RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy300
(451 letters)
>1e9g_A Ppase, inorganic pyrophosphatase; pyrophosphate phosphohydrolase,
hydrolase, manganese; HET: PO4; 1.15A {Saccharomyces
cerevisiae} SCOP: b.40.5.1 PDB: 1e6a_A* 1wgi_A 1wgj_A
2ihp_A* 8prk_A 2ik6_A 2ik2_A 2ik4_A 117e_A 2ik1_A*
2ik9_A 2ik0_A 2ik7_A 1m38_A 1ypp_A 1huk_A 1huj_A 1pyp_A
Length = 286
Score = 262 bits (672), Expect = 1e-85
Identities = 121/185 (65%), Positives = 146/185 (78%)
Query: 156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
Y + +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI E LNPI QD KKG L
Sbjct: 18 YIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKL 77
Query: 216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
R+V N FPHHGYI NYGA PQTWE+P+ + T GD DPIDVLEIGE IA G++ QV
Sbjct: 78 RFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQV 137
Query: 276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
KALG++ L+DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDG
Sbjct: 138 KALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDG 197
Query: 336 KPENV 340
KPEN
Sbjct: 198 KPENQ 202
Score = 67.2 bits (164), Expect = 1e-12
Identities = 24/39 (61%), Positives = 32/39 (82%)
Query: 380 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
+ +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 21 KDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59
>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 = 113 bits (286), Expect = 5e-30
Identities = 29/157 (18%), Positives = 64/157 (40%), Gaps = 34/157 (21%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL---KGCGFINYANKISAVK 88
++F+ +P +E++ +E F QYG + + +L++ KGC F+ + + +A++
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 89 AILKSN---------------------KKPYKGK----------ITEEEFKEHFGQYGDI 117
A + + + TE + + F +G I
Sbjct: 63 AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
+ ++L+ DG +GC F+ + + A AI ++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Score = 91.5 bits (228), Expect = 6e-22
Identities = 22/96 (22%), Positives = 42/96 (43%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
L K + K + +K + + +LFI + K TE + + F +G I
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 61 DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 96
+ ++L+ DG +GC F+ + + A AI ++
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
>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 = 114 bits (286), Expect = 4e-29
Identities = 39/165 (23%), Positives = 73/165 (44%), Gaps = 26/165 (15%)
Query: 19 KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
K ++ + T+R RLF+ NLP ITEE+FK F +YG+ + + ++ +G GFI
Sbjct: 9 KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFI 63
Query: 79 NYANKISAVKAILKSNKKPYKGK---------------------ITEEEFKEHFGQYGDI 117
++ A A + + K + ++ E ++ F Q+G +
Sbjct: 64 RLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPV 123
Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENG 162
A ++ + G+ G GF+ +A K A KA+ + + +
Sbjct: 124 EKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTP 168
Score = 70.9 bits (174), Expect = 5e-14
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 2/88 (2%)
Query: 14 FKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK 73
+ + + L +KNL ++ E ++ F Q+G + A ++ + G+
Sbjct: 80 GTILKSRPLRIRFATHGAA--LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137
Query: 74 GCGFINYANKISAVKAILKSNKKPYKGK 101
G GF+ +A K A KA+ + +
Sbjct: 138 GKGFVEFAAKPPARKALERCGDGAFLLT 165
>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 = 112 bits (283), Expect = 2e-28
Identities = 34/166 (20%), Positives = 64/166 (38%), Gaps = 28/166 (16%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
++ +K++E + R ++ I+ LP +T +E + Y + + K KG
Sbjct: 5 PEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY-----KG 58
Query: 75 CGFINYANKISAVKAILKSNKKPYKGK---------------------ITEEEFKEHFGQ 113
F+ N A AI ++ + + +T+++F+E
Sbjct: 59 TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRP 118
Query: 114 YGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+G + L+ + G+ KG GF Y K SA +A KP
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164
Score = 111 bits (280), Expect = 5e-28
Identities = 33/175 (18%), Positives = 60/175 (34%), Gaps = 37/175 (21%)
Query: 17 KGKK-KIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKG 74
