RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14476
(303 letters)
>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical
domain, RNA binding protein; NMR {Saccharomyces
cerevisiae} SCOP: a.144.1.1
Length = 92
Score = 122 bits (307), Expect = 2e-35
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 218 QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEH 275
P + Q+Q+Q LGE+L+ + E AGKITGM+L++ E+ +LE
Sbjct: 4 GSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLES 63
Query: 276 NESLKSKVEEAVAVLQAHQAKQAAVKKE 303
+E + +EA A ++ + +Q ++
Sbjct: 64 DELFEQHYKEASAAYESFKKEQEQQTEQ 91
>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding
protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1
Length = 85
Score = 119 bits (301), Expect = 1e-34
Identities = 36/84 (42%), Positives = 51/84 (60%)
Query: 212 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 271
+ Q ST+LA P++QK +LGERL+ I + P A K+TGMLLE+DN E+L
Sbjct: 1 GSSLASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60
Query: 272 MLEHNESLKSKVEEAVAVLQAHQA 295
+L+ L +KV+EA+ VL H
Sbjct: 61 LLDTPGLLDAKVQEALEVLNRHMN 84
>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding
protein; NMR {Triticum aestivum}
Length = 85
Score = 114 bits (287), Expect = 2e-32
Identities = 33/82 (40%), Positives = 55/82 (67%)
Query: 215 VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLE 274
+ ++ LA + P+ Q+ MLGE L+PL+ ++ + A K+TGMLLE+D E+L++LE
Sbjct: 3 LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62
Query: 275 HNESLKSKVEEAVAVLQAHQAK 296
++LK+KV EA+ VL++ Q
Sbjct: 63 SPDALKAKVAEAMEVLRSAQQH 84
>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo
sapiens} SCOP: a.144.1.1 PDB: 3ntw_A
Length = 61
Score = 109 bits (273), Expect = 1e-30
Identities = 30/60 (50%), Positives = 44/60 (73%)
Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 293
+Q LGERL+P +Q M P A KITGMLLE+ A+LL +L +SL+++V+EA+ ++ AH
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 106 bits (267), Expect = 3e-29
Identities = 44/55 (80%), Positives = 50/55 (90%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R++ +S
Sbjct: 48 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPSS 102
>3kuj_A Polyadenylate-binding protein 1; protein-protein complex,
methylation, mRNA processing, mRNA nucleus,
phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo
sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A
2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A
Length = 88
Score = 105 bits (263), Expect = 5e-29
Identities = 66/83 (79%), Positives = 75/83 (90%)
Query: 217 GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 276
PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE
Sbjct: 3 LGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 62
Query: 277 ESLKSKVEEAVAVLQAHQAKQAA 299
ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 63 ESLRSKVDEAVAVLQAHQAKEAA 85
>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 = 104 bits (262), Expect = 1e-26
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIA 62
+DG+ KGF + + + E A +A + +G +G L V+ ++ LA+ +
Sbjct: 221 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQAT 280
Query: 63 NM 64
+
Sbjct: 281 AL 282
Score = 74.6 bits (184), Expect = 1e-15
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
G+SKG+GF + + A +A +++ G+ +G + LYV + A L S+
Sbjct: 132 RTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185
Score = 58.1 bits (141), Expect = 5e-10
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+ KG FV + E+A A+ + + + L V L
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95
>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 = 99.3 bits (248), Expect = 2e-26
Identities = 16/65 (24%), Positives = 33/65 (50%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
+DG+S+G G V F EA +A++ NG+++ +P++V + +R + + Q+
Sbjct: 49 EDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108
Query: 61 IANMR 65
Sbjct: 109 SGPSS 113
>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 = 97.0 bits (242), Expect = 2e-25
Identities = 22/53 (41%), Positives = 29/53 (54%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
+ SK FGFV + +P A A+ MNG IG K L V L + K D K+ +S
Sbjct: 62 QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 92.0 bits (229), Expect = 1e-23
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKEDRKAHLASQ 56
+ G SKG+GFV F+ E +A+TE G + +GSKP+ +++A K R + S
Sbjct: 46 QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESG 100
>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 = 92.1 bits (229), Expect = 2e-23
Identities = 14/56 (25%), Positives = 23/56 (41%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
GRS G V F +A KA+ + G + +P+ + L + D + H
Sbjct: 69 YDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124
>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 = 88.1 bits (219), Expect = 4e-22
Identities = 13/55 (23%), Positives = 22/55 (40%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
G S+G GF S E+ + NG+ I + P A + + + +S
Sbjct: 59 RDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 88.7 bits (219), Expect = 6e-22
Identities = 81/141 (57%), Positives = 92/141 (65%), Gaps = 10/141 (7%)
Query: 159 GPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQ 218
GP G P +Y PQ + AVHVQGQ
Sbjct: 1 GPLGSAAAATPAV----------RTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQ 50
Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE ES
Sbjct: 51 EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 110
Query: 279 LKSKVEEAVAVLQAHQAKQAA 299
L+SKV+EAVAVLQAHQAK+AA
Sbjct: 111 LRSKVDEAVAVLQAHQAKEAA 131
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 87.2 bits (216), Expect = 4e-21
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
GRS G V F +A KA+ + G + +P+ + L + D + H
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177
>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 = 84.6 bits (210), Expect = 5e-21
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
S GFGFV + PE+A KA+ ++ G + L V +++R + +S
Sbjct: 47 LLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97
>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 = 88.5 bits (220), Expect = 1e-20
Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
E + F+ F + + A +A+ +MN ++G++ + V+LA +K
Sbjct: 247 QKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291
Score = 70.0 bits (172), Expect = 5e-14
Identities = 12/55 (21%), Positives = 23/55 (41%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQY 57
S+ F ++ +S E+A V ++NG I L ++ E K ++
Sbjct: 154 RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL 208
Score = 56.1 bits (136), Expect = 3e-09
Identities = 6/45 (13%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
++ F + F+ + A A+T+ + + + V+
Sbjct: 74 ADSLKKNFRFARIEFARYDGALAAITKTHKVVGQ-NEIIVSHLTE 117
>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 = 83.5 bits (207), Expect = 2e-20
Identities = 17/59 (28%), Positives = 38/59 (64%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
+ ++ SKG+GFV F + E A +A+ +MNG ++ + ++V + +++R+A L ++ +
Sbjct: 38 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 96
>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 = 81.6 bits (202), Expect = 8e-20
Identities = 12/54 (22%), Positives = 26/54 (48%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
K + F+ F + A KA+ EMNG+ + + + + A+ + ++ +Q
Sbjct: 44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97
>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 = 80.7 bits (200), Expect = 2e-19
Identities = 15/53 (28%), Positives = 23/53 (43%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL 53
+S + +G FV F AT A+ M G KP+ + A+ D A +
Sbjct: 44 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
>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 = 80.8 bits (200), Expect = 2e-19
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
GRS G V F +A KA+ + NG + +P+ + L
Sbjct: 63 YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
>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 = 84.7 bits (210), Expect = 2e-19
Identities = 17/103 (16%), Positives = 35/103 (33%), Gaps = 4/103 (3%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII----GSKPLYVALAQRKEDRKAHLASQYM 58
+ GR+ G GFV F++ A KA+ +P+ V ++ +D
Sbjct: 132 DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQ 191
