RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3343
(274 letters)
>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 = 114 bits (288), Expect = 1e-32
Identities = 51/108 (47%), Positives = 67/108 (62%)
Query: 88 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 147
+ RSK +IL KNLP TL +++ F FG LGRVL+P GIT +VEFL+ +A+
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61
Query: 148 AFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEE 195
AF LAY+KF VPLYLEWAP GVF A +K + ++ E+ E
Sbjct: 62 AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPS 109
Score = 43.6 bits (103), Expect = 5e-06
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
T + KNL + I+ F + G + V +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG 46
>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 = 75.3 bits (185), Expect = 1e-16
Identities = 36/171 (21%), Positives = 63/171 (36%), Gaps = 18/171 (10%)
Query: 99 ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTK 156
+LV NL P R P L LF +GD+ RV + LV+ NQA+ A + L K
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 157 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENV 216
P+ + + +E + + K+ K+ ++
Sbjct: 66 LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI--------- 116
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
P TL++ N+ + +E+ ++ F G + +KD K
Sbjct: 117 -------FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 160
Score = 36.0 bits (83), Expect = 0.006
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 3/74 (4%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 154
+ + N+P DLK LF G + G L++ +A A L
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180
Query: 155 TKFKE-VPLYLEWA 167
E L + ++
Sbjct: 181 HDLGENHHLRVSFS 194
Score = 32.6 bits (74), Expect = 0.080
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 227 DTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKK 263
++ L + NLN T S+ F G + V + K
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
>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 = 73.9 bits (181), Expect = 7e-16
Identities = 36/173 (20%), Positives = 64/173 (36%), Gaps = 18/173 (10%)
Query: 97 RIILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 154
++LV NL P R P L LF +GD+ RV + LV+ NQA+ A + L
Sbjct: 35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 94
Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
K P+ + + +E + + K+ K+ ++
Sbjct: 95 HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF------ 148
Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
P TL++ N+ + +E+ ++ F G + +KD K
Sbjct: 149 ----------PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 191
Score = 35.0 bits (80), Expect = 0.017
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 223 EPEPDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKK 263
++ L + NLN T S+ F G + V + K
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 71
>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 = 66.7 bits (162), Expect = 2e-13
Identities = 19/177 (10%), Positives = 46/177 (25%), Gaps = 16/177 (9%)
Query: 97 RIILVKNLPYRTL-PTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 154
+++V L + + +F +G++ +V +VE A L
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64
Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
+ + + K+ E + ++ ++
Sbjct: 65 NFMFGQKMNVCVS--------------KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST 110
Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
+ + R P L+ N TE++ + G +V
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSS 167
Score = 37.4 bits (86), Expect = 0.002
Identities = 7/39 (17%), Positives = 12/39 (30%), Gaps = 1/39 (2%)
Query: 226 PDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVARKK 263
L + L+ D + F G + V + K
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41
Score = 35.1 bits (80), Expect = 0.013
Identities = 11/72 (15%), Positives = 22/72 (30%), Gaps = 6/72 (8%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKA 147
++ N P + + + G V + GL+E+ K+ A
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 148 AFNSLAYTKFKE 159
L + + K
Sbjct: 181 TLGFLNHYQMKN 192
>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 = 57.3 bits (139), Expect = 5e-11
Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
+ L+IKNLNF++TE++++ F K G I S T+ K G LSM
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSM 50
Score = 36.8 bits (86), Expect = 0.001
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 9/78 (11%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-----PPYGIT----GLVEFLQKNQAKAAF 149
+ +KNL + T LK +F G + + + G VE+ + QA+ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 150 NSLAYTKFKEVPLYLEWA 167
L L + +
Sbjct: 68 KQLQGHTVDGHKLEVRIS 85
>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 = 58.5 bits (142), Expect = 1e-10
Identities = 28/186 (15%), Positives = 53/186 (28%), Gaps = 46/186 (24%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQ 141
A ++R+ V N+P+ + F LG + P +EF
Sbjct: 2 AMARRL-YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
++ A + F+ L + + +
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRP-------------------------HDYQPLPGM 94
Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
E+ VP V V P+ L+I L +D ++ GP+ + +
Sbjct: 95 SENPSVYVPGVVSTVV------PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV- 147
Query: 262 KKDPKS 267
KD +
Sbjct: 148 -KDSAT 152
Score = 41.2 bits (97), Expect = 1e-04
Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 6/78 (7%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ + LP +K L FG L + TGL E++ N A L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 153 AYTKFKEVPLYLEWAPEG 170
+ + L ++ A G
Sbjct: 177 NGMQLGDKKLLVQRASVG 194
>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 = 59.2 bits (144), Expect = 1e-10
Identities = 31/187 (16%), Positives = 50/187 (26%), Gaps = 55/187 (29%)
Query: 90 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKN 143
V + ++ V NLP + L PFG L R + TG E+++K+
Sbjct: 89 VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Query: 144 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
A A + L LY+ W G A S+
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR----------------------- 185
Query: 204 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARK 262
L + L + D++ R +A
Sbjct: 186 -------------------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG 220
Query: 263 KDPKSPG 269
+D + G
Sbjct: 221 QDGQLKG 227
Score = 48.4 bits (116), Expect = 7e-07
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
+ R++R IL++ LP ++ L + + G T V L QA+AA N+
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKG-TAFVTLLNGEQAEAAINA 76
Query: 152 LAYTKFKEVPLYLEWAPEG 170
++ +E L ++ P
Sbjct: 77 FHQSRLRERELSVQLQPTD 95
Score = 39.2 bits (92), Expect = 8e-04
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 1/46 (2%)
Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
E ER+ + I+ L + T + + V + K
Sbjct: 13 EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK 57
Score = 34.2 bits (79), Expect = 0.035
Identities = 10/85 (11%), Positives = 19/85 (22%), Gaps = 12/85 (14%)
Query: 92 EARSKRIILVKNLPYRTLPTD-LKALFEPFGDLGRVLVPP--------YGITGLVEFLQK 142
R + V LP D L + + + +E+
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAV---LEYETA 236
Query: 143 NQAKAAFNSLAYTKFKEVPLYLEWA 167
A+ A L + +
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFC 261
>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 = 58.5 bits (142), Expect = 3e-10
Identities = 22/183 (12%), Positives = 49/183 (26%), Gaps = 51/183 (27%)
Query: 91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQ 144
V ++ + + N P +++ L + + + P ++ K
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED 171
Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED 204
A+ L K + L + + EK K + E +
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVS------------NPLEKSKRTDSATLEGR-------- 211
Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST-EDSIRRHFKKCGPIASVTVARKK 263
+ I+NL+ E+ +R F+ G I + + +
Sbjct: 212 ------------------------EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ 247
Query: 264 DPK 266
Sbjct: 248 KEH 250
Score = 48.1 bits (115), Expect = 1e-06
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 190 GEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK 249
G + +E + + E R E TT+ +KNL + ++ + ++FK
Sbjct: 5 GHHARPDSKRPLDEGSPAAAGLTSKKANEALTRNRE-LTTVLVKNLPKSYNQNKVYKYFK 63
Query: 250 KCGPIASVTVARKKD 264
CGPI V VA
Sbjct: 64 HCGPIIHVDVADSLK 78
Score = 43.1 bits (102), Expect = 5e-05
Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
+ TL++ N + T+ +IR + +A S+ + + S
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160
Score = 33.8 bits (78), Expect = 0.043
Identities = 19/116 (16%), Positives = 42/116 (36%), Gaps = 23/116 (19%)
Query: 74 RAFLEENGVQLDAFNQVVEARSK--------------RIILVKNLPYRTLP-TDLKALFE 118
+ NG++++ + V + + R I+++NL L L+ FE
Sbjct: 174 YCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFE 233
Query: 119 PFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
FG + ++ +P + F K+ A+ A + + + + A
Sbjct: 234 GFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA 288
>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 = 54.3 bits (131), Expect = 4e-10
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 1/76 (1%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 152
+ ILVKNLP + ++ L + + L V T V L QA+ A
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 153 AYTKFKEVPLYLEWAP 168
F+ L ++ P
Sbjct: 61 HQYSFRGKDLIVQLQP 76
Score = 32.4 bits (74), Expect = 0.026
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ + +KNL +S + K + V R K
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK 40
>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 = 54.3 bits (131), Expect = 8e-10
Identities = 21/106 (19%), Positives = 42/106 (39%), Gaps = 4/106 (3%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLA 153
RI+ ++NLPY+ ++ +F +G + ++ V T V + AK A + L+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 154 YTKFKEVPLYLEWA-PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKE 198
L + + F + K K ++ + +E G
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPP 114
Score = 52.4 bits (126), Expect = 4e-09
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 270
PE + LYI+NL + T + + F K GPI + V P++ G
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGT 49
>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 = 54.3 bits (131), Expect = 1e-09
Identities = 15/73 (20%), Positives = 28/73 (38%)
Query: 192 GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC 251
+ T + E EE++ ++Y+ N+++ ST + HF C
Sbjct: 1 AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 252 GPIASVTVARKKD 264
G I +T+ K
Sbjct: 61 GSINRITILCDKF 73
Score = 40.9 bits (96), Expect = 6e-05
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 6/87 (6%)
Query: 68 EIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVL 127
K A G + + KR + V N+ Y + DL+A F G + R+
Sbjct: 8 TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67
Query: 128 VPPYGITGL------VEFLQKNQAKAA 148
+ +G +EF ++N AA
Sbjct: 68 ILCDKFSGHPKGYAYIEFAERNSVDAA 94
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 55.4 bits (134), Expect = 2e-09
Identities = 25/173 (14%), Positives = 51/173 (29%), Gaps = 48/173 (27%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 154
V ++ Y ++ F PFG + + + +T VE+ A+ A +
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
+ + + D
Sbjct: 93 VMLGGRNIKVGRP--------------------------SNIGQAQPIIDQLA------- 119
Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
E +Y+ +++ + ++D I+ F+ G I S T+AR DP +
Sbjct: 120 -------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR--DPTT 163
Score = 43.8 bits (104), Expect = 2e-05
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ +Y+ ++ + ED+IR+ F GPI S+ ++
Sbjct: 23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW 62
Score = 33.8 bits (78), Expect = 0.033
Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
I V ++ D+K++FE FG + + TG +E+ + ++ A +S+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 153 AYTKFKEVPLYLEWA 167
L + A
Sbjct: 188 NLFDLGGQYLRVGKA 202
>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 = 54.0 bits (130), Expect = 2e-09
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
E++E+ + TLY+ NL+F +TE+ I F K G I + + K K+
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80
Score = 49.0 bits (117), Expect = 1e-07
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 6/76 (7%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ V NL + T + LF GD+ ++++ + VE+ + A+ A +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 153 AYTKFKEVPLYLEWAP 168
T+ + + +W
Sbjct: 102 NGTRLDDRIIRTDWDA 117
>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 = 56.0 bits (134), Expect = 3e-09
Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 5/107 (4%)
Query: 170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVE-----EDEEREP 224
G+ +E ++ E EE+ E E ++ EVE ++ D +
Sbjct: 40 GIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQG 99
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
+ TL++ +N+++TE +RR F+ GPI + + K P +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Score = 37.1 bits (85), Expect = 0.005
Identities = 20/175 (11%), Positives = 56/175 (32%), Gaps = 7/175 (4%)
Query: 60 TRLAMGETEIVEKTRAFLEENGVQLDAFNQV-VEARSKRIILVKNLPYRTLPTDLKALFE 118
R+ E +E+ + +E D N + + + + V + Y T + L+ FE
Sbjct: 65 ERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124
Query: 119 PFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
+G + R+ + +G +E+ + +A+ K + ++
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
+ + G G + + + ++ ++ + +
Sbjct: 185 KGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRER 239
>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 = 52.1 bits (125), Expect = 4e-09
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
++ V+ L + DL E FG + V++ P+ LVEF + AK A
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75
Query: 157 F--KEVPLYLEWA 167
+ ++
Sbjct: 76 VYIAGQQAFFNYS 88
Score = 44.8 bits (106), Expect = 1e-06
Identities = 7/41 (17%), Positives = 16/41 (39%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ ++++ L + E + +K G I V + K
Sbjct: 11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK 51
>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 = 53.4 bits (129), Expect = 5e-09
Identities = 28/173 (16%), Positives = 46/173 (26%), Gaps = 57/173 (32%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