+ ++ ++ + D L + NLP +T+++F+E +G + L+ + G+ KG
Sbjct: 83 RERELSVQLQPTD----ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138
Query: 75 CGFINYANKISAVKAILKSNKKPYKGK------------------------------ITE 104
GF Y K SA +A KP + +
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFND 198
Query: 105 EE-FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ QL DG+LKG + Y A +A +++ G
Sbjct: 199 VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG 253
Score = 73.5 bits (181), Expect = 8e-15
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 1/79 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEE-FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
+ P L + LP + + QL DG+LKG + Y
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYET 235
Query: 83 KISAVKAILKSNKKPYKGK 101
A +A +++ G
Sbjct: 236 AEMAEEAQQQADGLSLGGS 254
Score = 41.9 bits (99), Expect = 2e-04
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 6/59 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+T +E + Y + + K KG F+ N A AI ++ + E
Sbjct: 34 VTNQEVHDLLSDYE-LKYCFVDKY-----KGTAFVTLLNGEQAEAAINAFHQSRLRERE 86
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 103 bits (258), Expect = 1e-25
Identities = 32/178 (17%), Positives = 68/178 (38%), Gaps = 40/178 (22%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLK 73
++ G+ +++ R+++ ++ +++ E+ ++ F +G I + ++ K K
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
Query: 74 GCGFINYANKISAVKAILKSNKKPYKGK-------------------------------- 101
G F+ Y +A A+ + N G+
Sbjct: 71 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 130
Query: 102 ------ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
+++++ K F +G I A L ++ GK KG GFI Y S+ A+ N
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 77.7 bits (192), Expect = 1e-16
Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 2/98 (2%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRG-RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
+ KV + + I + ++ + R+++ ++ +++++ K F +G I A L
Sbjct: 98 RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATL 157
Query: 65 LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
++ GK KG GFI Y S+ A+ N G+
Sbjct: 158 ARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195
Score = 44.6 bits (106), Expect = 2e-05
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E+ ++ F +G I + ++ K KG F+ Y +A A+ + N G
Sbjct: 40 LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97
>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 = 99.6 bits (249), Expect = 7e-25
Identities = 32/154 (20%), Positives = 62/154 (40%), Gaps = 29/154 (18%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
L + LP +T+ E F G I +++++ G G F+++ +++ + +AI
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 94 NKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDAQLLK-N 125
N + K IT+++ FG+YG I+ +L+
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125
Query: 126 ADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
G+ +G F+ Y + A +AI N +G
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 159
Score = 72.2 bits (178), Expect = 3e-15
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYAN 82
R + K L++ NLP IT+++ FG+YG I+ +L+ G+ +G F+ Y
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 83 KISAVKAILKSNKKPYKG 100
+ A +AI N +G
Sbjct: 141 REEAQEAISALNNVIPEG 158
Score = 49.5 bits (119), Expect = 3e-07
Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+T+ E F G I +++++ G G F+++ +++ + +AI N +
Sbjct: 15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
>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 = 102 bits (257), Expect = 8e-25
Identities = 27/176 (15%), Positives = 58/176 (32%), Gaps = 23/176 (13%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGR--LFIKNLPFKITEEEFKEHFGQYGDIIDA 62
+K+ + G + + R + +KNLP + + ++F G II
Sbjct: 12 SKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV 71
Query: 63 QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKI-------------------T 103
+ + I +A A+ AI K++K + +I T
Sbjct: 72 DVADSLKKN-FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYT 130
Query: 104 EEEFKEHFGQYGDI-IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ ++ + + +L + +I+ +K A + K N +G
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG 186