Query: 59 QRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQI 101
+ + ++ F T + + + Q Q+
Sbjct: 192 KTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQV 234
Score = 58.2 bits (141), Expect = 5e-10
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
R +GFGF+ S A A E++G I+ S+PL + A
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95
Score = 28.9 bits (65), Expect = 2.1
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 23 KAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
KA+ EM + + A+ K + + A Q
Sbjct: 221 KALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQ 257
>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 = 82.3 bits (204), Expect = 3e-19
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+S+DG+SKG ++ F S +A K + E G I + + + K
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 65.7 bits (161), Expect = 3e-13
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
G ++ FG+V F S E+ KA+ E+ G + + + + ++ +K
Sbjct: 49 RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKV 96
>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 = 84.2 bits (207), Expect = 4e-19
Identities = 27/169 (15%), Positives = 45/169 (26%), Gaps = 2/169 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
+S + +G FV F AT A+ M G KP+ + A+ D A + +++R
Sbjct: 45 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVER 104
Query: 61 IANMRMQQMGQLFQPGSTGGY--FVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQ 118
++ P + T M + PR +P
Sbjct: 105 DRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM 164
Query: 119 TAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ 167
G P + P S P +
Sbjct: 165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLT 213
Score = 51.4 bits (122), Expect = 1e-07
Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQR 45
FV F + +A A + G +I + + ++ A++
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 80.1 bits (198), Expect = 5e-19
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
+ SK FGFV F +P+ A A+ MNG +G+K L V L +
Sbjct: 77 QTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>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 = 80.3 bits (198), Expect = 8e-19
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ ++GR KG F+ + + A KA+ E NG ++ KP+ V A+ ++
Sbjct: 85 LMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQD 135
Score = 30.6 bits (69), Expect = 0.34
Identities = 9/45 (20%), Positives = 12/45 (26%)
Query: 21 ATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
EM I + L R+E + Y N R
Sbjct: 3 LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCR 47
>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 = 76.5 bits (189), Expect = 5e-18
Identities = 16/53 (30%), Positives = 34/53 (64%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
+ G SKG+ F+ F+S + + A+ MNG+ + ++P+ V+ A +K+ + + +S
Sbjct: 43 DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95
>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 = 78.3 bits (194), Expect = 6e-18
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
+ G S+G+GFV F+S ++A A+ M G+ + +PL + A +
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 58.7 bits (143), Expect = 9e-11
Identities = 8/45 (17%), Positives = 21/45 (46%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
++ + FV + +A A+ +NG+ I + + + A + +
Sbjct: 38 NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS 82
>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 = 78.0 bits (193), Expect = 9e-18
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALA 43
DG S+G FV F++ A A+ M+ S P+ V A
Sbjct: 129 RGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 53.4 bits (129), Expect = 6e-09
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+SKG FV F + + A +A ++ + + + + K
Sbjct: 43 PPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEK 89
>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 = 77.2 bits (191), Expect = 2e-17
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALA 43
GR +G FV ++ EEA +A++ +N I GS+PL V LA
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 66.4 bits (163), Expect = 1e-13
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+ G S G+ FV F+S ++ +A+ +NG + +K L V+ A+ +
Sbjct: 40 KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGES 86
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 74.9 bits (185), Expect = 2e-17
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
E+G+SKG G V F SPE A +A MNG + + + V + + +
Sbjct: 41 KMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91
>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 = 74.5 bits (184), Expect = 2e-17
Identities = 16/45 (35%), Positives = 28/45 (62%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
+ G S+G+GFV F+S ++A A+ M G+ + +PL + A + E
Sbjct: 38 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82
>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 = 74.2 bits (183), Expect = 4e-17
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
+G+ K FGFVCF PE + A+ +NG + +P+ V+
Sbjct: 52 REGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 77.4 bits (191), Expect = 5e-17
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
G+ KG+GF+ + + + AV+ MN +G + L V A
Sbjct: 162 TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 64.3 bits (157), Expect = 2e-12
Identities = 13/55 (23%), Positives = 24/55 (43%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
+ KGF FV + PE A A+ +MN ++G + + V + + +
Sbjct: 67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121
>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 = 76.9 bits (190), Expect = 6e-17
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
+ ++ SKG+GFV F + E A +A+ +MNG ++ + ++V + +++R+A L ++
Sbjct: 136 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARA--- 192
Query: 61 IANMRMQQMGQLFQP 75
+
Sbjct: 193 -KEFYPYDVPDYAGS 206
Score = 56.9 bits (138), Expect = 6e-10
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
RS G+ +V F P +A +A+ MN +I KP+ + +QR
Sbjct: 54 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD 95
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 73.5 bits (181), Expect = 6e-17
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
+ FV + E A +AV E+NG + S L V +A+++ + +S
Sbjct: 46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPSS 96
>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 = 73.1 bits (180), Expect = 1e-16
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALAQRKEDR 49
DG SKG FV FSS EA A+ ++G S L V A ++
Sbjct: 51 PDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100
>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 = 73.1 bits (180), Expect = 1e-16
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
G ++ FG+V F S E+ KA+ E+ G + + + + ++ +
Sbjct: 53 RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTRG 100
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 73.1 bits (180), Expect = 1e-16
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
GF FV F E A KA+ E++G+ ++PL V ++ R
Sbjct: 65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
>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 = 73.1 bits (180), Expect = 1e-16
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
GR +G F+ F + E A +A+ +NG + K L + + K+ R +
Sbjct: 64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110
>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 = 73.1 bits (180), Expect = 2e-16
Identities = 14/57 (24%), Positives = 26/57 (45%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
+S+GF F+ F +P +A A +MNG+ + K + V A++ +
Sbjct: 43 RTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPAS 99
>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 = 75.9 bits (186), Expect = 2e-16
Identities = 18/120 (15%), Positives = 37/120 (30%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIA 62
+G+SKGF V S + K + + R + + V ++ + + S+ +
Sbjct: 107 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSG 166
Query: 63 NMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQG 122
M + S + + + + P P+GQT
Sbjct: 167 QMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHH 226
>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 = 71.9 bits (177), Expect = 3e-16
Identities = 13/46 (28%), Positives = 28/46 (60%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ + + FV FS+ E+A +A+ +NG+++ P+ V LA+ + +