E+ + + + NL +LK + V TG V+F
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67
Query: 146 KAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDN 205
+ A L K + LE
Sbjct: 68 EKALE-LTGLKVFGNEIKLEKP-------------------------------------- 88
Query: 206 QQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
+ + ++ TL KNL+FN TED ++ F+ I V+
Sbjct: 89 -----------KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 130
Score = 50.7 bits (122), Expect = 5e-08
Identities = 9/51 (17%), Positives = 17/51 (33%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E E L+I NLN N + ++ + + V + +
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 55
Score = 38.0 bits (89), Expect = 0.001
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 5/79 (6%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAA 148
+ R+ R +L KNL + +LK +FE ++ LV G + +EF + A+
Sbjct: 95 KVRAARTLLAKNLSFNITEDELKEVFEDALEI--RLVSQDGKSKGIAYIEFKSEADAEKN 152
Query: 149 FNSLAYTKFKEVPLYLEWA 167
+ + L +
Sbjct: 153 LEEKQGAEIDGRSVSLYYT 171
>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 = 53.0 bits (128), Expect = 6e-09
Identities = 32/179 (17%), Positives = 49/179 (27%), Gaps = 59/179 (32%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 148
S ++V LP +L ALF G + + TG V+F + ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
L + L + +A
Sbjct: 62 IKVLNGITVRNKRLKVSYA----------------------------------------- 80
Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
E DT LY+ NL T+D + F K G I + R D +
Sbjct: 81 ----------RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR--DKLT 127
>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 = 51.1 bits (123), Expect = 7e-09
Identities = 12/49 (24%), Positives = 24/49 (48%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ E D T+++ NL E+ + F + GP+ VT+ + ++ K
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58
Score = 41.5 bits (98), Expect = 2e-05
Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 7/85 (8%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQA 145
+ + R + V NL R L LF G L +V + P G V F
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF-GFVCFKHPESV 70
Query: 146 KAAFNSLAYTKFKEVPLYLEWAPEG 170
A L + P+ + G
Sbjct: 71 SYAIALLNGIRLYGRPINVSGPSSG 95
>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 = 50.8 bits (122), Expect = 1e-08
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E + L+I LN + E ++ F K GPI+ V + + + KS G
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG 49
Score = 36.9 bits (86), Expect = 0.001
Identities = 17/71 (23%), Positives = 24/71 (33%), Gaps = 13/71 (18%)
Query: 91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---------GLVEFLQ 141
VEA + + L T LKA+F G + VL+ I + F
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLL----IKDRTSKSRGFAFITFEN 57
Query: 142 KNQAKAAFNSL 152
AK A +
Sbjct: 58 PADAKNAAKDM 68
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 16/51 (31%), Positives = 22/51 (43%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E D L++ LN +E+ + R F+ G I TV R D S G
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG 57
Score = 40.7 bits (96), Expect = 5e-05
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 155
V L + D+ LF+PFG + VL P G + V+F +A+AA ++L +
Sbjct: 20 VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
Query: 156 KFKE---VPLYLEWA 167
+ L +++A
Sbjct: 80 QTMPGASSSLVVKFA 94
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 12/48 (25%), Positives = 22/48 (45%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+E LY++NL +++E+ I + F P A V + +D
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52
Score = 41.9 bits (99), Expect = 1e-05
Identities = 15/73 (20%), Positives = 24/73 (32%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 154
S +I+ V+NL T ++ F V V F + A A +L
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 155 TKFKEVPLYLEWA 167
P+ + A
Sbjct: 74 KVLDGSPIEVTLA 86
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 50.1 bits (120), Expect = 2e-08
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
P + LN N E ++ +K G + V +
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR 43
Score = 42.8 bits (101), Expect = 1e-05
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAF 149
+ + L T LK + +G++ V + + T V F AK
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 150 NSLAYTKFKEVPLYLEWAPEG 170
+L T ++ + +G
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKG 86
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 8/45 (17%), Positives = 22/45 (48%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ + + + + ++N+ F + + IR F G + +V + +K
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT 52
Score = 49.6 bits (119), Expect = 3e-08
Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 8/99 (8%)
Query: 89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGL------VEFLQ 141
QV + ++ ILV+N+P++ +++ LF FG+L V +P TG V+F+
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 142 KNQAKAAFNSLA-YTKFKEVPLYLEWAPEGVFAEAKEKS 179
K AK AFN+L T L LEWA V ++ S
Sbjct: 68 KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 9/53 (16%), Positives = 18/53 (33%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ E E L+I NLN N + ++ + + V + +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 59
Score = 29.9 bits (68), Expect = 0.25
Identities = 15/86 (17%), Positives = 26/86 (30%), Gaps = 12/86 (13%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLV--PPYGIT---GLVEFLQKNQAKAAFNSLAYT 155
+ NL +LK + V G G V+F + A L
Sbjct: 22 IGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGL 80
Query: 156 KFKEVPLYLEWAPEGVFAEAKEKSKG 181
K + LE + ++ ++G
Sbjct: 81 KVFGNEIKLEK------PKGRDGTRG 100
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 49.6 bits (119), Expect = 3e-08
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 210 PEVEENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P+V + R P TT YI N+ +TE + F+ G I +K
Sbjct: 9 PQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
Score = 45.0 bits (107), Expect = 1e-06
Identities = 16/67 (23%), Positives = 26/67 (38%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
+ N+P+ DL LF+ FG + P +++ QA +LA F+
Sbjct: 32 IGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91
Query: 161 PLYLEWA 167
L W
Sbjct: 92 NLRTGWG 98
>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 = 49.4 bits (118), Expect = 3e-08
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
R++ ++ LP T++ AL PFG + +L+ +E + A N +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75
Query: 157 --FKEVPLYLEWA 167
+ P+Y++++
Sbjct: 76 PHLRNQPIYIQYS 88
Score = 41.0 bits (96), Expect = 3e-05
Identities = 8/45 (17%), Positives = 19/45 (42%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
++ + P L+I+ L TE + G + ++ + + K
Sbjct: 7 GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51
>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 = 51.1 bits (123), Expect = 4e-08
Identities = 32/177 (18%), Positives = 48/177 (27%), Gaps = 55/177 (31%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--------VEFLQKNQAKAAFNSL 152
V +P DL+ LFE +G + + V V F + A A N+L
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 153 AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEV 212
K P +
Sbjct: 68 HNMKV----------------------------------------------LPGMHHP-I 80
Query: 213 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ + E+ D L+I ++ TE+ IR F G I + R D S G
Sbjct: 81 QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG 137
Score = 44.1 bits (105), Expect = 8e-06
Identities = 7/41 (17%), Positives = 18/41 (43%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
+++ + +E +R F++ G + + V R + P
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPP 44
Score = 33.4 bits (77), Expect = 0.040
Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 155
+ + + D++ +F FG + R+L P G++ V F + A+ A ++
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Query: 156 KFKEV---PLYLEWA 167
+ E P+ +++A
Sbjct: 160 QTMEGCSSPMVVKFA 174
>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 = 50.6 bits (121), Expect = 4e-08
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
+A K ++ N+ G E +D + E + + E
Sbjct: 16 TTTEAVDAATAEKVFKQYANDNGVDGEWT-----YDDATKTFTVTEGSHHHHHHMDVEGM 70
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
T+L + NL + ++ D++RR F+K G + V + R
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104
Score = 42.9 bits (101), Expect = 2e-05
Identities = 34/126 (26%), Positives = 50/126 (39%), Gaps = 8/126 (6%)
Query: 33 GTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVE 92
G E E +A AE + A GE + T+ F G + VE
Sbjct: 9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE 68
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAK 146
+ + V NL YRT P L+ +FE +G +G V +P T V F K A+
Sbjct: 69 GMTS--LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 147 AAFNSL 152
A +++
Sbjct: 127 DAMDAM 132
>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 = 49.2 bits (118), Expect = 4e-08
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
E+ + L++ NL + TE+ +R+ F+K G V + + K
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
Score = 48.0 bits (115), Expect = 9e-08
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYT 155
+ V NLP +++ LFE +G G V + + G + + A+ A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF---GFIRLETRTLAEIAKVELDNM 74
Query: 156 KFKEVPLYLEWAPEG 170
+ L + +A
Sbjct: 75 PLRGKQLRVRFACHS 89
>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 = 50.2 bits (121), Expect = 7e-08
Identities = 27/179 (15%), Positives = 53/179 (29%), Gaps = 62/179 (34%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAA 148
R++ V NL LK F+ G + + + Y VE+ Q + A A
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA---FVEYHQSHDANIA 57
Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
+L + + + + WA
Sbjct: 58 LQTLNGKQIENNIVKINWA----------------------------------------- 76
Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ ++ + L++ +LN N ++++R FK S V D ++
Sbjct: 77 --------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQT 125
Score = 39.8 bits (94), Expect = 2e-04
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
LY+ NL+ TED ++++F+ GPIA++ + K+ K+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN 42
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 48.6 bits (116), Expect = 7e-08
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
++ ++ L + DL + FG + V+V P LVEF A A N A +
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQ 81
Query: 157 FKEV--PLYLEWA 167
P ++ ++
Sbjct: 82 IYIAGHPAFVNYS 94
Score = 45.1 bits (107), Expect = 1e-06
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
D+ + ++I+ L E + ++ GPI+ V V KK
Sbjct: 13 DDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 48.2 bits (115), Expect = 8e-08
Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 3/92 (3%)
Query: 86 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQK 142
+ V + + R + ++N+P L +L +G +V V + K
Sbjct: 5 SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64
Query: 143 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE 174
+QA+ A + L + + L + + P+ + A+
Sbjct: 65 DQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
Score = 38.6 bits (90), Expect = 2e-04
Identities = 5/44 (11%), Positives = 14/44 (31%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
+ + L I+N+ + + + + G + S
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET 54
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 48.7 bits (116), Expect = 8e-08
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
R+I ++ LP ++ +L PFG + +L+ +E + A N
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76
Query: 157 --FKEVPLYLEWA 167
+ P+Y++++
Sbjct: 77 PVLRGQPIYIQFS 89
Score = 42.5 bits (100), Expect = 1e-05
Identities = 7/40 (17%), Positives = 17/40 (42%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P ++I+ L + TE + G + ++ + + K
Sbjct: 13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52
>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 = 48.0 bits (115), Expect = 8e-08
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TTLY+ L TE +R HF + G I ++TV +++
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
Score = 39.2 bits (92), Expect = 1e-04
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQA-KAAFNSL 152
++ + V L TDL+ F FG++ + V ++F + A AA S
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSF 69
Query: 153 AYTKFKEVPLYLEWA 167
L ++W
Sbjct: 70 NKLIVNGRRLNVKWG 84
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 49.0 bits (117), Expect = 1e-07
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
P+P+ L + L+ +TE +R F K GPIA V++ D +S
Sbjct: 36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY--DQQS 84
Score = 42.0 bits (99), Expect = 3e-05
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 6/64 (9%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 148
+ V L T DL+ +F +G + V + + V F + AK A
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 149 FNSL 152
Sbjct: 105 KERA 108
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 10/59 (16%), Positives = 22/59 (37%)
Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ + E+ + + T+Y + T+ +R+ F G I + V +K
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
Score = 43.5 bits (103), Expect = 5e-06
Identities = 14/69 (20%), Positives = 22/69 (31%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
+ ++ F PFG + + V P V F A A S+ T +
Sbjct: 30 CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89
Query: 161 PLYLEWAPE 169
+ W E
Sbjct: 90 VVKCYWGKE 98
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 2/48 (4%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
D +Y+ NL + I F K G I + + K P
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--KNRRGGPP 62
Score = 40.4 bits (95), Expect = 6e-05
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 3/81 (3%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAF 149
+ I V NLP D++ +F +G + + + VEF A+ A
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 150 NSLAYTKFKEVPLYLEWAPEG 170
+ L +E+ G
Sbjct: 79 YGRDGYDYDGYRLRVEFPRSG 99
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 6/60 (10%), Positives = 16/60 (26%)
Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ ++ E T++ L + F G + V + ++
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62
Score = 36.9 bits (86), Expect = 0.001
Identities = 15/63 (23%), Positives = 21/63 (33%), Gaps = 6/63 (9%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
