIE 123
+ I+
Sbjct: 67 DSKTID 72
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 26.9 bits (60), Expect = 1.7
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 47 NESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVD---INYKNGRPSGEADVYFATH 103
+ SSGP +++ + L V++ + +FF V P + + G G V F
Sbjct: 3 SGSSGP-EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61
Query: 104 EDAMQAM 110
+ +A+
Sbjct: 62 LEQKRAL 68
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 26.4 bits (59), Expect = 1.8
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPV-----VPVYVDINYKNGRPS-GEADVYFAT 102
SSG + ++ L F E+ + FS V + N S G V +
Sbjct: 2 SSGSS--GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
Query: 103 HEDAMQAMSK 112
E A +A+ +
Sbjct: 60 PEQAQKALKQ 69
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 27.8 bits (62), Expect = 1.9
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 79 VPVYVD--INYKNGRPSGEADVY-FATHEDAMQAMSKDRTN 116
+P+Y + IN +G+ G+ D + FA E+A + M++D N
Sbjct: 116 LPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERN 156
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 26.5 bits (59), Expect = 2.2
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL ++ ++ + ++F V V + R G V F + +++ R +
Sbjct: 32 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 91
Query: 118 RHRYIE 123
+ I+
Sbjct: 92 DSKTID 97
>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG,
thermus thermophilus HB8, structural genomics, NPPSFA;
2.30A {Thermus thermophilus}
Length = 268
Score = 26.4 bits (59), Expect = 3.4
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 17/53 (32%)
Query: 60 RGLPFRVNEKDIVDFFSPVVPVYVD--INYKNGRPSGEADVYFATHEDAMQAM 110
G+ R + + + PV VD + G PS A + M
Sbjct: 160 WGVRTRALLELFAREKASLPPVVVDAGL----GLPS-----------HAAEVM 197
>2ory_A Lipase; alpha/beta hydrolase, hydrolase; 2.20A {Photobacterium SP}
Length = 346
Score = 26.7 bits (58), Expect = 3.5
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 12/41 (29%)
Query: 36 FAGPRPGD----RWVNESSGPGHHTVHMRGLPFRVNEKDIV 72
FAGP G+ + ++ G + N DIV
Sbjct: 206 FAGPTAGNADFADYFDDCLGDQCTRI--------ANSLDIV 238
>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 148
Score = 26.3 bits (57), Expect = 3.7
Identities = 14/76 (18%), Positives = 23/76 (30%), Gaps = 5/76 (6%)
Query: 18 GGGRGCFNNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVH-MRGLPFRVNEKDI----V 72
G G R + G AG R + PG+ M+ + N+ +
Sbjct: 16 SHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNL 75
Query: 73 DFFSPVVPVYVDINYK 88
D +V +N
Sbjct: 76 DKPWTLVSEQTRVNAA 91
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 25.7 bits (57), Expect = 4.1
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL F E+ + +++ + V + + R G V F++ + AM+ +I
Sbjct: 34 GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSI 93
Query: 118 RHRYIELFLNSSSPRGGVGGSGFS 141
R +E + R G S
Sbjct: 94 DGRVVE--PKRAVAREESGSGPSS 115
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 25.2 bits (56), Expect = 4.2
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL + ++KD+ D+F+ VV + ++ GR G + F + + + +
Sbjct: 18 GLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRL 77
Query: 118 RHRYIE 123
R I+
Sbjct: 78 DGRVID 83
>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase;
NMR {Thermoplasma acidophilum} PDB: 2k22_A
Length = 90
Score = 25.5 bits (56), Expect = 4.4