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSS 94
>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 = 73.9 bits (182), Expect = 6e-16
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
S G SKG+ F + +A+ +NG +G K L V A
Sbjct: 150 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 195
Score = 60.4 bits (147), Expect = 3e-11
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ + K F F+ F S +E T+A+ +G I + L + +
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPG 93
>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 = 70.7 bits (174), Expect = 4e-15
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALA 43
G S+G GF+ F EA +A+ +NG+ ++P+ V A
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 60.3 bits (147), Expect = 2e-11
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
G+S G+GFV + P++A KA+ +NG + +K + V+ A+
Sbjct: 41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS 85
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 68.1 bits (167), Expect = 1e-14
Identities = 13/46 (28%), Positives = 26/46 (56%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+ + SKGFGFV F + +A +A +++G ++ + + V A +
Sbjct: 62 IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
G SKG+GFV F + + K V + K L + A RK++ +
Sbjct: 43 TDRTGVSKGYGFVSFYNDVDVQKIV--ESQINFHGKKLKLGPAIRKQNLSTYHVQP 96
>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 = 65.4 bits (160), Expect = 7e-14
Identities = 13/51 (25%), Positives = 27/51 (52%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ + SKGFGFV F + +A +A +++G ++ + + V A + +
Sbjct: 48 IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98
>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 = 64.9 bits (159), Expect = 7e-14
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
G+SKG+GFV F + +A A+ +M G+ +G + + A RK
Sbjct: 43 ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 64.7 bits (158), Expect = 2e-13
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
G+SKG+GFV F + +A A+ +M G+ +G + + A RK ++
Sbjct: 54 GKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109
>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 = 65.3 bits (160), Expect = 4e-13
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
S G SKG+ F + +A+ +NG +G K L V A
Sbjct: 130 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 55.3 bits (134), Expect = 1e-09
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
+ K F F+ F S +E T+A+ +G I + L + +
Sbjct: 48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGA 94
>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 = 62.5 bits (153), Expect = 5e-13
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
+ KG+GFV F SP A KAVT + + ++ +
Sbjct: 44 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS 83
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 63.6 bits (155), Expect = 5e-13
Identities = 8/51 (15%), Positives = 19/51 (37%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL 53
+ G V F+S A + V ++ + ++ L + + R +
Sbjct: 43 RTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY 93
>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 = 62.7 bits (153), Expect = 6e-13
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+DG+SKG ++ F S +A K + E G I + + + K +
Sbjct: 48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 63.8 bits (155), Expect = 6e-13
Identities = 9/51 (17%), Positives = 20/51 (39%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ + G ++ F++ E A V G PL + ++ + + A
Sbjct: 65 VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVA 115
>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 = 62.3 bits (152), Expect = 9e-13
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
+E G G V F S +EAT AV ++N R IGS+ + + L
Sbjct: 50 YNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
E RS+GFGFV F + ++A A+ MNG+ + + + V A + D ++
Sbjct: 49 ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
E G SKGFGFV F+S E+A A M I + + A+ K +
Sbjct: 49 ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95
>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 = 61.4 bits (150), Expect = 1e-12
Identities = 14/48 (29%), Positives = 22/48 (45%)
Query: 2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
SKG+ +V F +P+EA KA+ M+G I + + R
Sbjct: 41 MHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 88
>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 = 61.8 bits (151), Expect = 1e-12
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+ GRSKG+GF+ FS E A +A+ ++NG + +P+ V + D
Sbjct: 42 DTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG 88
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
++G+SKG+ F+ F+S E+A +A+ N R I + + + L +
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 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 = 61.4 bits (150), Expect = 2e-12
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+G+SKGF V S + K + + R + + V + + E
Sbjct: 40 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH 86
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+ KGF FV F PE A KA E++G++ + L+V + K++
Sbjct: 45 LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
E + +GF FV F E+A A+ MN + + + V LA+ +++
Sbjct: 49 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97
>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 = 61.6 bits (150), Expect = 3e-12
Identities = 8/68 (11%), Positives = 27/68 (39%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
+ ++G +V + +A AV ++G + ++ L V + + ++
Sbjct: 40 VGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ 99
Query: 61 IANMRMQQ 68
+ ++ +
Sbjct: 100 LKLLKEKY 107
>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 = 61.3 bits (149), Expect = 3e-12
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
E G+ KG V + P A AV +G+ L V+LA++K
Sbjct: 60 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 60.9 bits (148), Expect = 5e-12
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
E G+ KG V F P A A+ +G+ P+ V+ A R+ D
Sbjct: 52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 60.0 bits (146), Expect = 6e-12
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
G+ KG +V + + +A++AV +M+G I + VA++
Sbjct: 55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99
>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 = 59.6 bits (145), Expect = 1e-11
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
E GRSKG+GF+ FS E A KA+ ++NG + +P+ V + D
Sbjct: 63 ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ GRSKG+ F+ F E + AV +NG +GS+ L + +
Sbjct: 39 QTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGV 87
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ KGFGF+ + A A E++ + K L V A +
Sbjct: 49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94
>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 = 60.1 bits (146), Expect = 2e-11
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
+S+G+GFV F S A +A+ +NG I +K L VALA R
Sbjct: 81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGI 128
>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 = 59.9 bits (145), Expect = 3e-11
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
S+GF FV F +A A+ M+G ++ + L V +A+ +H
Sbjct: 107 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156
>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 = 58.1 bits (141), Expect = 3e-11
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
+E G G V F S +EAT AV ++N R IGS+ + ++
Sbjct: 50 YNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
G+SKGF F+ F E+A +A+ ++G L V A+ +
Sbjct: 52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 12/47 (25%), Positives = 19/47 (40%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+GF FV F +A A M+G + + L V +A+
Sbjct: 50 HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
+ RS+GF FV F + ++A +A NG + + + V+
Sbjct: 52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>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 = 58.0 bits (141), Expect = 4e-11
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
E G+ KG+GF + E A A+ +NGR + L V A +++++
Sbjct: 45 ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92
>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 = 57.2 bits (139), Expect = 6e-11
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