E R R + L R P DL+ F G + V + + VEF +
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 146 KAA 148
A
Sbjct: 81 PLA 83
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 11/48 (22%), Positives = 23/48 (47%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ T++I+NL+F+S E+++ ++ G + V V D
Sbjct: 5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD 52
Score = 38.9 bits (91), Expect = 2e-04
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
+ + + ++NL + + L + + FGDL V V + T +F+ + A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 146 KAAFNSL 152
+ +
Sbjct: 71 QKCLAAA 77
>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 = 50.1 bits (120), Expect = 2e-07
Identities = 11/47 (23%), Positives = 23/47 (48%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ E+ L++ NL + TE+ +R F++ G + V + R +
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58
Score = 41.6 bits (98), Expect = 1e-04
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKF 157
V NLP D K LFE +G+ V + + G + + A+ A L T
Sbjct: 27 VGNLPTDITEEDFKRLFERYGEPSEVFINRDRGF---GFIRLESRTLAEIAKAELDGTIL 83
Query: 158 KEVPLYLEWAPEG 170
K PL + +A G
Sbjct: 84 KSRPLRIRFATHG 96
Score = 37.7 bits (88), Expect = 0.002
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
R L +KNL+ + + + + F + GP+ V ++ G
Sbjct: 91 RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 138
Score = 29.3 bits (66), Expect = 1.1
Identities = 30/149 (20%), Positives = 53/149 (35%), Gaps = 14/149 (9%)
Query: 89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKN 143
++ A + VKNL L+ F FG + V+V G G VEF K
Sbjct: 89 RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKP 148
Query: 144 QAKAAFNSLAYTKF----KEVPLYLEWAP-----EGVFAEAKEKSKGKEKEKNEEGEGEE 194
A+ A F P+ +E +G+ + +K++ KE+ + +
Sbjct: 149 PARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQ 208
Query: 195 EKKENTAEEDNQQGVPEVEENVEEDEERE 223
+ + E+E+ E +R
Sbjct: 209 PGTFEFEYASRWKALDEMEKQQREQVDRN 237
>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 = 48.0 bits (114), Expect = 2e-07
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
R+I ++ LP ++ +L PFG + +L+ +E + A N
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91
Query: 157 --FKEVPLYLEWA 167
+ P+Y++++
Sbjct: 92 PVLRGQPIYIQFS 104
Score = 42.2 bits (99), Expect = 2e-05
Identities = 8/51 (15%), Positives = 19/51 (37%)
Query: 213 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ D P ++I+ L + TE + G + ++ + + K
Sbjct: 17 RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 67
>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 = 47.1 bits (113), Expect = 2e-07
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
++Y+ N+++ +T + + HF CG + VT+ K
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF 43
Score = 40.6 bits (96), Expect = 4e-05
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKA 147
R I V N+ Y +L+A F G + RV + +G +EF K +
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 148 A 148
+
Sbjct: 64 S 64
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 10/48 (20%), Positives = 21/48 (43%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ +T+++ NL++ ++ F G + + KD KS G
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG 57
Score = 38.4 bits (90), Expect = 4e-04
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 152
+ V NL Y+ LK +F G + R + G G V F Q +A A +
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
>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 = 46.8 bits (112), Expect = 3e-07
Identities = 10/43 (23%), Positives = 24/43 (55%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
R + + T+ + NL+ ++ E ++ F+ G I+ + +A+ K
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT 52
Score = 45.7 bits (109), Expect = 8e-07
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
I V NL T TDL+ LF PFG + R+ + TG + F ++ A A +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 153 AYTKFKEVPLYLEWA 167
+ + + L +EWA
Sbjct: 78 SGFGYDHLILNVEWA 92
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 46.5 bits (111), Expect = 4e-07
Identities = 8/45 (17%), Positives = 18/45 (40%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
T+ ++N+ ++ DSI +A + KD ++
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQT 49
Score = 36.1 bits (84), Expect = 0.002
Identities = 9/62 (14%), Positives = 19/62 (30%), Gaps = 8/62 (12%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGITGL------VEFLQKNQAKAAFN 150
I+++N+ T+ + P+ L + + T V+ A
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 151 SL 152
L
Sbjct: 72 IL 73
>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 = 46.5 bits (111), Expect = 4e-07
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P T L++ L N++ ++ R F + G I ++ +
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
Score = 40.3 bits (95), Expect = 5e-05
Identities = 10/52 (19%), Positives = 19/52 (36%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 152
V L T L F+ FG + + +++ + A+AA +
Sbjct: 22 VGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKM 73
>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 = 46.7 bits (111), Expect = 5e-07
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 72
Query: 154 YTKFKEVPLYLEWA 167
TKF+ +
Sbjct: 73 NTKFRSHEGETAYI 86
Score = 32.9 bits (75), Expect = 0.030
Identities = 5/41 (12%), Positives = 15/41 (36%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
+ + + L + + ++ H ++ G + V R
Sbjct: 11 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 51
>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 = 46.1 bits (110), Expect = 5e-07
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V+NL Y + DL+ LF +G L + P +T V F+ A A+ +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Score = 44.1 bits (105), Expect = 2e-06
Identities = 8/44 (18%), Positives = 20/44 (45%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L+++NL++ S+E+ + + F GP++ +
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL 45
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 46.5 bits (111), Expect = 5e-07
Identities = 7/45 (15%), Positives = 16/45 (35%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ +T L+++ + E + F GP+ V +
Sbjct: 21 MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 65
Score = 45.4 bits (108), Expect = 1e-06
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
+ V+ P ++L +F PFG + V + G VEF + A A + F
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-G-FAFVEFEEAESAAKAIEEVHGKSFA 91
Query: 159 EVPLYLEWA 167
PL + ++
Sbjct: 92 NQPLEVVYS 100
>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 = 46.1 bits (110), Expect = 5e-07
Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 4/84 (4%)
Query: 88 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----VEFLQKN 143
+ + R + V NL + LF G + + VEF +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66
Query: 144 QAKAAFNSLAYTKFKEVPLYLEWA 167
A AA ++ K + + WA
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWA 90
Score = 41.9 bits (99), Expect = 2e-05
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ TLY+ NL+ + TE I + F + GP S + +
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT 52
>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 = 46.1 bits (110), Expect = 6e-07
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ + TL + NL + ++ DS+RR F+K G + V + R+
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH 50
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V NL YRT P L+ +FE +G +G V +P T V F + A+ A ++
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
>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 = 45.7 bits (109), Expect = 7e-07
Identities = 11/50 (22%), Positives = 20/50 (40%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E L + NL+F ++ I+ F + G + V + +S G
Sbjct: 22 GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG 71
Score = 40.7 bits (96), Expect = 4e-05
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 152
+LV NL + D++ LF FG L + V G T V F +K A A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90
>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 = 45.7 bits (109), Expect = 7e-07
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
P+P+ L + L+ +TE +R F K GPIA V++
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 47
Score = 40.3 bits (95), Expect = 5e-05
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V L T DL+ +F +G + V + + V F + AK A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 46.0 bits (109), Expect = 8e-07
Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 15/112 (13%)
Query: 85 DAFNQVVEARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLV---PPYGITGLV 137
D + +++L+ N+ L+ AL GD+ ++V +
Sbjct: 18 DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77
Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE 189
F + A+A + F+ PL + + ++ ++ + E
Sbjct: 78 VFATQESAQAFVEAFQGYPFQGNPLVITF--------SETPQSQVAEDGSLE 121
Score = 42.2 bits (99), Expect = 2e-05
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 9/78 (11%)
Query: 197 KENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH----FKKCG 252
KE A + +Q + + EP + I N+N ++ ++ G
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPH---TEPSQVVLITNINPEVPKEKLQALLYALASSQG 58
Query: 253 PIASVTVARKKDPKSPGQ 270
I + V + G+
Sbjct: 59 DILDIVV--DLSDDNSGK 74
>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 = 46.8 bits (112), Expect = 9e-07
Identities = 27/179 (15%), Positives = 54/179 (30%), Gaps = 59/179 (32%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 148
SK ++V LP + ++LF G++ + ITG V ++ A+ A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
N+L + + + + +A S ++ N
Sbjct: 61 INTLNGLRLQTKTIKVSYA---------RPSSASIRDAN--------------------- 90
Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
LY+ L T+ + + F + G I + + D +
Sbjct: 91 ---------------------LYVSGLPKTMTQKELEQLFSQYGRIITSRILV--DQVT 126
Score = 26.8 bits (60), Expect = 5.4
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDL--GRVLV-PPYGIT---GLVEFLQKNQAKAAFNSL 152
+ V LP +L+ LF +G + R+LV G++ G + F ++ +A+ A L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 153 --AYTKFKEVPLYLEWA 167
P+ +++A
Sbjct: 151 NGQKPSGATEPITVKFA 167
>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 = 45.2 bits (107), Expect = 1e-06
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 71
Query: 154 YTKFKEVPLYLEWA 167
TKF+ +
Sbjct: 72 NTKFRSHEGETAYI 85
Score = 32.8 bits (75), Expect = 0.025
Identities = 5/41 (12%), Positives = 15/41 (36%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
+ + + L + + ++ H ++ G + V R
Sbjct: 10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 50
>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 = 46.4 bits (110), Expect = 1e-06
Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 1/91 (1%)
Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP-DTTL 230
EA + + ++ K + + + + V E + R+ P D +
Sbjct: 17 TTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKV 76
Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
Y+ NL N + + R F GP+ SV VAR
Sbjct: 77 YVGNLGNNGNKTELERAFGYYGPLRSVWVAR 107
Score = 38.7 bits (90), Expect = 4e-04
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTK 156
+ V NL T+L+ F +G L V V P G VEF A A L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAADAVRELDGRT 134
Query: 157 FKEVPLYLEWA 167
+ +E +
Sbjct: 135 LCGCRVRVELS 145
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQ 270
E P+ T+YI NLN +D +++ F + G I + V + K GQ
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQ 53
Score = 44.1 bits (105), Expect = 2e-06
Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 15/102 (14%)
Query: 92 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 144
E R I + NL + +LK A+F FG + +LV V F + +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 186
A A S+ F + P+ +++ AK S K K
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMK 97
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 46.4 bits (110), Expect = 1e-06
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 153
+LV NL + D++ LF FG L + V G T V F ++ A A
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 154 YTKFKEVPLYLEWAPE 169
P+ ++
Sbjct: 151 GVPLDGRPMDIQLVAS 166
Score = 44.8 bits (106), Expect = 5e-06
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E L + NL+F ++ I+ F + G + V + +S G
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 130
>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 = 44.6 bits (106), Expect = 2e-06
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 214 ENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
+E+ + TL KNL+FN TED ++ F+ I V+
Sbjct: 2 HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 47
Score = 37.2 bits (87), Expect = 6e-04
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFG------DLGRVLVPPYGITGLVEFLQKNQA 145
+ R+ R +L KNL + +LK +FE G+ GI +EF + A
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK----SKGI-AYIEFKSEADA 66
Query: 146 KAAFNSL 152
+
Sbjct: 67 EKNLEEK 73
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
+ T++++ L N T +S+ +FK+ G I +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKT 42
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 45.5 bits (108), Expect = 2e-06
Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 9/106 (8%)
Query: 56 SGAATRLAMGETEIVEKT---RAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTD 112
S + E V T +G + A +KR++ V L
Sbjct: 20 SDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKV 79
Query: 113 LKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
L A F PFGD+ + +P T VEF A AA +++
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Score = 41.7 bits (98), Expect = 4e-05
Identities = 6/59 (10%), Positives = 14/59 (23%)
Query: 201 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
+ + + LY+ L + + F G I + +
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95
>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 = 46.5 bits (111), Expect = 2e-06
Identities = 28/180 (15%), Positives = 49/180 (27%), Gaps = 55/180 (30%)
Query: 88 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQ 141
N + + V +L L F P G + + V IT V F Q
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
A+ A +++ + K P+ + W+ ++ K
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWS---------QRDPSLRKSG--------------- 102
Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
++IKNL+ + ++ F G I S V
Sbjct: 103 -------------------------VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137
Score = 41.9 bits (99), Expect = 7e-05