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFSPV 78
G++ M+GL + + D +D F PV
Sbjct: 62 GNNITSMKGLDTEIKDDDKIDLFPPV 87
>2zwn_A Two-domain type laccase; muticopper oxidase, oxidoreductase; 1.70A
{Metagenomes}
Length = 339
Score = 26.2 bits (58), Expect = 4.8
Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 9/75 (12%)
Query: 18 GGGRGCFNNDRWNDRPGGFAGP---RPGD----RWVNESSGPGHHTVHMRGLPFRVNEKD 70
G + N + P + GD R+ +G G H +H G V KD
Sbjct: 159 GTPMNVADYFSVNAKSFPLTQPLRVKKGDVVKIRFFG--AGGGIHAMHSHGHDMLVTHKD 216
Query: 71 IVDFFSPVVPVYVDI 85
+ SP V +
Sbjct: 217 GLPLDSPYYADTVLV 231
>2uxt_A Protein SUFI, SUFI; oxidoreductase, periplasmic, cupredoxin-like,
FTS mutant suppressor; 1.90A {Escherichia coli} PDB:
2uxv_A
Length = 451
Score = 26.1 bits (57), Expect = 6.2
Identities = 7/68 (10%), Positives = 17/68 (25%), Gaps = 2/68 (2%)
Query: 3 DANTTTTTTTGANRFGGGRGCFNNDRWNDRPGGFAGPRPGDRWVNESSGPGHHTVHMRGL 62
+ + + G G +R + G H+ G+
Sbjct: 317 EIMAGSPIRSRDISLGDDPGINGQLWDVNRI--DVTAQQGTWERWTVRADEPQAFHIEGV 374
Query: 63 PFRVNEKD 70
F++ +
Sbjct: 375 MFQIRNVN 382
>2j5w_A Ceruloplasmin, ferroxidase; oxidoreductase, plasma protein, copper
transport, copper, transport, polymorphism, glycoprotein,
multi-copper oxidase; HET: NAG; 2.80A {Homo sapiens}
SCOP: b.6.1.3 b.6.1.3 b.6.1.3 b.6.1.3 b.6.1.3 PDB:
1kcw_A*
Length = 1065
Score = 26.1 bits (56), Expect = 6.7
Identities = 11/56 (19%), Positives = 16/56 (28%), Gaps = 7/56 (12%)
Query: 24 FNNDRWNDRPGGFAGP---RPGD----RWVNESSGPGHHTVHMRGLPFRVNEKDIV 72
N R G GD + + HTVH G F+ + +
Sbjct: 956 NKMHAINGRMFGNLQGLTMHVGDEVNWYLMGMGNEIDLHTVHFHGHSFQYKHRGVY 1011
>3tl2_A Malate dehydrogenase; center for structural genomics of infectious
diseases, csgid dehydrogenase, oxidoreductase, citric
acid cycle; 1.70A {Bacillus anthracis}
Length = 315
Score = 25.5 bits (57), Expect = 6.8
Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 13/58 (22%)
Query: 64 FRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRY 121
F + +K++ D V VDI G+A D ++A +
Sbjct: 25 FLLAQKELADV------VLVDIPQLENPTKGKA-------LDMLEASPVQGFDANIIG 69
>2xu9_A Laccase; oxidoreductase, multicopper oxidases; 1.50A {Thermus
thermophilus} PDB: 2xuw_A 2xvb_A 2yae_A 2yaf_A 2yah_A
2yam_A 2yao_A 2yap_A 2yaq_A 2yar_A 4ai7_A
Length = 439
Score = 25.6 bits (56), Expect = 7.6
Identities = 12/55 (21%), Positives = 18/55 (32%), Gaps = 1/55 (1%)
Query: 17 FGGGRGCFNNDRWNDRPGGFAGPRPG-DRWVNESSGPGHHTVHMRGLPFRVNEKD 70
R N ++ R G + W E+ G H H+ PF+V
Sbjct: 331 MMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVG 385
>3g5w_A Multicopper oxidase type 1; two domain, laccase, nitrifier, metal B
protein; 1.90A {Nitrosomonas europaea}
Length = 318
Score = 25.4 bits (56), Expect = 8.5
Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 9/79 (11%)
Query: 14 ANRFGGGRGCFNNDRWNDRPGGFAGP---RPGD----RWVNESSGPGHHTVHMRGLPFRV 66
G F+ N + P + GD R + +G H +H G ++
Sbjct: 154 PGEGGIPGDVFDYYTINAKSFPETQPIRVKKGDVIRLRLIG--AGDHVHAIHTHGHISQI 211
Query: 67 NEKDIVDFFSPVVPVYVDI 85
KD P+ V I
Sbjct: 212 AFKDGFPLDKPIKGDTVLI 230
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.136 0.435
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,513,080
Number of extensions: 145724
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 549
Number of HSP's successfully gapped: 207
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)