+ +SKG F+ F + A +N + + + + ++A
Sbjct: 53 DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>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 = 58.7 bits (142), Expect = 8e-11
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
G SKG+ V + + ++A A +NG I + + V K ++
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRV 157
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 57.8 bits (140), Expect = 8e-11
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
S+GF FV F +A A+ M+G ++ + L V +A+ +H
Sbjct: 84 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133
>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 = 56.4 bits (137), Expect = 9e-11
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
E + +GF FV F E+A A+ MN + + + V LA+
Sbjct: 44 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
G SKG+ V + + ++A A +NG I + + V K ++
Sbjct: 63 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>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 = 56.7 bits (137), Expect = 2e-10
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+ FV + E A +AV E+NG + S L V +A+++
Sbjct: 71 PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 111
>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 = 56.6 bits (137), Expect = 2e-10
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 6/52 (11%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMN------GRIIGSKPLYVALAQRKEDRK 50
SKG F F + E A K + + G + + L V LA +++
Sbjct: 54 EHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
G+ +G+GFV F S E+A A+ M+ + KP+ V A +
Sbjct: 52 VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 55.5 bits (134), Expect = 2e-10
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK 36
EDG++KG+ F+ ++SP A AV +G + +
Sbjct: 40 PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75
>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 = 56.2 bits (136), Expect = 2e-10
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRKEDRKAHLAS 55
G +GFGFV F + ++A KA + + + + L + A + ++ +S
Sbjct: 55 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
>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 = 55.8 bits (135), Expect = 2e-10
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
E G+ KG V F P A A+ +G+ P+ V+ A
Sbjct: 58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 56.9 bits (137), Expect = 3e-10
Identities = 11/48 (22%), Positives = 24/48 (50%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+G+SKG+ V +S K + + G+++ + + V A R+ +
Sbjct: 94 ANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141
>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 = 56.3 bits (136), Expect = 3e-10
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
+ RS+GF FV F + ++A +A NG + + + V + ++ H
Sbjct: 83 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT---KRPH 129
>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 = 55.4 bits (134), Expect = 4e-10
Identities = 14/50 (28%), Positives = 22/50 (44%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
KG+ FV FS+ E A A+ +NG I + + D + +S
Sbjct: 59 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 55.1 bits (133), Expect = 4e-10
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA-----LAQRKEDRKA 51
KG FV F S E A K V E G+ L + A++ E+RK
Sbjct: 47 LHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKDDYFAKKNEERKQ 99
>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 = 55.5 bits (134), Expect = 6e-10
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
G KG+ V + + +EA A+ +NG+ + +P+ V + K
Sbjct: 59 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGK 108
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 55.6 bits (134), Expect = 7e-10
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
E + +GF FV F E+A A+ MN + + + V LA
Sbjct: 100 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 53.8 bits (130), Expect = 9e-10
Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKEDRKA 51
G+ FV + A +A+ ++G++ + K + V + K+ R +
Sbjct: 41 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSS 88
>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 = 54.2 bits (131), Expect = 9e-10
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
S R KGFG+ F + A+ +N +G+K + V +A + +D+
Sbjct: 50 PSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK 97
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 54.3 bits (131), Expect = 9e-10
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK 36
EDG++KG+ F+ ++SP A AV +G + +
Sbjct: 56 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89
>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 = 53.8 bits (130), Expect = 1e-09
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
R KGFG+ F + A+ +N +G++ + V +A + +D
Sbjct: 56 NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 53.8 bits (130), Expect = 1e-09
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
G KG+ V + + +EA A+ +NG+ + +P+ V +
Sbjct: 60 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 53.4 bits (129), Expect = 2e-09
Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+ + KGF +V F + +A+ +G ++G + L V +A+ ++ K
Sbjct: 51 DTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDK 97
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 53.1 bits (128), Expect = 2e-09
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGR----IIGSKPLYVALAQR 45
+++GF FV SS +A++ + + I K + V A+
Sbjct: 50 QQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>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 = 52.2 bits (126), Expect = 4e-09
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
E + KGFGFV E ++A+ +++ + + V A K+
Sbjct: 38 ETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSL 83
>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 = 51.4 bits (124), Expect = 6e-09
Identities = 10/44 (22%), Positives = 22/44 (50%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
K + FV +A A+ ++NG+ + K + V L+ + + +
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
>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 = 51.9 bits (125), Expect = 6e-09
Identities = 14/43 (32%), Positives = 19/43 (44%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+ FV F +A A+ MNGR I K + V A +K
Sbjct: 55 DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97
>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 = 52.3 bits (126), Expect = 6e-09
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
RSKG +V F + A+ + G+ + P+ V +Q +++R +
Sbjct: 62 NSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLS 109
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 51.7 bits (124), Expect = 6e-09
Identities = 10/47 (21%), Positives = 21/47 (44%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
V +SS ++A +A+ ++NG + + L VA + +
Sbjct: 50 TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
>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 = 51.7 bits (124), Expect = 8e-09
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
GR+ G G V F SP++ +A+ + N ++ + + V+ A ++ A
Sbjct: 49 KDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAA 98
>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 = 51.0 bits (123), Expect = 8e-09
Identities = 8/43 (18%), Positives = 16/43 (37%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
K +GFV A A+ ++ + + V ++ K
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKAS 84
>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 = 51.7 bits (124), Expect = 1e-08
Identities = 8/60 (13%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
+ +G+ G V F + ++A K+ ++ + + + +V + ++ R+ +
Sbjct: 50 VDNNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGK 108
>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 = 53.4 bits (128), Expect = 1e-08
Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 3/97 (3%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
K V + +A A++ +NG + KP+ + L++ + + Q Q +
Sbjct: 39 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR-EGQEDQGLTKDY 97
Query: 66 MQQMGQLFQPGSTGGYFVPTLPQPQRFYG--PTQMTQ 100
F+ + + P P +++
Sbjct: 98 GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSE 134
Score = 51.4 bits (123), Expect = 4e-08
Identities = 7/42 (16%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQRK 46
+ + + S EEA +A+ +++ + + L V+ ++
Sbjct: 156 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197