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
P +LY+ +L+ + TE + F GPI S+ V R
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM 51
>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 = 46.1 bits (110), Expect = 2e-06
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ +EPE L+I L+F +T++S+R HF++ G + V +DP +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNT 51
Score = 34.2 bits (79), Expect = 0.024
Identities = 5/52 (9%), Positives = 19/52 (36%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
+ +++ + ++ E +R +F++ G I + + +
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK 145
>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 = 47.7 bits (113), Expect = 2e-06
Identities = 49/284 (17%), Positives = 85/284 (29%), Gaps = 97/284 (34%)
Query: 36 AIAEAMAETY-----NATKA-EVLTGSGAATRLAMGETEIVEKTRAFLEENG-------- 81
A+A A +++ + KA VL G A T + EN
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 82 ---------VQ--LDAFNQVVEARSKRI-ILVKNLPYRTLPTDLKALFEPFGDLGRVLV- 128
VQ ++ N + K++ I + N + LV
Sbjct: 340 SISNLTQEQVQDYVNKTNSHL-PAGKQVEISLVNGA-------------------KNLVV 379
Query: 129 --PPYGITGLVEFLQK-------NQAKAAFNSLA---YTKFKEV--PL---YLEWAPEGV 171
PP + GL L+K +Q++ F+ +F V P L A + +
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKK--ENTAE-EDNQQGVPEVEENVEEDEEREP---E 225
+ + N ++ + +T + D + + E + + R P E
Sbjct: 440 NKDL--------VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE 491
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGP-----IASVTVARKKD 264
F +T H GP + +T R KD
Sbjct: 492 -------TTTQFKAT------HILDFGPGGASGLGVLT-HRNKD 521
Score = 31.2 bits (70), Expect = 0.50
Identities = 15/69 (21%), Positives = 21/69 (30%), Gaps = 23/69 (33%)
Query: 203 EDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
E + +PE E D+ EP L K L + V+
Sbjct: 35 EQFNKILPEPTEGFAADD--EPTTPAELVGKFLGY---------------------VSSL 71
Query: 263 KDPKSPGQF 271
+P GQF
Sbjct: 72 VEPSKVGQF 80
Score = 29.6 bits (66), Expect = 1.3
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 17/56 (30%)
Query: 235 LNFNSTEDSI-------------RRHFKKCGPIASVTVARKKDPKSP----GQFLS 273
L+ S E + + F K P + A +P +P G+FL
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG 66
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 44.7 bits (106), Expect = 3e-06
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Score = 44.3 bits (105), Expect = 4e-06
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ E T+L + NL + ++ D++RR F+K G + V + R
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81
>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 = 45.2 bits (107), Expect = 3e-06
Identities = 17/103 (16%), Positives = 43/103 (41%), Gaps = 2/103 (1%)
Query: 164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED--NQQGVPEVEENVEEDEE 221
++ A E E ++ + KEK + +G ++ E + + V +++ E
Sbjct: 7 IDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGP 66
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ L++ +++ + ED I+ F G I ++ + +
Sbjct: 67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109
Score = 41.0 bits (96), Expect = 9e-05
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
I+ V ++ +++ F +G++ + + TG LVE+ QA AA +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 152 LAYTKFKEVPLYLEWA 167
L + + ++W
Sbjct: 134 LNGAEIMGQTIQVDWC 149
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.0 bits (104), Expect = 4e-06
Identities = 9/48 (18%), Positives = 21/48 (43%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ + ++YIK ++T D I+ + G + ++ + R G
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 53
Score = 40.9 bits (96), Expect = 4e-05
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 6/98 (6%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAK 146
R + +K P D+K E G + + + + V F AK
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 147 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 184
K+KE L + + + + +E+ + K +
Sbjct: 67 KFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA-RKKDPKSPGQ-FLSM 274
EP+ LY+KNL+ TE + F + + R + GQ F++
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITF 74
Score = 43.8 bits (104), Expect = 4e-06
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 154
+KNL R DL +LF F + + +TG + F K A A + +
Sbjct: 30 LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG 89
Query: 155 TKFKEVPLYLEWA 167
K L +E+
Sbjct: 90 YKLYGKILVIEFG 102
>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 = 44.3 bits (105), Expect = 4e-06
Identities = 11/50 (22%), Positives = 20/50 (40%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
E L + NL+F ++ I+ F + G + V + +S G
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77
Score = 42.0 bits (99), Expect = 2e-05
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 153
+LV NL + D++ LF FG L + V G T V F ++ A A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 154 YTKFKEVPLYLEWAPE 169
P+ ++
Sbjct: 98 GVPLDGRPMDIQLVAS 113
>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 = 43.3 bits (103), Expect = 4e-06
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAK 146
A +KR++ V L L A F PFGD+ + +P T VEF A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 147 AAFNSL 152
AA +++
Sbjct: 64 AAIDNM 69
Score = 36.7 bits (86), Expect = 6e-04
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
LY+ L + + F G I + +
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 39
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 43.9 bits (104), Expect = 4e-06
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
E++ + T++++ L N T +S+ +FK+ G I +
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKT 36
Score = 27.0 bits (60), Expect = 3.1
Identities = 11/68 (16%), Positives = 17/68 (25%), Gaps = 14/68 (20%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------------GLVEFLQKNQ 144
I V+ L + F+ G + + V F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 145 AKAAFNSL 152
AKAA +
Sbjct: 70 AKAAIDWF 77
>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 = 44.1 bits (104), Expect = 5e-06
Identities = 9/70 (12%), Positives = 24/70 (34%), Gaps = 1/70 (1%)
Query: 201 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTV 259
+ + ++ + D + ++ L F T++ I + F + +T+
Sbjct: 16 PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75
Query: 260 ARKKDPKSPG 269
+ K G
Sbjct: 76 PVDPEGKITG 85
Score = 38.3 bits (89), Expect = 5e-04
Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 6/76 (7%)
Query: 79 ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG--- 135
G Q+ + ++ + + ++ LP+ ++ F + + P G
Sbjct: 25 TGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84
Query: 136 ---LVEFLQKNQAKAA 148
V+F + A+ A
Sbjct: 85 GEAFVQFASQELAEKA 100
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 42.9 bits (102), Expect = 6e-06
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
++++NL F+ T ++ F +CG + +
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM 42
Score = 35.2 bits (82), Expect = 0.003
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 10/61 (16%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNS 151
I V+NLP+ LK F G + + G+ V+F A+ A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGV---VKFESPEVAERACRM 67
Query: 152 L 152
+
Sbjct: 68 M 68
>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 = 43.0 bits (102), Expect = 7e-06
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TL + NL++++TE++++ F+K + V + ++ KS G
Sbjct: 5 SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSKG 54
Score = 34.9 bits (81), Expect = 0.005
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 86 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEF 139
+ N SK ++ + NL Y L+ +FE + VP G +EF
Sbjct: 6 SGNSTWSGESKTLV-LSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSKGY-AFIEF 60
Query: 140 LQKNQAKAAFNSL 152
AK A NS
Sbjct: 61 ASFEDAKEALNSC 73
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 43.4 bits (102), Expect = 7e-06
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 93 ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
+ + + ++V N L L + E G + +L+PP + ++K A+
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81
Query: 151 SLAYTKF-----KEVPLYLEWA 167
+L + +++ LYL +
Sbjct: 82 TLNGKEVVDDLGQKITLYLNFV 103
Score = 37.2 bits (86), Expect = 9e-04
Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 217 EEDEEREPEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVARKK 263
E E +L + N L + + + +KCG + ++ + K
Sbjct: 15 HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK 63
>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 = 45.3 bits (106), Expect = 7e-06
Identities = 26/123 (21%), Positives = 46/123 (37%), Gaps = 15/123 (12%)
Query: 92 EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 144
E R I + NL + +LK A+F FG + +LV V F + +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED 204
A A S+ F + P+ +++ AK S K K E + ++++ +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMKGTFVERDRKREKRKPKSQ 116
Query: 205 NQQ 207
Sbjct: 117 ETP 119
Score = 42.9 bits (100), Expect = 5e-05
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQ 270
E P+ T+YI NLN +D +++ F + G I + V + K GQ
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMRGQ 54
Score = 42.2 bits (98), Expect = 9e-05
Identities = 26/145 (17%), Positives = 44/145 (30%), Gaps = 2/145 (1%)
Query: 25 HTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQL 84
+ + + + G + +I + Q+
Sbjct: 136 AVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQM 195
Query: 85 DAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPPYGITGLVEFLQKN 143
+ E I+ + NLP T L LF F LVP VEF +
Sbjct: 196 PPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEV 255
Query: 144 QAKAAFNSLAYTKF-KEVPLYLEWA 167
QA AA ++L K + + + +A
Sbjct: 256 QAGAARDALQGFKITQNNAMKISFA 280
>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 = 43.0 bits (102), Expect = 7e-06
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
+ L++ L+F++ E S+ + F K G I+ V V
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV 44
Score = 35.7 bits (83), Expect = 0.003
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V L + T L+ +F +G + V+V T G V F + AK A ++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
>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 = 43.2 bits (102), Expect = 8e-06
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
+ E ++ +Y++ LN + T D + FK+CG +
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKM 44
Score = 28.9 bits (65), Expect = 0.78
Identities = 16/90 (17%), Positives = 23/90 (25%), Gaps = 14/90 (15%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------------GLV 137
E I V+ L DL F+ G + + V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
+ AKAA F+ L + A
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 42.2 bits (100), Expect = 9e-06
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+T+Y+ NL F+ T + + R F K G + VT+ + KD
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD 53
Score = 40.7 bits (96), Expect = 4e-05
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 145
A SK + V NLP+ DL +F +G + +V + T + FL K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 146 KAAFNSL 152
+ ++
Sbjct: 72 QNCTRAI 78
>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 = 42.6 bits (101), Expect = 9e-06
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 217 EEDEEREPEPDT---TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
R P + T ++ NL ++ TE+SI+ F+ I++V + R +P +P +
Sbjct: 6 HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL 60
Score = 29.1 bits (66), Expect = 0.41
Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 7/79 (8%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 150
+ NLPY +K F L EF + +A +
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 151 SLAYTKFKEVPLYLEWAPE 169
L + ++ A +
Sbjct: 80 -LNEESLGNRRIRVDVADQ 97
>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 = 42.1 bits (100), Expect = 9e-06
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 270
T ++I L N T+D I F G I + + + P
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP--VERMHPHL 45
Score = 36.4 bits (85), Expect = 0.001
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 9/62 (14%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAAFN 150
+ + L + +F +G + + +P G VEF ++A+ A
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG-YAYVEFENPDEAEKALK 65
Query: 151 SL 152
+
Sbjct: 66 HM 67
>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 = 42.6 bits (101), Expect = 9e-06
Identities = 22/113 (19%), Positives = 33/113 (29%), Gaps = 20/113 (17%)
Query: 86 AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEF 139
+ + E + V L + L LF G + +P +TG VEF
Sbjct: 5 SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64
Query: 140 LQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEG 192
L + A A + K P+ + A KN G
Sbjct: 65 LSEEDADYAIKIMDMIKLYGKPIRVNKA--------------SAHNKNLSGPS 103
Score = 39.9 bits (94), Expect = 8e-05
Identities = 9/43 (20%), Positives = 20/43 (46%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
E D T+Y+ L+ +E + F + GP+ + + + +
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV 52
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
A +KR++ V L L A F PFGD+ + +P T VEF A
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 146 KAAFNSL 152
AA +++
Sbjct: 68 AAAIDNM 74
Score = 38.7 bits (91), Expect = 2e-04
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
LY+ L + + F G I + +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 44
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ E R P TLY+ + T +R F G I +++ +
Sbjct: 27 SDSFPERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR 73
Score = 36.7 bits (85), Expect = 0.002
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 2/88 (2%)
Query: 80 NGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEF 139
+ D+F + R + V PT L+ F PFG++ + + P V +
Sbjct: 23 PFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTY 80
Query: 140 LQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
+ A A L T+ + V L + A
Sbjct: 81 EKMESADQAVAELNGTQVESVQLKVNIA 108
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 42.3 bits (100), Expect = 1e-05
Identities = 9/48 (18%), Positives = 18/48 (37%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L+I L F+ T++ + K G + + + + K G
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59
Score = 40.3 bits (95), Expect = 6e-05
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAA 148
K + + LP+ +L+ + + G + + + P G+ VE+ ++QA A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL-AYVEYENESQASQA 74
Query: 149 FNSL 152
+
Sbjct: 75 VMKM 78
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 42.3 bits (100), Expect = 1e-05
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+Y+ NL + + + R F GP+ +V +AR
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR 34
Score = 40.4 bits (95), Expect = 5e-05
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
V NL +L+ F +G L V + P G VEF A+ A L
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF-AFVEFEDPRDAEDAVRGLDGKVIC 63
Query: 159 EVPLYLEWA 167
+ +E +
Sbjct: 64 GSRVRVELS 72
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
L+++NL TE+ + + F + G + V +
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK 45
Score = 41.5 bits (98), Expect = 2e-05
Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYT 155
+++ V+NL L+ F FG L RV Y + F +++ A A +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY---AFIHFDERDGAVKAMEEMNGK 68
Query: 156 KFKEVPLYLEWA 167
+ + + +A
Sbjct: 69 DLEGENIEIVFA 80
>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 = 43.3 bits (103), Expect = 1e-05
Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ ++I LN+++TED++R +F K G + + + KDP +
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI--MKDPAT 41
Score = 37.5 bits (88), Expect = 0.001
Identities = 6/43 (13%), Positives = 14/43 (32%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
E + +++ + + F + G I + KD
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 219 DEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
R P P T ++ NL ++ TE+SI+ F+ I++V + R +P +P +
Sbjct: 6 SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL 56
Score = 31.1 bits (71), Expect = 0.095
Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 7/79 (8%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFN 150
+ NLPY +K F L EF + +A +
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 151 SLAYTKFKEVPLYLEWAPE 169
L + ++ A +
Sbjct: 76 -LNEESLGNKRIRVDVADQ 93
>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 = 41.9 bits (99), Expect = 2e-05
Identities = 8/41 (19%), Positives = 16/41 (39%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
L++ N+ F + +R+ F + G I V +
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 47
Score = 38.4 bits (90), Expect = 3e-04
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 12/62 (19%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 150
+ V N+P+R DL+ +F FG + V + I G V F A A
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRARE 73
Query: 151 SL 152
L
Sbjct: 74 KL 75
>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 = 42.9 bits (101), Expect = 2e-05
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 1/79 (1%)
Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIR 245
+ + + + E + + E E + EP EP+ +Y+KNL + E ++
Sbjct: 4 GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLK 63
Query: 246 RHFKKCGPIASVTVARKKD 264
F + +S T D
Sbjct: 64 YIFGRYVDFSSETQRIMFD 82
Score = 35.6 bits (82), Expect = 0.005
Identities = 20/113 (17%), Positives = 32/113 (28%), Gaps = 13/113 (11%)
Query: 83 QLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGIT------- 134
L F I VKNL DLK +F + D + I
Sbjct: 32 TLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRM 91
Query: 135 ---GLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 184
+ + A A P+ +++A ++ +GK K
Sbjct: 92 KGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA--RPKQDPKEGKRK 142
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 8/38 (21%), Positives = 19/38 (50%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ T L++ N++ T +R F++ GP+ + +
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK 44
Score = 38.0 bits (89), Expect = 3e-04
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSL 152
++ + V N+ +L+A FE +G + +V Y V + A A L
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGL 64
Query: 153 AYTKFKEVPLYLEWA 167
T+F+ ++++ +
Sbjct: 65 DNTEFQGKRMHVQLS 79
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T+++ ++ E IR F + G + V + + S G
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG 51
Score = 29.1 bits (66), Expect = 0.46
Identities = 5/24 (20%), Positives = 12/24 (50%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGD 122
+ V + R T++++ F +G
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGS 35
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 41.9 bits (99), Expect = 2e-05
Identities = 8/48 (16%), Positives = 17/48 (35%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ N+ F + +R+ F + G I V + +
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER 66
Score = 37.7 bits (88), Expect = 5e-04
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 12/60 (20%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFNSL 152
V N+P+R DL+ +F FG + V + I G V F A A L
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRAREKL 89
>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 = 42.1 bits (99), Expect = 2e-05
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 210 PEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKS 267
+ + R P E +Y+K L F + + FKK + S+ +A + K+
Sbjct: 7 GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 66
Query: 268 PG 269
G
Sbjct: 67 TG 68
Score = 36.0 bits (83), Expect = 0.003
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 6/63 (9%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 145
+ + +K LP+ + F+ + + YG G VEF +
Sbjct: 21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80
Query: 146 KAA 148
KAA
Sbjct: 81 KAA 83
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
++ LY+ +L+FN TED +R F+ G I S+ +
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQL 58
Score = 39.6 bits (93), Expect = 1e-04
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V +L + L+ +FEPFG + + + TG + F AK A L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
E R P TLY+ + T +R F G I +++ +
Sbjct: 8 ERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR 49
Score = 32.6 bits (75), Expect = 0.028
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 111 TDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
T L+ F PFG++ + + P V + + A A L T+ + V L + A
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
>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 = 42.2 bits (100), Expect = 3e-05
Identities = 21/184 (11%), Positives = 42/184 (22%), Gaps = 65/184 (35%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQKN 143
S R + V N+P+ + F LG + P +EF +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 144 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
+ A + F+ L + +
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRP---------------------------HDYQPLPGA 94
Query: 204 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
L+I L +D ++ GP+ + + +
Sbjct: 95 HK------------------------LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK-- 128
Query: 264 DPKS 267
D +
Sbjct: 129 DSAT 132
Score = 33.0 bits (76), Expect = 0.058
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ + LP +K L FG L + TGL E++ N A L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 153 AYTKFKEVPLYLEWA 167
+ + L ++ A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 41.1 bits (97), Expect = 4e-05
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+++ + T LYI NL + E + K G + S + R S G
Sbjct: 18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 67
Score = 35.7 bits (83), Expect = 0.003
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 155
+ NLP +L+ + +PFG + R+L G + G + +A
Sbjct: 30 ISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGK 89
Query: 156 KFKEVPLY 163
K P
Sbjct: 90 FIKTPPGV 97
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
+I V+N+P+ ++ F + + + Y G +V F +++A AA
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 149 FNSLAYTKFKEVPLYLEWAPEG 170
L + L G
Sbjct: 74 VIDLNDRPIGSRKVKLSGPSSG 95
Score = 37.7 bits (88), Expect = 4e-04
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTVARKKDPKSPG 269
T + ++N+ F + D I F I SV + + G
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
>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 = 41.6 bits (98), Expect = 4e-05
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFN 150
I+ V + D+ F +G++ + + G LVE+ +A+AA
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY-TLVEYETYKEAQAAME 82
Query: 151 SLAYTKFKEVPLYLEWA 167
L P+ ++W
Sbjct: 83 GLNGQDLMGQPISVDWC 99
Score = 35.4 bits (82), Expect = 0.004
Identities = 7/40 (17%), Positives = 18/40 (45%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ ++ +TE+ I F + G I ++ + +
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 59
>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 = 40.2 bits (95), Expect = 4e-05
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ LYI+ L +T+ + + + G I S K
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT 42
Score = 38.7 bits (91), Expect = 1e-04
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
++ L T DL L +P+G + T V+F + A+ A +L
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 40.3 bits (95), Expect = 4e-05
Identities = 6/40 (15%), Positives = 16/40 (40%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+++ N++ T +R F++ G + V +
Sbjct: 4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK 43
Score = 37.2 bits (87), Expect = 6e-04
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
I V N+ +L++LFE G + +V Y V ++ AKAA L +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY---AFVHMEKEADAKAAIAQLNGKEV 68
Query: 158 KEVPLYLEWA 167
K + +E +
Sbjct: 69 KGKRINVELS 78
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 7/39 (17%), Positives = 18/39 (46%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
P +Y+ ++ ++ TE+ I GP+ ++ +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ 39
Score = 33.4 bits (77), Expect = 0.014
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFN 150
R++ + ++PY + L G + + + TG +EF + +A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 151 SL 152
+L
Sbjct: 63 NL 64
>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 = 41.4 bits (97), Expect = 4e-05
Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ + + ++++ L + +TE+ I F P+ V + D + G
Sbjct: 36 DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGRVTG 87
Score = 36.4 bits (84), Expect = 0.003
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYG-ITG--LVEFLQKNQAKA 147
++ + + ++ LPY+ D+ F P + + + P G +TG VEF +A A
Sbjct: 42 QSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVA 101
Query: 148 A 148
A
Sbjct: 102 A 102
>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 = 40.2 bits (95), Expect = 5e-05
Identities = 9/49 (18%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ + E +++ L++++++ ++ +F K G + T+ K DP +
Sbjct: 3 NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI--KMDPNT 49
>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 = 40.4 bits (95), Expect = 5e-05
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
II V+N+P+ ++ F + + + Y G +V F +++A AA
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 149 FNSL 152
L
Sbjct: 74 VIDL 77
Score = 36.5 bits (85), Expect = 0.001
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTVARKKDPKSPG 269
T + ++N+ F + D I F I SV + + G
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
>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 = 40.7 bits (95), Expect = 6e-05
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 97 RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
R+I + NLP+ + + L EP+G + ++ +E + A A +
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVD----- 80
Query: 156 KFKEVPLYLEWAP 168
+ L+ +
Sbjct: 81 HCLKKALWFQGRC 93
Score = 31.4 bits (71), Expect = 0.097
Identities = 8/55 (14%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 210 PEVEENVEEDEEREPEPDTTLYIKNL-NFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ E ++ +++ E +++ NL + ++ ++ + + G I + + R K
Sbjct: 8 KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>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 = 40.7 bits (96), Expect = 6e-05
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 204 DNQQGVPEVEENV-EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
G+ + E V E ++RE E L+I L+F +TE+S+R ++++ G + V
Sbjct: 3 SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV--M 60
Query: 263 KDPKS 267
+DP S
Sbjct: 61 RDPAS 65
>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 = 42.4 bits (99), Expect = 6e-05
Identities = 10/80 (12%), Positives = 21/80 (26%), Gaps = 2/80 (2%)
Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR 246
+ E ++ G + LYI NL + +T++ +
Sbjct: 28 SANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTE 87
Query: 247 HFKKCGP--IASVTVARKKD 264
G I + +
Sbjct: 88 AVHSLGVNDILEIKFFENRA 107
Score = 32.8 bits (74), Expect = 0.080
Identities = 16/102 (15%), Positives = 33/102 (32%), Gaps = 8/102 (7%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 150
+ + NL + T DL G D+ + G LV + +K +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 151 SLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEG 192
L + + + ++ + +S+ + GEG
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172
>1x4d_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 = 102
Score = 40.2 bits (94), Expect = 6e-05
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 96 KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
+R++ + + + L L L EPFG + L+ +E A+AA +
Sbjct: 15 RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 40.6 bits (95), Expect = 7e-05
Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 4/57 (7%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVARKKDPKSPG 269
E + E + ++ L F +T + + F + PI + D + G
Sbjct: 13 EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG 69
Score = 31.0 bits (70), Expect = 0.18
Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG------RVLVPPYGI---TGLVEF 139
Q + ++ I+ ++ LP+ ++ A F + + P G V F
Sbjct: 16 QFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLF 75
Query: 140 LQKNQAKAA 148
+ A+ A
Sbjct: 76 ACEEYAQNA 84
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 39.9 bits (94), Expect = 8e-05
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
I+ V + D+ F +G++ + + TG LVE+ +A+AA
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 152 LAYTKFKEVPLYLEWA 167
L P+ ++W
Sbjct: 85 LNGQDLMGQPISVDWC 100
Score = 34.2 bits (79), Expect = 0.008
Identities = 7/41 (17%), Positives = 18/41 (43%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ ++ +TE+ I F + G I ++ + +
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 40.4 bits (95), Expect = 8e-05