>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 = 51.2 bits (123), Expect = 1e-08
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALAQRKEDRKA 51
G KG F+ + E A KA + ++ + ++P+ V A + +
Sbjct: 50 FTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101
>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 = 50.9 bits (122), Expect = 1e-08
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ GRS G FV F+S E A KA+ + + IG + + + + R E R +
Sbjct: 50 VDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99
>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 = 52.7 bits (127), Expect = 1e-08
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
G+ +GF FV F + K V + V A K++ + +SQ
Sbjct: 141 GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMASASSSQ 193
Score = 48.1 bits (115), Expect = 5e-07
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI 61
RS+GFGFV +++ EE A+ + + + A +ED + A +++I
Sbjct: 52 KRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI 107
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 9/43 (20%), Positives = 19/43 (44%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
K + FV E+A +A+ ++ K ++V L+ +
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA 86
>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 = 52.8 bits (126), Expect = 2e-08
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII----GSKPLYVALA 43
S G + + S +A + + +N + G P + L
Sbjct: 158 FSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204
Score = 46.2 bits (109), Expect = 3e-06
Identities = 6/87 (6%), Positives = 20/87 (22%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRM 66
G V + +A+T +N + + + V ++++ +
Sbjct: 41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDF 100
Query: 67 QQMGQLFQPGSTGGYFVPTLPQPQRFY 93
+ +
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLH 127
>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 = 50.6 bits (121), Expect = 3e-08
Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+G++ G GFV F + + A+ + + +G++ + V +K +
Sbjct: 60 YGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEK 109
>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 = 51.3 bits (123), Expect = 3e-08
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ-RI 61
+ GF FV + S +A A+ +NG + + + ++ + QY + R
Sbjct: 76 MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR-----QYGRGRS 130
Query: 62 ANMRMQQMGQLFQPGSTGGY 81
+ Q + G GGY
Sbjct: 131 GGQVRDEYRQDYDAGR-GGY 149
>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 = 49.6 bits (119), Expect = 4e-08
Identities = 11/46 (23%), Positives = 14/46 (30%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
F FV F P +A AV +G L V +
Sbjct: 57 RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102
>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 = 49.0 bits (118), Expect = 4e-08
Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
G KGF ++ FS E ++ ++ + + + V +
Sbjct: 43 FSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR 83
>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 = 49.3 bits (118), Expect = 4e-08
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ DGR G V F++ E+A A+ + + + + + L +
Sbjct: 48 IGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGTSGS 97
>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 = 50.2 bits (120), Expect = 5e-08
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI 61
DGR G V F++ EEA A+ + + + + + L +SQ MQ +
Sbjct: 81 PDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGM 138
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 49.5 bits (118), Expect = 6e-08
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 11/70 (15%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
DGR G FV F+ E A A+ + ++G + + + + E +Q+
Sbjct: 61 TYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAE----------VQQ 109
Query: 61 IANMRMQQMG 70
+ N G
Sbjct: 110 VLNRFSSASG 119
>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 = 50.2 bits (121), Expect = 6e-08
Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+ G+S+GFGFV + S + + + + + + A+ +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPR 166
Score = 47.1 bits (113), Expect = 1e-06
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
GRS+GFGF+ F P + V + I+ K + A ++++
Sbjct: 42 GRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQ 84
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 48.6 bits (116), Expect = 8e-08
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII-GSKPLYVALAQRKE 47
G++KGF FV S +A K + +G+ + L++ + E
Sbjct: 49 ATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVE 94
>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 = 48.6 bits (116), Expect = 9e-08
Identities = 12/44 (27%), Positives = 17/44 (38%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
G G V F E+ T AV +++ S A + K D
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
G G+ FV F+ A K + ++NG+ +
Sbjct: 49 GIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF 86
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
+ G G+ FV FS+ EE +A+ + N +G + + V +
Sbjct: 43 RNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEVFREKSGP 88
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
G SKGFGFV F+ E K +++ + +I + L K+ + +
Sbjct: 54 GHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDS 98
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 47.9 bits (114), Expect = 1e-07
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+ F+ + A +AV+ + G +G+ L VALA+++ D+
Sbjct: 54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
R +GFGF+ F + +AV M+ I K + V A+ ++ + +
Sbjct: 49 QRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKSS 94
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 48.1 bits (115), Expect = 1e-07
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
G+S+G+GFV + A +A + N I G + V LA ++
Sbjct: 56 GKSRGYGFVTMADRAAAERACKDPNPIIDG-RKANVNLAYLGAKPRSL 102
>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 = 47.8 bits (114), Expect = 2e-07
Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
G KG+ ++ F+ AV M+ + + + V +
Sbjct: 73 FSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNM 116
>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 = 47.5 bits (113), Expect = 3e-07
Identities = 13/46 (28%), Positives = 18/46 (39%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
D G G V F E+ T AV +++ S A + K D
Sbjct: 47 DVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 92
>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 = 47.5 bits (113), Expect = 3e-07
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
+V + E+A +A+ +N ++ + L +L K
Sbjct: 61 GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTK 101
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 47.4 bits (113), Expect = 3e-07
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
KG+ FV +S+ A AV NGR++ + L + +A + +
Sbjct: 61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDR 104
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 46.8 bits (112), Expect = 3e-07
Identities = 8/44 (18%), Positives = 18/44 (40%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
FGF+ F +P+ A+ + + K L + ++ +
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQ 87
>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 = 46.9 bits (112), Expect = 3e-07
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALAQRK 46
+ F ++ + S + A A +M G +G + L V A+
Sbjct: 51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 46.5 bits (111), Expect = 4e-07
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
GF FV F P +A AV ++G++I + V L+ R
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR 78
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 45.5 bits (109), Expect = 5e-07
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 5 GRSKGFGFVCFSSPEEATKAVT----EMNGRII 33
R +GFGFV F S + K E+N +++
Sbjct: 38 NRHRGFGFVTFESEDIVEKVCEIHFHEINNKMV 70
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 46.7 bits (111), Expect = 5e-07
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 5/47 (10%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
G G + F S E +A+ +N + V + D
Sbjct: 62 NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV-----ERDD 103
>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 = 46.8 bits (111), Expect = 5e-07