Identities = 10/45 (22%), Positives = 17/45 (37%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
++ E L+I +L T+ + F G + S V K
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77
Score = 32.7 bits (75), Expect = 0.030
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ + +LP TDL + F PFG++ V T L V F + A+ A ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
>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 = 40.0 bits (94), Expect = 8e-05
Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 14/111 (12%)
Query: 63 AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
A+ E V E G Q + I+ V ++ +++ F +G+
Sbjct: 1 AIHSYERVRNEDDDELEPGPQ--------RSVEGWILFVTSIHEEAQEDEIQEKFCDYGE 52
Query: 123 LGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
+ + + TG LVE+ QA AA +L + + ++W
Sbjct: 53 IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103
Score = 36.5 bits (85), Expect = 0.001
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 214 ENVEEDEEREPEPDT-------TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
E V +++ E EP L++ +++ + ED I+ F G I ++ + +
Sbjct: 6 ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 63
>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 = 39.5 bits (93), Expect = 9e-05
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
L+I NL +TE IR F++ G + + +
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
Score = 38.3 bits (90), Expect = 2e-04
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNS 151
+ + + NLP ++++LFE +G + ++ Y G V K A+ A +
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---GFVHIEDKTAAEDAIRN 61
Query: 152 LAYTKFKEVPLYLEWA 167
L + K V + +E +
Sbjct: 62 LHHYKLHGVNINVEAS 77
>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 = 39.6 bits (93), Expect = 9e-05
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
T+ ++ FN TE ++ P+ ++ + R G
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTG 51
Score = 33.8 bits (78), Expect = 0.011
Identities = 8/61 (13%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYGIT---GLVEFLQKNQAKA 147
+ + ++ P+ ++ P + R++ +G V+F + + K
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQ 65
Query: 148 A 148
A
Sbjct: 66 A 66
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
R + + L + L + +TE ++ +F G + V V KKD K+
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV--KKDLKT 53
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 39.6 bits (93), Expect = 1e-04
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
EP T Y+ NL FN+ + I FK I SV + R KD
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD 51
Score = 27.2 bits (61), Expect = 2.2
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 15/64 (23%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFG----------DLGRVLVPPYGITGLVEFLQKNQAK 146
V NLP+ T+ D+ A+F+ D + G VEF + + K
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDK----FKGF-CYVEFDEVDSLK 70
Query: 147 AAFN 150
A
Sbjct: 71 EALT 74
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
+ LY+KNL+ ++ +R+ F G I S V
Sbjct: 8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM 49
Score = 32.2 bits (74), Expect = 0.039
Identities = 19/75 (25%), Positives = 25/75 (33%), Gaps = 12/75 (16%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFNSL 152
VKNL L+ F PFG + V + G V F +A A +
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKV----MMEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 153 AYTKFKEVPLYLEWA 167
PLY+ A
Sbjct: 76 NGRIVATKPLYVALA 90
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 39.1 bits (92), Expect = 1e-04
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 226 PDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
P + L+I NL + +++ + R F G I + +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45
Score = 32.2 bits (74), Expect = 0.033
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 99 ILVKNLPYRTL-PTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
+ + NLP + + DL +F P+G + ++ + + G ++F + A +
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIECESQEM 69
Query: 157 FKEVPLYLEWA 167
L LE +
Sbjct: 70 NFGKKLILEVS 80
>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 = 39.3 bits (92), Expect = 1e-04
Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ ++++ L + +TE+ I F P+ V + D + G
Sbjct: 5 SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTG 56
Score = 35.5 bits (82), Expect = 0.003
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 88 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYG---ITGLVEFLQKN 143
++ + + ++ LPYR D+ F P + + + P G VEF
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHE 66
Query: 144 QAKAA 148
A AA
Sbjct: 67 DAVAA 71
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
E +I N+ F+ T+ + + + +V V + + G
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLG 58
Score = 39.0 bits (91), Expect = 2e-04
Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 147
+K + N+P+ D+ E + G LV+F ++ A+
Sbjct: 13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72
Query: 148 A 148
+
Sbjct: 73 S 73
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
+ D + ++ L F +++ I + F + +T+ +S G
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG 58
Score = 36.6 bits (85), Expect = 0.001
Identities = 9/63 (14%), Positives = 22/63 (34%), Gaps = 6/63 (9%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 145
+ + + ++ LP+ ++ F + + P G V+F + A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 146 KAA 148
+ A
Sbjct: 71 EKA 73
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 8/54 (14%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 214 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+ L++ L++++T++++R +F + G + + KD +
Sbjct: 3 SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI--MKDKTT 54
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 9/46 (19%), Positives = 17/46 (36%)
Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
++E L+I +L + + + F G + S V K
Sbjct: 17 GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62
Score = 33.4 bits (77), Expect = 0.022
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ + +LP DL +F PFG++ V T L V + A+AA S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
>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 = 40.2 bits (93), Expect = 2e-04
Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 8/87 (9%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNS 151
R + +K P D+K E G + + + + V F AK +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
Query: 152 LAYTKFKEVPLYLEWAPEGVFAEAKEK 178
K+KE L + + + + K +
Sbjct: 170 PG-QKYKETDLLILFKDD--YFAKKNE 193
Score = 36.0 bits (82), Expect = 0.007
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 210 PEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
P DE + + ++YIK ++T D I+ + G + ++ + R G
Sbjct: 92 PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 151
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 9/45 (20%), Positives = 19/45 (42%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ L+I + N E ++ F++ G I +TV + +
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF 50
Score = 33.5 bits (77), Expect = 0.015
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
+ +P DLK LFE FG + + V TG+ + + ++ A A ++L
Sbjct: 18 IGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 39.3 bits (92), Expect = 3e-04
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 199 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
++ QQ +P + N EP+ L + + E +R+ F++ GPI SV
Sbjct: 20 QQLQQQQQQHIPPTQMN------PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73
Query: 259 VARKKD 264
+ ++
Sbjct: 74 IVCDRE 79
Score = 35.5 bits (82), Expect = 0.005
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
++V +P L+ LFE +G + V + T V+F + A+ A L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
>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 = 38.7 bits (90), Expect = 3e-04
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPG 269
E E + + + L ++ T + + F C + +D K G
Sbjct: 5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRG 56
Score = 29.8 bits (67), Expect = 0.32
Identities = 11/65 (16%), Positives = 19/65 (29%), Gaps = 8/65 (12%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-----RVLVPPYGIT---GLVEFLQKN 143
E +I + LP+ D+ F L+ G L+E +
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
Query: 144 QAKAA 148
+ A
Sbjct: 67 DVQKA 71
>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 = 38.3 bits (90), Expect = 3e-04
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ LY+ +L+FN TED +R F+ G I ++ + + D
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD 42
Score = 37.5 bits (88), Expect = 5e-04
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ V +L + L+ +FEPFG + +++ TG + F A+ A L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 38.1 bits (89), Expect = 3e-04
Identities = 7/35 (20%), Positives = 16/35 (45%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
++++ + +F GP+ASV + + K
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK 44
Score = 34.2 bits (79), Expect = 0.007
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAA 148
+ R + V P L F FG + V++ G+ +VE +A
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAV 61
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 38.0 bits (89), Expect = 3e-04
Identities = 11/40 (27%), Positives = 15/40 (37%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
LYI NL+ T D +R+ F + V K
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS 44
Score = 36.1 bits (84), Expect = 0.002
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 3/69 (4%)
Query: 101 VKNLPYRTLPTDLKALFEPFGD-LGRVLVPPYGITGLVEFLQKNQAKAAFNSL-AYTKFK 158
+ NL DL+ LF L ++ G V++ +N A A +L +
Sbjct: 13 IGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGY-AFVDYPDQNWAIRAIETLSGKVELH 71
Query: 159 EVPLYLEWA 167
+ ++++
Sbjct: 72 GKIMEVDYS 80
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 10/46 (21%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
++ T +++ L +++T+ S+R++F+ G I V D ++
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV--ITDRQT 55
Score = 26.9 bits (60), Expect = 3.4
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
I V LPY T L+ FE FGD+ +V
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVV 49
>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 = 38.4 bits (89), Expect = 4e-04
Identities = 6/52 (11%), Positives = 19/52 (36%), Gaps = 3/52 (5%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPG 269
E + ++ L ++ + + ++ C +A V ++ + G
Sbjct: 11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62
Score = 30.7 bits (69), Expect = 0.18
Identities = 10/66 (15%), Positives = 20/66 (30%), Gaps = 10/66 (15%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPF---GDLGRVLVP------PYGITGLVEFLQK 142
E ++ ++ LP+ D++ + V G VE +
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGE-AFVELESE 71
Query: 143 NQAKAA 148
+ K A
Sbjct: 72 DDVKLA 77
>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 = 38.1 bits (89), Expect = 5e-04
Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 207 QGVPEVEENVEEDEEREPEPD-TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
G+ + + +P+ + ++I NLN + + F K G +A +V +
Sbjct: 6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62
Score = 33.5 bits (77), Expect = 0.017
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 101 VKNLPY-RTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK 158
+ NL +D++ +F +G + V Y V++ + A+AA
Sbjct: 32 IGNLNTALVKKSDVETIFSKYGRVAGCSVHKGY---AFVQYSNERHARAAVLGENGRVLA 88
Query: 159 EVPLYLEWA 167
L + A
Sbjct: 89 GQTLDINMA 97
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 99 ILVKNLPYRTL-PTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
+ + NLP + + DL +F P+G + ++ + + G ++F + A +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIEXESQEM 81
Query: 157 FKEVPLYLEWA 167
L LE +
Sbjct: 82 NFGKKLILEVS 92
Score = 37.3 bits (87), Expect = 7e-04
Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 222 REPEPDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
R + L+I NL + +++ + R F G I + +
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>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 = 37.6 bits (88), Expect = 5e-04
Identities = 7/45 (15%), Positives = 23/45 (51%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ ++++ N+ + +TE+ ++ F + GP+ S + ++
Sbjct: 1 DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE 45
Score = 33.8 bits (78), Expect = 0.013
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 147
RS R + V N+PY LK +F G + + TG E+ + A +
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 148 AFNSL 152
A +L
Sbjct: 66 AMRNL 70
>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 = 37.5 bits (87), Expect = 6e-04
Identities = 9/88 (10%), Positives = 24/88 (27%), Gaps = 10/88 (11%)
Query: 90 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGD--LGRVLVPPYGITG------LVEFLQ 141
+ + + +P ++ + L ++ VE+
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 142 KNQAKAAFNSLAYTKFK--EVPLYLEWA 167
A A L + + + ++WA
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDWA 89
Score = 37.5 bits (87), Expect = 7e-04
Identities = 6/48 (12%), Positives = 12/48 (25%), Gaps = 3/48 (6%)
Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQF 271
+ L+I + + I K + V V +
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIV--YASAADKMKN 51
>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 = 37.6 bits (88), Expect = 7e-04
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
P ++IKNL+ + ++ F G I S V
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 39
Score = 33.4 bits (77), Expect = 0.017
Identities = 22/153 (14%), Positives = 44/153 (28%), Gaps = 55/153 (35%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 150
I +KNL L F FG++ V + G V F + A+ A
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKV----VCDENGSKGYGFVHFETQEAAERAIE 63
Query: 151 SLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVP 210
+ + +++ +++++ + + + +E
Sbjct: 64 KMNGMLLNDRKVFVGR------FKSRKEREAELGARAKEF-------------------- 97
Query: 211 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS 243
T +YIKN ST +
Sbjct: 98 -----------------TNVYIKNFGPGSTRAA 113
>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 = 37.4 bits (87), Expect = 8e-04
Identities = 7/47 (14%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
D + + + F++ E+ +R F + +V + + ++ G
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNG 57
Score = 31.3 bits (71), Expect = 0.090
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYGI---TGLVEFLQKNQAKAA 148
+ V +P+ + D++ F +L G GLV+FL A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEA 72
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 36.7 bits (85), Expect = 0.001
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 3/78 (3%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLV--PPYGITGLVEFLQKNQAKAAF 149
A + V NLP +DLK G + L P + + A+ A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRR-AFLHYPDSAAAQQAV 73
Query: 150 NSLAYTKFKEVPLYLEWA 167
+ L + L + A
Sbjct: 74 SCLQGLRLGTDTLRVALA 91
Score = 34.8 bits (80), Expect = 0.005
Identities = 5/43 (11%), Positives = 15/43 (34%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
+Y+ NL ++ ++R ++ G + +
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG 54
>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 = 36.9 bits (86), Expect = 0.001
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
+P TL++K L+ ++TE++++ F +
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARI 44
Score = 29.5 bits (67), Expect = 0.40
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 9/60 (15%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
+ VK L T LK E F R + TG V+F + AKAA ++
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>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 = 36.9 bits (86), Expect = 0.001
Identities = 7/45 (15%), Positives = 20/45 (44%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
++++ +++ +L+ T + I+ F G I+ V +
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA 52
Score = 35.4 bits (82), Expect = 0.004
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V +L D+KA F PFG + V T G V F K A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 153 AYTKFKEVPLYLEWA 167
+ WA
Sbjct: 78 GGQWLGGRQIRTNWA 92
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 35.9 bits (84), Expect = 0.001
Identities = 9/38 (23%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
++I L++ +T++ +R +F + G + V +DP +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT 38
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 37.3 bits (86), Expect = 0.001
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 2/71 (2%)
Query: 80 NGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLV 137
+ +DA + I+V+NL Y L +F FG + +++ L+
Sbjct: 12 SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALL 71
Query: 138 EFLQKNQAKAA 148
++ A+ A
Sbjct: 72 QYADPVSAQHA 82
Score = 34.2 bits (78), Expect = 0.013
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 218 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ L ++NL + T D + + F K G + + K
Sbjct: 17 DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64
>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 = 35.7 bits (83), Expect = 0.002
Identities = 4/43 (9%), Positives = 17/43 (39%)
Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ +++ + T + +++ F + G + V + +
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
Score = 26.0 bits (58), Expect = 5.0
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 129
+ V +L+ F +G++ V +P
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIP 44
>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 = 36.5 bits (85), Expect = 0.002
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
++I L++ +T++ +R +F + G + V +DP +
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV--MRDPLT 63
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 37.8 bits (87), Expect = 0.002
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 9/45 (20%)
Query: 228 TTLYIKNLNFNST---------EDSIRRHFKKCGPIASVTVARKK 263
TLY+ ++ E IR F + G I + K
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK 179
Score = 35.1 bits (80), Expect = 0.013
Identities = 11/68 (16%), Positives = 25/68 (36%)
Query: 102 KNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP 161
K+L + + ++ +F GD+ R+ G V+F + A+ A +++
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPS 208
Query: 162 LYLEWAPE 169
Sbjct: 209 DKEWDDRR 216
>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 = 35.6 bits (83), Expect = 0.002
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+++ + N E +R +FKK G + V + D +
Sbjct: 6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVM--IYDAEK 48
Score = 25.6 bits (57), Expect = 9.0
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 129
I V +P+ T+L+ F+ FG + V++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMI 43
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 36.0 bits (83), Expect = 0.003
Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 3/80 (3%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
+ I +KNLP DLK L V + TG +EF + A
Sbjct: 26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALE 85
Query: 151 SLAYTKFKEVPLYLEWAPEG 170
L +F+ + +E
Sbjct: 86 RLNNIEFRGSVITVERDDNP 105
Score = 31.7 bits (72), Expect = 0.076
Identities = 6/53 (11%), Positives = 15/53 (28%), Gaps = 2/53 (3%)
Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
+ P + +KNL + ++ ++ T + G
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDG 68
>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 = 36.6 bits (84), Expect = 0.003
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 2/84 (2%)
Query: 70 VEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 129
V+ L + +DA + I+V+NL Y L +F FG + +++
Sbjct: 20 VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79
Query: 130 P--YGITGLVEFLQKNQAKAAFNS 151
L+++ A+ A S
Sbjct: 80 TKNNQFQALLQYADPVSAQHAKLS 103
Score = 35.1 bits (80), Expect = 0.009
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 218 EDEEREPEPDTTL--YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ L ++NL + T D + + F K G + + K
Sbjct: 35 DAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 82
>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 = 34.4 bits (80), Expect = 0.005
Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V +L L+ F+ F V T G V F ++ A+ A +S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 153 AYTKFKEVPLYLEWA 167
PL + WA
Sbjct: 64 QGQDLNGRPLRINWA 78
Score = 34.4 bits (80), Expect = 0.005
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
L++ +LN N ++++R FK S V
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ 38
>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 = 35.7 bits (82), Expect = 0.005
Identities = 10/92 (10%), Positives = 25/92 (27%), Gaps = 7/92 (7%)
Query: 181 GKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST 240
G + G + + A Q E + ++ L ++ +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQ----MGRGSMMLGPEGGEGFVVKLRGLPWSCS 57
Query: 241 EDSIRRHFKKC---GPIASVTVARKKDPKSPG 269
+ ++ C A V ++ + G
Sbjct: 58 VEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG 89
Score = 27.7 bits (61), Expect = 2.4
Identities = 9/65 (13%), Positives = 19/65 (29%), Gaps = 8/65 (12%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-----RVLVPPYGIT---GLVEFLQKN 143
E ++ ++ LP+ D++ + G VE ++
Sbjct: 40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99
Query: 144 QAKAA 148
K A
Sbjct: 100 DVKMA 104
>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 = 34.6 bits (80), Expect = 0.006
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKD-PKSPG 269
+L++ +L E+ I R F G + SV + R + G
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG 53
>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 = 34.1 bits (79), Expect = 0.007
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+++ + TED +R F + G + V + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41
Score = 26.0 bits (58), Expect = 5.6
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP 129
+ V +L+ F +GD+ V +P
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIP 38
>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 = 33.7 bits (78), Expect = 0.010
Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKDPKS 267
+ ++I NL+ E + F G I + R DP +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR--DPDT 44
>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 = 33.7 bits (78), Expect = 0.011
Identities = 7/31 (22%), Positives = 19/31 (61%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
+Y+ NL +++T + ++ F + G + +V +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKL 33
Score = 32.1 bits (74), Expect = 0.032
Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
I V NL Y +K LF FG + V + T VE Q+ A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 33.2 bits (77), Expect = 0.011
Identities = 6/38 (15%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+++ L+ N+T + ++ +F++ G + + D +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAML--MFDKTT 37
>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 = 33.3 bits (77), Expect = 0.011
Identities = 7/41 (17%), Positives = 15/41 (36%)
Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+++ +L+ T +I F G I+ V +
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA 43
Score = 32.5 bits (75), Expect = 0.026
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V +L + A F PFG + V T G V F K A+ A +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 153 AYTKFKEVPLYLEWA 167
+ WA
Sbjct: 69 GGQWLGGRQIRTNWA 83
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 34.5 bits (79), Expect = 0.012
Identities = 6/93 (6%), Positives = 22/93 (23%), Gaps = 6/93 (6%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIK 233
+ + P + R +Y+
Sbjct: 6 HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRR----AAVYVG 61
Query: 234 NLNFNSTEDSIRRHFKKCGP--IASVTVARKKD 264
+ ++ +T+ + + + G + + A +
Sbjct: 62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Score = 30.7 bits (69), Expect = 0.28
Identities = 9/62 (14%), Positives = 16/62 (25%), Gaps = 8/62 (12%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 150
+ V + + T L + G D+ + G V +N
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 151 SL 152
L
Sbjct: 118 LL 119
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 33.2 bits (76), Expect = 0.019
Identities = 17/68 (25%), Positives = 22/68 (32%), Gaps = 12/68 (17%)
Query: 97 RIILVKNLPY------RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQ 144
+ I+V P L L +LF G + + P TG VE N
Sbjct: 7 QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66
Query: 145 AKAAFNSL 152
AK S
Sbjct: 67 AKKIIKSF 74
Score = 27.8 bits (62), Expect = 1.7
Identities = 4/34 (11%), Positives = 12/34 (35%)
Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
I + + ++ F K G + ++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA 49
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 33.0 bits (75), Expect = 0.025
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+++ L + ED I F++ GP+ + +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSY 48
Score = 26.1 bits (57), Expect = 6.8
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
+ S+++ V LP ++ A F FG L
Sbjct: 5 SSGSRKV-FVGGLPPDIDEDEITASFRRFGPL 35
>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 = 32.9 bits (75), Expect = 0.031
Identities = 6/45 (13%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 229 TLYIKNLNFNSTEDSIRR---HFKKCGPIASVTVARKKDPKSPGQ 270
+++ L+ + + + +F K G I V +
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG 61
Score = 27.5 bits (61), Expect = 1.9
Identities = 11/70 (15%), Positives = 23/70 (32%), Gaps = 12/70 (17%)
Query: 95 SKRIILVKNLPYRTLPTDL---KALFEPFGDLGRVLVPPYGITGL---------VEFLQK 142
K ++ V L R ++ F FG + +V++ V +++
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 143 NQAKAAFNSL 152
A A +
Sbjct: 74 EDALRAIQCV 83
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 34.6 bits (78), Expect = 0.032
Identities = 13/63 (20%), Positives = 25/63 (39%)
Query: 167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP 226
A E + E + + E + EE+ E AE + + P+ ++ E E +
Sbjct: 71 ASETASPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEATNQG 130
Query: 227 DTT 229
D +
Sbjct: 131 DES 133
Score = 27.6 bits (60), Expect = 5.0
Identities = 10/43 (23%), Positives = 14/43 (32%)
Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
+ G + EN + + VPE E E E T
Sbjct: 4 HHHHHGHHHQLENLYFQGEETAVPENSGANTELVSGESEHSTN 46
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.0 bits (77), Expect = 0.032
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 3/67 (4%)
Query: 165 EWAPEGVFAEA-KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
+W E + +E + + E E ++ E + ++Q N D+
Sbjct: 89 KWREE--QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFY 146
Query: 224 PEPDTTL 230
+PD +
Sbjct: 147 QQPDADI 153
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 31.7 bits (73), Expect = 0.033
Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
+++ L+ ++ E+ IR +F G + S+ + D K+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIEL--PMDNKT 37
>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 = 32.3 bits (73), Expect = 0.033
Identities = 6/46 (13%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKD 264
+ + N+++ + +++ F + G + SV ++ D
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD 50
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 32.6 bits (75), Expect = 0.033
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPG 269
P+ +L++ +L + + + F K P V + S G
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKG 52
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.8 bits (79), Expect = 0.034
Identities = 40/242 (16%), Positives = 68/242 (28%), Gaps = 75/242 (30%)
Query: 51 EVLTGSGAATRLAMGETEIVEKTRAFLE--EN--GVQLDAFNQVVEARSKRIILVKNLPY 106
EVLT + L++ I E R L +N V D ++E+ S + L
Sbjct: 321 EVLTTNPRR--LSI----IAESIRDGLATWDNWKHVNCDKLTTIIES-S-----LNVLE- 367
Query: 107 RTLPTDLKALFEPFG----DLGRVLVPP--------YGITGLVE-FLQKNQAKAAFNSLA 153
P + + +F+ +P I V + K SL
Sbjct: 368 ---PAEYRKMFDRLSVFPPS---AHIPTILLSLIWFDVIKSDVMVVVNKLHKY----SLV 417
Query: 154 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKK-----ENTAEEDNQQG 208
+ KE + + ++ E K K E E + D+
Sbjct: 418 EKQPKESTISI----PSIYLELKVKL---------ENEYALHRSIVDHYNIPKTFDSDDL 464
Query: 209 VPEVEEN------------VEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
+P + +E E ++ L+F E IR S
Sbjct: 465 IPPYLDQYFYSHIGHHLKNIEHPERMTLFRM--VF---LDFRFLEQKIRHDSTAWNASGS 519
Query: 257 VT 258
+
Sbjct: 520 IL 521
Score = 34.4 bits (78), Expect = 0.041
Identities = 21/134 (15%), Positives = 44/134 (32%), Gaps = 44/134 (32%)
Query: 157 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGE------EEKKENTAEEDNQQGVP 210
K+V P+ + + KE+ K+ K+E ++
Sbjct: 35 CKDVQDM----PKSILS--KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK------- 81