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
+ +G+ G FV F+S E A KA+ + IG + + V + ++E
Sbjct: 77 VDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEE 122
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 45.6 bits (109), Expect = 5e-07
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 5 GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSK 36
RS+GFGFV F K + E++ + I K
Sbjct: 39 KRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 46.1 bits (110), Expect = 6e-07
Identities = 6/34 (17%), Positives = 13/34 (38%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
KG F+ + + E+A + + + L
Sbjct: 60 YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 47.2 bits (112), Expect = 6e-07
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
GF FV F P +A AV E++GR + + V L+ +
Sbjct: 108 NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148
>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 = 46.3 bits (110), Expect = 7e-07
Identities = 11/41 (26%), Positives = 13/41 (31%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
V F P EA KA + PLY+ A
Sbjct: 44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG 84
>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 = 45.6 bits (108), Expect = 1e-06
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKEDRKAHLASQYM 58
+++GF FV + S A A ++ + + V A+ + D +
Sbjct: 49 MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVS 104
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEM----NGRIIGSK 36
GRS+GFGF+ F K + + +GR+I K
Sbjct: 50 GRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK 85
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 11/44 (25%), Positives = 16/44 (36%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
R+K FV + E+A A+ + K L V L
Sbjct: 35 YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78
>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 = 46.9 bits (111), Expect = 2e-06
Identities = 13/93 (13%), Positives = 31/93 (33%), Gaps = 9/93 (9%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
K V + +A A++ +NG + KP+ + L++ + +
Sbjct: 70 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR---------EGQE 120
Query: 66 MQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQM 98
Q + + + + P Q + P+
Sbjct: 121 DQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 153
Score = 46.1 bits (109), Expect = 4e-06
Identities = 7/42 (16%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQRK 46
+ + + S EEA +A+ +++ + + L V+ ++
Sbjct: 187 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 44.5 bits (106), Expect = 2e-06
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+S+GFGFV F P + + + + + + +
Sbjct: 55 NQSRGFGFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPRGMQPS 100
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 44.2 bits (105), Expect = 2e-06
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
FGF+ F +P+ A+ + + K L + ++
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92
>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 = 43.6 bits (104), Expect = 3e-06
Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 4/33 (12%)
Query: 5 GRSKGFGFVCFSSPEEATKAVT----EMNGRII 33
+ +GF F+ F E K + +
Sbjct: 38 NKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKC 70
>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 = 44.5 bits (105), Expect = 3e-06
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ +GR G FV S ++ A+ + + +G + + V + R E
Sbjct: 54 YTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKSHRTEMDWV 103
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 44.1 bits (104), Expect = 3e-06
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
G +V F E+A KAV ++N R +P++ L
Sbjct: 63 LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
>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 = 43.8 bits (104), Expect = 5e-06
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 5 GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSKPLYVALAQRKEDR 49
RS+GFGFV F K + E++ + I K +A + +
Sbjct: 64 KRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK-----VAFPRRAQ 107
>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 = 43.7 bits (103), Expect = 5e-06
Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
++ DG+ +G + S ++ KA+ E + +G + + V ++
Sbjct: 48 LNRDGKRRGDALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEINNEDVDAL 97
>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 = 45.2 bits (106), Expect = 6e-06
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 1/50 (2%)
Query: 2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ KG FV F S E A K V + L + +K
Sbjct: 144 TLHKAFKGSIFVVFDSIESAKKFVETPGQKYKE-TDLLILFKDDYFAKKN 192
>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 = 43.4 bits (103), Expect = 6e-06
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 5 GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSKPLYVALAQRKEDRKA 51
RS+GFGFV FSS E A+ ++GR++ K A +E+ +
Sbjct: 66 KRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR-----AVAREESGS 111
>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 = 42.6 bits (100), Expect = 1e-05
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIG-----SKPLYVALAQR 45
+K + F + + EE+ +A +NG+ + LY+ ++
Sbjct: 61 PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+ +GR G FV S ++ A+ + + +G + + V + R E
Sbjct: 81 YTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWV 130
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 41.8 bits (99), Expect = 2e-05
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
+ F FV F+ + A E II ++++ A+ K ++
Sbjct: 46 PFRAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPKHNKL 88
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 44.8 bits (105), Expect = 3e-05
Identities = 26/151 (17%), Positives = 38/151 (25%), Gaps = 5/151 (3%)
Query: 87 PQPQRFYG----PTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVI 142
PQ Q YG P Q P+ AA M +P + Q +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 143 RGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGT-QPQAQIG 201
A + A V + P+ P QP A +G
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129
Query: 202 GIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQ 232
+ + + + P T L P
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160
Score = 41.0 bits (95), Expect = 4e-04
Identities = 27/185 (14%), Positives = 49/185 (26%), Gaps = 5/185 (2%)
Query: 55 SQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMR 114
S + +R+ Q GQ P F+P PQ G + P A P M
Sbjct: 2 SHHKKRVYPQAQLQYGQNATPLQQPAQFMP--PQDPAAAGMSYGQMGMPPQ--GAVPSMG 57
Query: 115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPG-PAS 173
+ Q S + + Q + + G P+Q P +
Sbjct: 58 QQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117
Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQE 233
A G+ + + P + + P + P ++ +
Sbjct: 118 APAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNA 177
Query: 234 QKQML 238
+
Sbjct: 178 SPDYI 182
Score = 35.2 bits (80), Expect = 0.029
Identities = 21/168 (12%), Positives = 33/168 (19%), Gaps = 5/168 (2%)
Query: 49 RKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWA 108
++ + +Q +QQ Q P + G + Q
Sbjct: 6 KRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMG-QQQFLTP 64
Query: 109 AAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQA 168
A Q+ A N + P G + A
Sbjct: 65 AQEQLHQQIDQATTSMNDMHLHNVPLVDPNA----YMQPQVPVQMGTPLQQQQQPMAAPA 120
Query: 169 PGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQ 216
G S + YP+ P P V
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168
>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 = 40.3 bits (95), Expect = 4e-05
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYV 40
+ + F+ F++ + A A + N I+ + L V
Sbjct: 46 QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 81
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 41.2 bits (97), Expect = 4e-05
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
D G V F PEEA + ++GR G + + D
Sbjct: 60 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD 104
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 40.6 bits (95), Expect = 7e-05
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 6 RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
+ K F+ ++ E A V ++ +P+Y+ + KE + +Q
Sbjct: 50 KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 39.9 bits (94), Expect = 7e-05
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
+ F FV F+ + A II ++++ A+ K +
Sbjct: 39 KPFRAFAFVTFADDQIAQSLC--GEDLIIKGISVHISNAEPKHNS 81
>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 = 39.7 bits (93), Expect = 9e-05
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
+ K F F+ F S +E T+A+ +G I + L +
Sbjct: 50 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI 84
>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 = 40.3 bits (94), Expect = 9e-05
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 6 RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
+ K F+ ++ E A V ++ +P+Y+ + KE + +Q
Sbjct: 65 KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 39.4 bits (92), Expect = 2e-04
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
+ G FV F+S + KA+ + GR ++ +
Sbjct: 54 VEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKE 47
+ K F+ ++ E A V + ++P+Y+ + KE
Sbjct: 49 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 37.8 bits (88), Expect = 4e-04
Identities = 9/44 (20%), Positives = 13/44 (29%), Gaps = 2/44 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKE 47
K V F A AV I P +V + ++
Sbjct: 55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif,
RRM, RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 37.4 bits (87), Expect = 8e-04
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGR 31
ED FV FS E KA+ +NGR
Sbjct: 65 EEDAEIIVKIFVEFSIASETHKAIQALNGR 94
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 37.3 bits (87), Expect = 9e-04
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 9 GFGFVCFSSPEEATKAVTEMNGR 31
G +V S A AV ++GR
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGR 78
>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 = 39.6 bits (92), Expect = 0.001
Identities = 48/312 (15%), Positives = 86/312 (27%), Gaps = 118/312 (37%)
Query: 16 SSP------EEATKAVTEMNG----RIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
+S A + G I+ + P+ + + H + +RI
Sbjct: 1638 TSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTI---------HFGGEKGKRIRENY 1688
Query: 66 MQQMGQLFQPGSTGGYFV-PTLPQPQR---FYGP------TQMTQIRPQP-----RWAAA 110
+ + G + + + F TQ TQ P AA
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ----PALTLMEKAAF 1744
Query: 111 PQMRPSGQTAQGFPNIPQFR--------SAPRASTG-----QTV----IRG---ANMSAR 150
++ ++G +A + V RG R
Sbjct: 1745 EDLK-----SKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR 1799
Query: 151 PITGQSTMGPRGGGPMQAPGPASVSA-------------AGRQTGG------YNKYPVRN 191
G+S G M A P V+A G++TG YN
Sbjct: 1800 DELGRSNYG------MIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN-----V 1848
Query: 192 PGTQPQAQIGGIQPAAAG-VQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMY 250
Q AAG ++A+ + +T+ +L + Q+ + L + +
Sbjct: 1849 ENQ----QY-----VAAGDLRAL-----DTVTN-VLNFIKLQKID------IIELQKSLS 1887
Query: 251 PELAGKITGMLL 262
E ++ G L
Sbjct: 1888 LE---EVEGHLF 1896
Score = 32.3 bits (73), Expect = 0.21
Identities = 24/125 (19%), Positives = 41/125 (32%), Gaps = 39/125 (31%)
Query: 198 AQIGGIQPAAAGVQAVHVQGQ---------EPLTSTM-LAAAQPQEQKQMLG-ERLFPLI 246
A + + + V+ V +G E S + A P E L ++
Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVV 1830
Query: 247 QRMYPELAGKITGMLLEIDNAELLYMLEHNES---------LKSKVEEAVAVLQAHQAKQ 297
+R GK TG L+EI N +N L++ ++ VL
Sbjct: 1831 ER-----VGKRTGWLVEIVN--------YNVENQQYVAAGDLRA-LDTVTNVL-----NF 1871
Query: 298 AAVKK 302
++K
Sbjct: 1872 IKLQK 1876
Score = 30.4 bits (68), Expect = 0.96
Identities = 40/277 (14%), Positives = 80/277 (28%), Gaps = 89/277 (32%)
Query: 35 SKPLYVALAQRKEDRKAHLASQYM--QRIANMRMQQMGQLFQPGSTG---GYFVPTLPQP 89
S PL + + Q LA Y+ ++ ++ + G+TG G
Sbjct: 237 SCPL-IGVIQ--------LA-HYVVTAKLLGFTPGELRSYLK-GATGHSQGLVTAVAIAE 285
Query: 90 ----QRFYGPTQ-----MTQI--RPQ---PRWAAAPQM-RPSGQTAQGFPNIPQF--RSA 132
+ F+ + + I R P + P + S + +G P+ P +
Sbjct: 286 TDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS-PMLSISNL 344
Query: 133 PRASTGQTVIRGANMSARPITGQSTM----GPRG---GGPMQAPGPAS---VSAAGRQTG 182
+ Q + N P Q + G + GP P S ++ R+
Sbjct: 345 TQEQV-QDYVNKTNSHL-PAGKQVEISLVNGAKNLVVSGP-----PQSLYGLNLTLRK-- 395
Query: 183 GYNKYPVRNPGTQPQAQIGGIQ----------------------PAAAGVQAVHVQGQEP 220
+ P Q++I + PA+ + V+
Sbjct: 396 ------AKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVS 449
Query: 221 LTSTMLA--------AAQPQEQKQMLGERLFPLIQRM 249
+ + + + + ER+ I R+
Sbjct: 450 FNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRL 486
>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 = 36.3 bits (84), Expect = 0.002
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKE 47
K V F + + A + VT I + + + K
Sbjct: 49 PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 36.1 bits (83), Expect = 0.002
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 13 VCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLA 54
+ FS+P A A ++ K + + AQ +HLA
Sbjct: 51 INFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 35.8 bits (83), Expect = 0.003
Identities = 8/47 (17%), Positives = 14/47 (29%), Gaps = 1/47 (2%)
Query: 4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
D F V + + +G L V ++KE +
Sbjct: 41 DKDKGVFAIVEMGDVGAREAVL-SQSQHSLGGHRLRVRPREQKEFQS 86
>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 = 35.7 bits (82), Expect = 0.003
Identities = 12/51 (23%), Positives = 22/51 (43%)
Query: 1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
+S + V + ++A AV ++ IGSK + V+LA +
Sbjct: 45 LSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPSS 95
>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 = 37.1 bits (85), Expect = 0.006
Identities = 9/74 (12%), Positives = 24/74 (32%)
Query: 3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIA 62
G+ +G+ F+ + + A +G+ I + + V + + + +
Sbjct: 139 RSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGG 198
Query: 63 NMRMQQMGQLFQPG 76
R + G
Sbjct: 199 TRRGGADVNIRHSG 212
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 33.3 bits (76), Expect = 0.024
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
F+ F E A KAV ++NGR G + +
Sbjct: 57 VRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 32.7 bits (74), Expect = 0.025
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
++G +++ EEA KA +N ++ + ++ E
Sbjct: 42 NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENE 82
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 31.2 bits (70), Expect = 0.10
Identities = 5/42 (11%), Positives = 15/42 (35%)
Query: 7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
+ + F + + A +A M + + V+ + +
Sbjct: 45 TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRE 86
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 30.7 bits (69), Expect = 0.19
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKEDRK 50
R K F+ + E+A V + + V L+++ +
Sbjct: 60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLV 106
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 31.3 bits (70), Expect = 0.28
Identities = 10/44 (22%), Positives = 15/44 (34%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
SK GFV F A A M+ + + +R+
Sbjct: 177 ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 29.5 bits (66), Expect = 0.48
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 6 RSKGFGFVCFSSPEEATKAVT----EMNGRIIGSKP 37
R G + F P +A + + E++G + +P
Sbjct: 45 RLGCGGVLTFREPADAERVLAQADHELHGAQLSLRP 80
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 30.7 bits (69), Expect = 0.58
Identities = 20/90 (22%), Positives = 28/90 (31%), Gaps = 4/90 (4%)
Query: 131 SAPRASTGQTVIRGANMSARPITGQSTMGPRGGG-PMQAPGPASVSAAGRQTGGYNKYPV 189
A ++ + M + Q+ P+G P Q P G GY P
Sbjct: 361 DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGY---PP 417
Query: 190 RNPGTQPQAQIGGIQPAAAGVQAVHVQGQE 219
+ PQ P AA Q V Q +
Sbjct: 418 QGYPPPPQGAPPQGAPPAAPPQGVDNQAYQ 447
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 29.8 bits (66), Expect = 0.99
Identities = 18/125 (14%), Positives = 38/125 (30%), Gaps = 3/125 (2%)
Query: 87 PQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGAN 146
+ ++ +M+ I Q++ + + + Q + G RG +
Sbjct: 199 SRDIQYLPILKMSTITGPVPREFKSQLQEAPLEWKALLEMQQTKMVLETFGGDGHARGDS 258
Query: 147 MSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPA 206
+S + G + P + G + G PG+ G +P