Query: 211 EVEENVEED----------EEREPEPDTTLYIKNLN--FNSTE-------------DSIR 245
VEE + + E+R+P T +YI+ + +N + +R
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
Query: 246 RHFKKCGPIASVTV 259
+ + P +V +
Sbjct: 142 QALLELRPAKNVLI 155
Score = 27.5 bits (60), Expect = 6.9
Identities = 3/20 (15%), Positives = 8/20 (40%)
Query: 231 YIKNLNFNSTEDSIRRHFKK 250
++ N + +D + K
Sbjct: 29 FVDNFDCKDVQDMPKSILSK 48
>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 = 32.0 bits (73), Expect = 0.034
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
LY+ N+ F TE+++ F + +T A
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA 39
Score = 30.9 bits (70), Expect = 0.083
Identities = 12/68 (17%), Positives = 20/68 (29%), Gaps = 11/68 (16%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQK 142
S R + V N+P+ + F LG + P +EF
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 143 NQAKAAFN 150
++ A
Sbjct: 64 DETTQAMA 71
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 32.0 bits (73), Expect = 0.034
Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 98 IILVKNLP------YRTLPTDLKALFEPFGDLGRVLVPPY-GIT---GLVEFLQKNQAKA 147
+I+V N+P L + +F FG + P G T +E+ A
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62
Query: 148 AFNSLAYTKF 157
A + K
Sbjct: 63 AVKNADGYKL 72
Score = 26.2 bits (58), Expect = 3.8
Identities = 10/49 (20%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 227 DTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
D+ + + N+ ++ I + F K G I + ++D K+ G
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKG 48
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 32.7 bits (74), Expect = 0.037
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV-PPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
+ ++N Y L + P G + R+++ GI +VEF A+ A +L
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI 87
Query: 158 --KEVPLYLEWA 167
L +E+A
Sbjct: 88 YAGCCTLKIEYA 99
Score = 30.8 bits (69), Expect = 0.16
Identities = 7/53 (13%), Positives = 17/53 (32%)
Query: 211 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
+ D+ L I+N + T D + G + + + ++
Sbjct: 9 RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN 61
>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 = 30.6 bits (70), Expect = 0.12
Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPYGITG------LVEFLQKNQAKAAFN 150
+ + NL + T DL G D+ + G LV + +K +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 151 SL 152
L
Sbjct: 64 LL 65
Score = 30.6 bits (70), Expect = 0.13
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGP--IASVTV 259
LYI NL + +T++ + G I +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKF 35
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 30.5 bits (69), Expect = 0.15
Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 12/72 (16%)
Query: 97 RIILVKNLPYRT------LPTDLKALFEPFGDLGRVLVP-----PYGITGLVEFLQKNQA 145
+I+V N+P L + +F FG + P G +E+ A
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGY-IFLEYASPAHA 74
Query: 146 KAAFNSLAYTKF 157
A + K
Sbjct: 75 VDAVKNADGYKL 86
Score = 27.8 bits (62), Expect = 1.6
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 217 EEDEEREPEPDTTLYIKNL------NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
++ + D+ + + N+ ++ I + F K G I + +D K+ G
Sbjct: 5 KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-EDGKTKG 62
>3bfj_A 1,3-propanediol oxidoreductase; opportunistic pathogens, decamer,
structural genomics,struct proteomics in europe, spine;
2.70A {Klebsiella pneumoniae}
Length = 387
Score = 31.8 bits (73), Expect = 0.22
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 30 LFLGTNAIAEA--MAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAF 87
F G NAI+ + KA ++T G L + V+KT +L E G+++ F
Sbjct: 14 NFFGPNAISVVGERCQLLGGKKALLVTDKG----LRAIKDGAVDKTLHYLREAGIEVAIF 69
Query: 88 NQVV 91
+ V
Sbjct: 70 DGVE 73
>3ox4_A Alcohol dehydrogenase 2; iron, NAD, oxidoreductase; HET: NAD;
2.00A {Zymomonas mobilis} PDB: 3owo_A*
Length = 383
Score = 30.6 bits (70), Expect = 0.47
Identities = 8/64 (12%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 30 LFLGTNAIAEAMAE--TYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAF 87
+G ++ +A+ + A +++ + M ++ +V++ L+ G+ +
Sbjct: 12 NEMGEGSLEKAIKDLNGSGFKNALIVSDAF------MNKSGVVKQVADLLKAQGINSAVY 65
Query: 88 NQVV 91
+ V+
Sbjct: 66 DGVM 69
>1rrm_A Lactaldehyde reductase; structural genomics, dehydrogenase, PSI,
protein structure initiative; HET: APR; 1.60A
{Escherichia coli} SCOP: e.22.1.2 PDB: 2bi4_A* 2bl4_A*
Length = 386
Score = 30.6 bits (70), Expect = 0.54
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 8/64 (12%)
Query: 30 LFLGTNAIAEAMAE--TYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAF 87
+ G A+ E KA ++T + + +V K ++ G+ +
Sbjct: 12 AWFGRGAVGALTDEVKRRGYQKALIVTDKT------LVQCGVVAKVTDKMDAAGLAWAIY 65
Query: 88 NQVV 91
+ VV
Sbjct: 66 DGVV 69
>3cx5_F Cytochrome B-C1 complex subunit 6; complex III, electron transfer
complex, cytochrome BC1 complex,
mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ
HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces
cerevisiae} SCOP: f.28.1.1 PDB: 3cxh_F* 1ezv_H* 1kb9_F*
1p84_F* 2ibz_H* 1kyo_F*
Length = 146
Score = 29.5 bits (65), Expect = 0.70
Identities = 14/63 (22%), Positives = 27/63 (42%)
Query: 163 YLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 222
Y E V ++ E+ EEK+E +ED + E +++ ++++E
Sbjct: 9 YWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDDDDDDEDEE 68
Query: 223 EPE 225
E E
Sbjct: 69 EEE 71
Score = 29.1 bits (64), Expect = 0.84
Identities = 15/61 (24%), Positives = 28/61 (45%)
Query: 170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
V A + ++ E++ E E EEE + +ED + + ++ EE+EE +
Sbjct: 20 VVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDDDDDDEDEEEEEEVTDQLED 79
Query: 230 L 230
L
Sbjct: 80 L 80
>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A
{Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A*
1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A*
1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A*
2ga2_A* 2oaz_A*
Length = 478
Score = 30.3 bits (68), Expect = 0.76
Identities = 11/54 (20%), Positives = 27/54 (50%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
EA +K + K+K+ E++ + + + ++E + ED+ER+ + +
Sbjct: 33 EAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDEDDE 86
>1v6t_A Hypothetical UPF0271 protein PH0986; TIM-barrel, lactam utilization
protein, structural genomics; 1.70A {Pyrococcus
horikoshii} SCOP: c.6.2.5
Length = 255
Score = 29.8 bits (68), Expect = 0.87
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 68 EIVEKTRAFLEENGVQLDAFNQVV 91
EI R LEE GV++ + +
Sbjct: 231 EITSYIRKVLEEEGVKIVPMKEFI 254
>1dkg_A Nucleotide exchange factor GRPE; HSP70, GRPE, nucleotide exchange
factor, coiled-coil, complex (HSP24/HSP70); 2.80A
{Escherichia coli} SCOP: b.73.1.1 h.1.9.1
Length = 197
Score = 29.3 bits (66), Expect = 1.1
Identities = 9/42 (21%), Positives = 16/42 (38%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
KE++ E EE + E + + E+ DE+
Sbjct: 4 KEQKTPEGQAPEEIIMDQHEEIEAVEPEASAEQVDPRDEKVA 45
>1xw8_A UPF0271 protein YBGL; NESG, northeast structural genomics
consortium, structural genomics, protein structure
initiative, PSI, X-RAY; 2.00A {Escherichia coli} SCOP:
c.6.2.5
Length = 252
Score = 29.0 bits (66), Expect = 1.5
Identities = 4/22 (18%), Positives = 8/22 (36%)
Query: 68 EIVEKTRAFLEENGVQLDAFNQ 89
+ R+ E G+ + A
Sbjct: 226 AFARRLRSAFAEKGIVVAALEH 247
>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis
lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A*
1u0y_A* 1yt2_A*
Length = 269
Score = 28.7 bits (65), Expect = 1.7
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEER 222
K + E EEE+ E+++ VEE EE + +
Sbjct: 215 SSKTETVEEPMEEEEAA-KEEKEDSDDEAAVEEEEEEKKPK 254
Score = 26.8 bits (60), Expect = 7.0
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 176 KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
K++ E+ EE +EEK+++ E E EE ++ + ++
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAV-----EEEEEEKKPKTKK 257
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 28.7 bits (64), Expect = 2.8
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 74 RAFLEENGV---QLDAFNQVVEARSKRII 99
+F EE + QL +F++ V+ + I+
Sbjct: 22 SSFFEETSLARQQLFSFDEFVQNTMQEIV 50
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Length = 423
Score = 28.3 bits (63), Expect = 2.9
Identities = 15/88 (17%), Positives = 35/88 (39%), Gaps = 9/88 (10%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKEN---TAEEDNQQGVPEVEENVEEDEEREPEPDTTL 230
+ ++ + +E E +E+ E E + + + + +E+D PE L
Sbjct: 2 KKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGL 61
Query: 231 YIK------NLNFNSTEDSIRRHFKKCG 252
++ + ST D +R++ + G
Sbjct: 62 DLEEEEEDLPIPKISTSDPVRQYLHEIG 89
>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal
nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO
MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G*
3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 3bdm_F* 1fnt_G* 2zcy_F*
Length = 288
Score = 27.7 bits (62), Expect = 3.6
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE 223
+KE N + + +E+ +N D++ N D+E +
Sbjct: 244 QKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGD 284
>2xzm_B RPS0E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_B
Length = 241
Score = 27.5 bits (61), Expect = 3.9
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEE 221
K E+ E EEE+ AEE + E +++
Sbjct: 201 KTLPTAEQKEAEEEEGAEGAEEKVAEVKEGEAEQNTDNKN 240
>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T*
1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S*
3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z
1pnu_T 1pny_T 1vor_W ...
Length = 237
Score = 27.4 bits (61), Expect = 4.7
Identities = 6/45 (13%), Positives = 17/45 (37%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
+ + + + E+ + V E + ++EE + E +
Sbjct: 181 LEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDN 225
>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 = 27.4 bits (60), Expect = 4.8
Identities = 9/41 (21%), Positives = 18/41 (43%)
Query: 112 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 152
L + E G + +L+PP + ++K A+ +L
Sbjct: 36 QLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTL 76
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 27.5 bits (61), Expect = 5.3
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 74 RAFLEENGV---QLDAFNQVVEARSKRII 99
AF E G+ QLD+FNQ V+ + II
Sbjct: 35 SAFFREKGLVSQQLDSFNQFVDYTLQDII 63
>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B*
3thy_B* 3thz_B*
Length = 918
Score = 27.6 bits (62), Expect = 5.4
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE 225
P + +A KSK E N + ++ + A+ ++++ EE E +
Sbjct: 863 PGEILKKAAHKSKELEGLINT----KRKRLKYFAKLWTMHNAQDLQKWTEEFNMEETQ 916
>3lo3_A Uncharacterized conserved protein; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 2.38A {Colwellia psychrerythraea}
Length = 94
Score = 26.1 bits (58), Expect = 5.6
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 12/57 (21%)
Query: 114 KALFEPFGDLGRVLV----------PPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
+ + G VLV + ++EF + A ++S Y
Sbjct: 27 ASTLAKYS--GEVLVKGSVEQLHGKFEHKAQVILEFPSREDAYNWYHSEEYQALIST 81
>3r38_A UDP-N-acetylglucosamine 1-carboxyvinyltransferase; biosynthesis and
degradation of murein sacculus and peptidog infectious
diseases; 2.23A {Listeria monocytogenes} PDB: 3sg1_A*
Length = 454
Score = 27.1 bits (61), Expect = 7.9
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 17/88 (19%)
Query: 33 GTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVE 92
GT IA A+ T VL ++ ++ K LEE GVQ+ +
Sbjct: 261 GTFMIAAAI------TGGNVLIEDAVPEHISS----LIAK----LEEMGVQIIEEENGIR 306
Query: 93 ARSKRIIL---VKNLPYRTLPTDLKALF 117
+ VK +P+ PTD+++
Sbjct: 307 VIGPDKLKAVDVKTMPHPGFPTDMQSQM 334
>2fiu_A Conserved hypothetical protein; alpha-beta, dimeric alpha-beta
barrels, structural genomics, protein structure
initiative; 2.00A {Agrobacterium tumefaciens str} SCOP:
d.58.4.16
Length = 99
Score = 25.7 bits (57), Expect = 7.9
Identities = 12/57 (21%), Positives = 17/57 (29%), Gaps = 12/57 (21%)
Query: 114 KALFEPFGDLGRVLV----------PPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
K FE FG L ++EF A +NS Y ++
Sbjct: 28 KPAFERFG--ANFLARGGSVTELEGTARARNVVIEFPSVQHAIDCYNSPEYQAAAKI 82
>2xqh_A Immunoglobulin-binding protein EIBD; cell adhesion, virulence,
beta-helix; 1.99A {Escherichia coli}
Length = 281
Score = 27.0 bits (59), Expect = 8.0
Identities = 12/48 (25%), Positives = 20/48 (41%)
Query: 28 NSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRA 75
NS+ LG N++ E Y K + TR+ G ++ + A
Sbjct: 119 NSVALGANSVTTRDNEVYIGYKTGTESDKTYGTRVLGGLSDGTRNSDA 166
>2cg9_A ATP-dependent molecular chaperone HSP82; chaperone complex, HSP90,
heat shock protein, ATP-binding, heat shock,
nucleotide-binding, acetylation; HET: ATP; 3.1A
{Saccharomyces cerevisiae}
Length = 677
Score = 27.0 bits (60), Expect = 8.4
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
KE +E EE+K++ ++D ++ + ++ E+ + E E
Sbjct: 210 TKEVEKEVPIPEEEKKDEEKKDEEKKDEDDKKPKLEEVDEEEEKK 254
>2dfa_A Hypothetical UPF0271 protein TTHB195; lactam utilization protein,
structural genomics, NPPSFA; 1.90A {Thermus
thermophilus} SCOP: c.6.2.5
Length = 250
Score = 26.7 bits (60), Expect = 8.9
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 68 EIVEKTRAFLEENGVQLDAF 87
E+ R LE+ GV++ AF
Sbjct: 231 EVARAVREALEQAGVEVRAF 250
>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral
twinning, leucine-rich repeat protein, LRR, merohedral
twinning; 2.2A {Schizosaccharomyces pombe} SCOP:
c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A
Length = 386
Score = 26.6 bits (59), Expect = 9.2
Identities = 12/47 (25%), Positives = 18/47 (38%)
Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDE 220
+ + + E + EE EEE+ E E EE E+ E
Sbjct: 330 STRGRGELDELDDMEELTDEEEEDEEEEAESQSPEPETSEEEKEDKE 376
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
0.309 0.129 0.357
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,153,132
Number of extensions: 256993
Number of successful extensions: 1064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 941
Number of HSP's successfully gapped: 454
Length of query: 274
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 182
Effective length of database: 4,133,061
Effective search space: 752217102
Effective search space used: 752217102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 56 (26.1 bits)