Sbjct: 259 VSQGTGLAPGSPRKPGTSSIGNVNP---GSYGPGSSGTWNPGRPEPGSAGTWNPGRPEPG 315
Query: 207 AAGVQ 211
+AG
Sbjct: 316 SAGTW 320
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.9 bits (64), Expect = 1.1
Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRKE 47
R+ V F S A KA +NG I G L + A+
Sbjct: 60 RNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 103
>1b3q_A Protein (chemotaxis protein CHEA); histine kinase, signal
transduction, multi-domai protein, transferase; 2.60A
{Thermotoga maritima} SCOP: a.30.2.1 b.40.7.1 d.122.1.3
PDB: 2ch4_A* 3ur1_A
Length = 379
Score = 29.8 bits (68), Expect = 1.1
Identities = 5/41 (12%), Positives = 15/41 (36%), Gaps = 8/41 (19%)
Query: 42 LAQRKEDRKAHLASQYMQRIA--------NMRMQQMGQLFQ 74
++ ++ + ++ RI +RM + +F
Sbjct: 31 TLKKYNIKELDESLSHLSRITLDLQNVVMKIRMVPISFVFN 71
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 29.0 bits (65), Expect = 1.4
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 12 FVCFSSPEEATKAVTEMNGRIIGSK 36
FV FS E KA+ +NGR +
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGR 203
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 29.4 bits (65), Expect = 1.6
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKP 37
+K + F + + EE+ +A +NG+ +
Sbjct: 54 PNKPYSFARYRTTEESKRAYVTLNGKEVVDDL 85
>3e6q_A Putative 5-carboxymethyl-2-hydroxymuconate isomer; structural
genomics, APC7683, isomerase, PSI-2, protein STRU
initiative; HET: GOL IMD; 1.75A {Pseudomonas aeruginosa}
Length = 146
Score = 28.4 bits (63), Expect = 2.0
Identities = 6/34 (17%), Positives = 13/34 (38%)
Query: 231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEI 264
+Q LGE L ++ + + +E+
Sbjct: 94 DAATRQALGESLCEVLAGAVAGGGEEGVQVSVEV 127
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 27.7 bits (61), Expect = 2.4
Identities = 6/44 (13%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRKE 47
++ + ++ P A A ++G+ I L + ++
Sbjct: 64 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 28.0 bits (62), Expect = 5.0
Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 22/115 (19%)
Query: 3 EDGRSKGFGFVCFSSPE-EATKAVTEM---NGRIIGSKPLYVALAQRKEDRKAHLASQYM 58
++ + + FG F+ + V E + + + P ++ + + + L +
Sbjct: 508 QEEKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASES 567
Query: 59 QRIANMRMQQ------------------MGQLFQPGSTGGYFVPTLPQPQRFYGP 95
R + + + Q GY P QPQ +G
Sbjct: 568 LRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGY 622
>3t43_A HIV epitope-scaffold 4E10_1XIZA_S0_006_C; putative
phosphotransferase system, transferase; 1.95A
{Artificial gene}
Length = 162
Score = 27.0 bits (60), Expect = 5.2
Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 225 MLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVE 284
MLA + +L + +IQ + + LL +++ E+ +S+ +++
Sbjct: 89 MLALGNWFDITNVL-WWIMDVIQD--ADFMQQ----LLVMNDDEIY------QSIYTRIS 135
Query: 285 EAVAVLQAHQAKQ 297
EA + H +
Sbjct: 136 EAAGMAGIHFRRH 148
>1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1sms_A
Length = 345
Score = 27.5 bits (61), Expect = 5.3
Identities = 4/20 (20%), Positives = 9/20 (45%)
Query: 51 AHLASQYMQRIANMRMQQMG 70
Y++ +A+ +Q G
Sbjct: 271 LKSIHTYIEFVADGLLQGFG 290
>1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase,
ribonucleotide reductase, dinuclear metal-cluster; 2.2A
{Mus musculus} SCOP: a.25.1.2 PDB: 1h0n_A 1w68_A 1w69_A
1xsm_A 2uw2_A 3hf1_A 2vux_A
Length = 390
Score = 27.6 bits (61), Expect = 6.0
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 51 AHLASQYMQRIANMRMQQMGQLFQPGST 78
L QY++ +A+ M ++G
Sbjct: 318 CTLMKQYIEFVADRLMLELGFNKIFRVE 345
>3cps_A Glyceraldehyde 3-phosphate dehydrogenase; GAPDH, glycolysis,
malaria, structural genomics; HET: NAD; 1.90A
{Cryptosporidium parvum iowa II} PDB: 1vsv_A* 1vsu_A*
3chz_A 3cie_A* 3cif_A* 3sth_A*
Length = 354
Score = 27.5 bits (62), Expect = 6.3
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 251 PELAGKITGM 260
P L GK+TGM
Sbjct: 240 PALNGKLTGM 249
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 27.0 bits (59), Expect = 6.6
Identities = 5/28 (17%), Positives = 13/28 (46%)
Query: 6 RSKGFGFVCFSSPEEATKAVTEMNGRII 33
++ + ++ P A A ++G+ I
Sbjct: 82 NNQFQALLQYADPVSAQHAKLSLDGQNI 109
>1gad_O D-glyceraldehyde-3-phosphate dehydrogenase; oxidoreductase
(aldehyde(D)-NAD+(A)); HET: NAD; 1.80A {Escherichia
coli} SCOP: c.2.1.3 d.81.1.1 PDB: 1dc4_A* 1dc3_A 1dc6_A*
1dc5_A* 1s7c_A* 1gae_O* 2vyn_A* 2vyv_A*
Length = 330
Score = 27.1 bits (61), Expect = 6.8
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 251 PELAGKITGM 260
PEL GK+TGM
Sbjct: 219 PELNGKLTGM 228
>1mxr_A Ribonucleotide reductase R2; radical protein, DI iron,
oxidoreductase; 1.42A {Escherichia coli} SCOP: a.25.1.2
PDB: 1jpr_A 1jqc_A 1xik_A 3uus_E* 1yfd_A 1piy_A 1r65_A
2xof_A* 1biq_B* 1rsv_A 1piz_A 1piu_A 1pim_A 1rsr_A
1biq_A* 1rib_A 1mrr_A 1rnr_A* 1pj0_A 1pj1_A ...
Length = 375
Score = 27.4 bits (61), Expect = 6.8
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 51 AHLASQYMQRIANMRMQQMG 70
+ QY++ I N+RMQ +G
Sbjct: 301 KDILCQYVEYITNIRMQAVG 320
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 26.9 bits (59), Expect = 6.9
Identities = 17/108 (15%), Positives = 25/108 (23%)
Query: 89 PQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMS 148
P P + R P + +G + + T
Sbjct: 115 PAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGG 174
Query: 149 ARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQP 196
P G+ P GP P G G + PG +P
Sbjct: 175 PPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRP 222
>3ids_C GAPDH, glyceraldehyde-3-phosphate dehydrogenase, glycoso;
irreversible inhibitor, protein-ligand complex,X-RAY,
glycol NAD, oxireductase; HET: NAD; 1.80A {Trypanosoma
cruzi} PDB: 1ml3_A* 1qxs_C* 3dmt_A* 1k3t_A* 2x0n_A*
1gga_O* 1i32_A* 1a7k_A* 1i33_A* 1gyp_A* 1gyq_A*
Length = 359
Score = 27.2 bits (61), Expect = 7.5
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 251 PELAGKITGM 260
P GK+TGM
Sbjct: 237 PSTQGKLTGM 246
>3h9e_O Glyceraldehyde-3-phosphate dehydrogenase, testis-; oxidoreductase,
structural genomics, structural genomics CON SGC,
glycolysis, NAD; HET: NAD; 1.72A {Homo sapiens} PDB:
3pfw_O* 2vyn_D* 2vyv_D*
Length = 346
Score = 27.1 bits (61), Expect = 7.6
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 251 PELAGKITGM 260
PEL GK+TGM
Sbjct: 226 PELKGKLTGM 235
>3pym_A GAPDH 3, glyceraldehyde-3-phosphate dehydrogenase 3; NAD(P)-binding
rossmann-fold domain, alpha and beta protein,
oxidoreductase; HET: NAD; 2.00A {Saccharomyces
cerevisiae} PDB: 2i5p_O*
Length = 332
Score = 27.1 bits (61), Expect = 8.0
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 251 PELAGKITGM 260
PEL GK+TGM
Sbjct: 220 PELQGKLTGM 229
>2b4r_O Glyceraldehyde-3-phosphate dehydrogenase; SGPP, structural
genomics, PSI, structural genomi pathogenic protozoa
consortium; HET: NAD AES; 2.25A {Plasmodium falciparum}
SCOP: c.2.1.3 d.81.1.1 PDB: 2b4t_O* 1ywg_O*
Length = 345
Score = 26.8 bits (60), Expect = 8.5
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 251 PELAGKITGM 260
PEL GK+TG+
Sbjct: 233 PELNGKLTGV 242
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1;
ribonucleotide reductase, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A
Length = 419
Score = 26.8 bits (59), Expect = 8.9
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 51 AHLASQYMQRIANMRMQQMG 70
A L +QY++ +A+ + G
Sbjct: 344 ADLMNQYVEFVADRLLVAFG 363
>3e5r_O PP38, glyceraldehyde-3-phosphate dehydrogenase, cytosolic; GAPDH,
RICE, oxidoreductase, cytoplasm, glycolysis, NAD; HET:
NAD; 2.30A {Oryza sativa subsp} PDB: 3e6a_O
Length = 337
Score = 26.8 bits (60), Expect = 9.7
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 251 PELAGKITGM 260
P+L GK+TGM
Sbjct: 224 PDLNGKLTGM 233
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
0.315 0.130 0.374
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: 4,452,338
Number of extensions: 265488
Number of successful extensions: 857
Number of sequences better than 10.0: 1
Number of HSP's gapped: 794
Number of HSP's successfully gapped: 255
Length of query: 303
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 210
Effective length of database: 4,105,140
Effective search space: 862079400
Effective search space used: 862079400
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 (21.6 bits)
S2: 57 (25.7 bits)