Score = 98.9 bits (247), Expect = 2e-23
Identities = 27/177 (15%), Positives = 53/177 (29%), Gaps = 41/177 (23%)
Query: 10 VKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI-IDAQLLKNA 68
+ K K G+ +I + L++ N P T+ ++ + + +L
Sbjct: 98 ITKTHKVVGQNEIIVSHLTEC---TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR 154
Query: 69 DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------------------------- 101
+ +I+ +K A + K N +G
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM 214
Query: 102 --------ITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAI 148
+ E +E F +G I + C F+ + NK SA +A+
Sbjct: 215 IRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271
Score = 66.2 bits (162), Expect = 2e-12
Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 5/97 (5%)
Query: 8 KKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEE-FKEHFGQYGDIIDAQLLK 66
+ + +K +R + + I+NL ++ +E +E F +G I +
Sbjct: 187 YTLVTKVSNPLEKS-KRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPA 245
Query: 67 NAD--GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
C F+ + NK SA +A+ + N+ +
Sbjct: 246 GQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNR 281
>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 = 98.8 bits (247), Expect = 1e-24
Identities = 44/154 (28%), Positives = 71/154 (46%), Gaps = 29/154 (18%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
L + LP +T+EEF+ FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 94 NKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDAQLLK-N 125
N + K +T++E ++ F QYG II +++L
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 126 ADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
G +G GFI + +I A +AI N + G+
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 158
Score = 72.2 bits (178), Expect = 4e-15
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYAN 82
R + L++ LP +T++E ++ F QYG II +++L G +G GFI +
Sbjct: 80 RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139
Query: 83 KISAVKAILKSNKKPYKG 100
+I A +AI N + G
Sbjct: 140 RIEAEEAIKGLNGQKPSG 157
>3q46_A TT-ippase; inorganic pyrophosphatase, hydrolase; HET: EPE; 0.99A
{Thermococcus thioreducens} PDB: 3r6e_A* 3q3l_A 3i98_A
3q4w_A 3q9m_A* 3r5u_A 3r5v_A* 3q5v_A* 1ude_A 1twl_A
Length = 178
Score = 98.5 bits (246), Expect = 2e-24
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 37/176 (21%)
Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
PFH++ V + + ++EIP+ + K E+ D G L+ Y
Sbjct: 3 PFHELEPGPEVPE-VVYALIEIPKGSRNKYEL-----------DKATGLLKLDRVLYSPF 50
Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
+P +YG +PQTW DGDP D++ I II+ + +G+
Sbjct: 51 FYPV-----DYGIIPQTWY------------DDGDPFDIMVIMREPVYPLTIIEARPIGI 93
Query: 281 IGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
+ + D G DWK++A+ V DP D++D+ F L +F+ YK GK
Sbjct: 94 MKMEDSGDKDWKVLAVPVEDPYFNDWKDISDVPKAF---LDEIAHFFQRYKELQGK 146
Score = 32.6 bits (75), Expect = 0.15
Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 387 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
PFH++ V + + ++EIP+ + K E+
Sbjct: 3 PFHELEPGPEVPE-VVYALIEIPKGSRNKYEL 33
>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 = 96.9 bits (242), Expect = 6e-24
Identities = 31/163 (19%), Positives = 53/163 (32%), Gaps = 34/163 (20%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
+ + T LFI NL + E K + D ++ G + G++++ +
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 85 SAVKAILKSNKKPYKGK-----------------------------ITEEEFKEHFGQYG 115
KA+ + G ITE+E KE F
Sbjct: 66 DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124
Query: 116 DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+I DGK KG +I + ++ A K + + G
Sbjct: 125 EIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163
Score = 67.6 bits (166), Expect = 1e-13
Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 4/83 (4%)
Query: 19 KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
+K R L KNL F ITE+E KE F +I DGK KG +I
Sbjct: 86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYI 141
Query: 79 NYANKISAVKAILKSNKKPYKGK 101
+ ++ A K + + G+
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGR 164
>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 = 96.8 bits (242), Expect = 7e-24
Identities = 41/157 (26%), Positives = 77/157 (49%), Gaps = 28/157 (17%)
Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKA 89
+ ++FI L + TE+ +E+FG+YG + D +++K+ G+ +G GF+++ S +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 90 ILKSNK----------------KPYKGKI---------TEEEFKEHFGQYGDIIDAQLLK 124
+ + + GKI +EF+E F Q+G IIDAQL+
Sbjct: 62 VKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121
Query: 125 NAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ D G+ +G GF+ Y + AV + ++ +K +
Sbjct: 122 DKDTGQSRGFGFVTYDSA-DAVDRVCQNKFIDFKDRK 157
Score = 69.1 bits (170), Expect = 4e-14
Identities = 28/84 (33%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 19 KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGF 77
K+ I R + DKT + +F+ + + +EF+E F Q+G IIDAQL+ + D G+ +G GF
Sbjct: 76 KRAIPRDEQDKTGK--IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133
Query: 78 INYANKISAVKAILKSNKKPYKGK 101
+ Y + AV + ++ +K +
Sbjct: 134 VTYDSA-DAVDRVCQNKFIDFKDR 156
>2prd_A Pyrophosphate phosphohydrolase; 2.00A {Thermus thermophilus} SCOP:
b.40.5.1
Length = 174
Score = 94.2 bits (235), Expect = 7e-23
Identities = 36/170 (21%), Positives = 67/170 (39%), Gaps = 37/170 (21%)
Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANV 221
+P+ + + +MV+E+PR + K E D G ++ A
Sbjct: 3 LKSLPVGDKAPE-VVHMVIEVPRGSGNKYEY-----------DPDLGAIKLDRVLPGAQF 50
Query: 222 FPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVI 281
+P +YG +P T DGDP+D L + G +++V+ +G++
Sbjct: 51 YPG-----DYGFIPSTLA------------EDGDPLDGLVLSTYPLLPGVVVEVRVVGLL 93
Query: 282 GLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ DE D K+I + D + D+ D+ + +F+ YK
Sbjct: 94 LMEDEKGGDAKVIGVVAEDQRLDHIQDIGDVPEGV---KQEIQHFFETYK 140
Score = 30.3 bits (69), Expect = 0.77
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 388 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
+P+ + + +MV+E+PR + K E
Sbjct: 3 LKSLPVGDKAPE-VVHMVIEVPRGSGNKYEY 32
>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 = 93.1 bits (232), Expect = 3e-22
Identities = 36/168 (21%), Positives = 70/168 (41%), Gaps = 36/168 (21%)
Query: 20 KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFI 78
K K+P++ +LFI L F+ T+E + HF Q+G + D ++++ + + +G GF+
Sbjct: 3 KSESPKEPEQL--RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 79 NYANKISAVKAILK----------------------------SNKKPYKG----KITEEE 106
YA A+ + KK + G E
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 107 FKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 153
+++F QYG I +++ + GK +G F+ + + S K +++
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
Score = 63.5 bits (155), Expect = 7e-12
Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 16 KKGKKKIERKKPDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLK 73
K+ + + ++P + +F+ + E +++F QYG I +++ + GK +
Sbjct: 87 KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR 146
Query: 74 GCGFINYANKISAVKAILKSNKKPYKGK 101
G F+ + + +V I+ G
Sbjct: 147 GFAFVTFDDH-DSVDKIVIQKYHTVNGH 173
>3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, S
structural genomics center for infectious disease,
ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei
1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A*
Length = 196
Score = 90.1 bits (224), Expect = 3e-21
Identities = 44/174 (25%), Positives = 71/174 (40%), Gaps = 40/174 (22%)
Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVA 219
F ++P ++ FN+++EIP + K E D G L
Sbjct: 23 SFSNVPAGKDLPQ-DFNVIIEIPAQSEPVKYEA-----------DKALGLLVVDRFIGTG 70
Query: 220 NVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALG 279
+P NYG +PQT GDGDP+DVL I G +++ +ALG
Sbjct: 71 MRYPV-----NYGFIPQTLS------------GDGDPVDVLVITPFPLLAGSVVRARALG 113
Query: 280 VIGLIDEGQTDWKIIAINVND--PNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
++ + DE D K++A+ + P A L + D+ + +F+ YK
Sbjct: 114 MLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYL---KDQIKHFFEQYK 164
Score = 29.6 bits (67), Expect = 1.4
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 365 VSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEV 418
++ + ++ F ++P ++ FN+++EIP + K E
Sbjct: 1 MAHHHHHHMGTLEAQTQGPGSMSFSNVPAGKDLPQ-DFNVIIEIPAQSEPVKYEA 54
>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid,
hydrolase; 1.75A {Anaplasma phagocytophilum} PDB: 3lo0_A
Length = 199
Score = 90.1 bits (224), Expect = 3e-21
Identities = 45/174 (25%), Positives = 71/174 (40%), Gaps = 40/174 (22%)
Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVA 219
DI SN + N+V+E+ + + K E D K G L A
Sbjct: 23 NLDDIGSGSNAPE-EVNVVIEVSQDSHPVKYEF-----------DEKNGALWVDRFLPTA 70
Query: 220 NVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALG 279
+P NYG +P T GDGDP+DVL + G +I V+ +G
Sbjct: 71 MYYPC-----NYGFIPNTIA------------GDGDPVDVLVLARFPVMPGAVICVRPVG 113
Query: 280 VIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
V+ + DE D K++A+ D + + +D+ + F L + + +F YK
Sbjct: 114 VLMMNDEKGEDAKVLAVPATKVDQYYGNIVNYSDLPSSF---LDSISHFFSFYK 164
Score = 28.1 bits (63), Expect = 5.3
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 387 PFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEV 418
DI SN + N+V+E+ + + K E
Sbjct: 23 NLDDIGSGSNAPE-EVNVVIEVSQDSHPVKYEF 54
>1sxv_A Inorganic pyrophosphatase; structural genomics, ppase,, hydrolase;
1.30A {Mycobacterium tuberculosis} PDB: 1wcf_A 2uxs_A
4ecp_A
Length = 172
Score = 88.4 bits (220), Expect = 8e-21
Identities = 35/157 (22%), Positives = 62/157 (39%), Gaps = 36/157 (22%)
Query: 180 IFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFPHHGYIWNYGAL 234
F++ +EIP+ K E+ D + G +R Y +P +YG +
Sbjct: 12 QFDVTIEIPKGQRNKYEV-----------DHETGRVRLDRYLYTPMAYPT-----DYGFI 55
Query: 235 PQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKII 294
T DGDP+D L + + G ++ + +G+ ++DE D K++
Sbjct: 56 EDTLG------------DDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVL 103
Query: 295 AINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ DP + D+ D+ L A +F YK
Sbjct: 104 CVPAGDPRWDHVQDIGDVPAFE---LDAIKHFFVHYK 137
>2au7_A Inorganic pyrophosphatase; hydrolase, mutant; 1.05A {Escherichia
coli} PDB: 1i40_A 1i6t_A 1igp_A 1obw_A 2au6_A 2au8_A
2au9_A 2auu_A 1mjy_A 1faj_A 1ino_A 1ipw_A 1jfd_A 2eip_A
1mjz_A 1mjx_A 1mjw_A 3i4q_A*
Length = 175
Score = 87.3 bits (217), Expect = 2e-20
Identities = 38/173 (21%), Positives = 64/173 (36%), Gaps = 40/173 (23%)
Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
++P ++ + +V+EIP K EI D + G L A
Sbjct: 2 LLNVPAGKDLPE-DIYVVIEIPANADPIKYEI-----------DKESGALFVDQFMSTAM 49
Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
+P NYG + T DGDP+DVL + G + + + +GV
Sbjct: 50 FYPC-----NYGYINHTLS------------LDGDPVDVLVPTPYPLQPGSVTRCRPVGV 92
Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ + DE D K++A+ + + DV D+ +F+ YK
Sbjct: 93 LKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELL---KAQIAHFFEHYK 142
>3fq3_A Inorganic pyrophosphatase:bacterial/archaeal INOR pyrophosphatase;
ssgcid, inorganic phosphatase; 1.90A {Brucella
melitensis biovar abortus 230ORGANISM_TAXID} PDB: 3sw5_A
Length = 197
Score = 87.4 bits (217), Expect = 3e-20
Identities = 47/173 (27%), Positives = 67/173 (38%), Gaps = 40/173 (23%)
Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
I + SN + N+++E+P K E+ D K G L Y
Sbjct: 24 IDAISIGSNPPE-DVNVIIEVPVGGQPIKYEM-----------DKKAGALIVDRFLYTPM 71
Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
+P NYG +P T DGDPIDVL R G +I V+ +GV
Sbjct: 72 TYPG-----NYGFVPHTLS------------EDGDPIDVLVCNTRPLIPGCVINVRPIGV 114
Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ + D D KIIA+ K++D D+ LK +F+ YK
Sbjct: 115 LVMEDNSGKDEKIIAVPSPHLTRRYEKIHDYTDMPEIT---LKQIAHFFEHYK 164
Score = 27.7 bits (62), Expect = 6.1
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 388 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEV 418
I + SN + N+++E+P K E+
Sbjct: 24 IDAISIGSNPPE-DVNVIIEVPVGGQPIKYEM 54
>2bqx_A Inorganic pyrophosphatase; hydrolase; 1.90A {Helicobacter pylori}
PDB: 1ygz_A 2bqy_A
Length = 173
Score = 86.5 bits (215), Expect = 3e-20
Identities = 41/172 (23%), Positives = 72/172 (41%), Gaps = 40/172 (23%)
Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANV 221
+ + + +V+EI + +N K E+ D + G L Y A
Sbjct: 3 LEKLEVSHDADS--LCVVIEISKHSNIKYEL-----------DKESGALMVDRVLYGAQN 49
Query: 222 FPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVI 281
+P NYG +P T DGDP+D L + + + G +++ + +GV+
Sbjct: 50 YPA-----NYGFVPNTLG------------SDGDPVDALVLSDVAFQAGSVVKARLVGVL 92
Query: 282 GLIDEGQTDWKIIAI--NVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ DE D K+IA+ + DP + + D+ D+ H L +F+ YK
Sbjct: 93 NMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHT---LDKIKHFFETYK 141
>1qez_A Ppase, S-ppase, protein (inorganic pyrophosphatase);
thermostability, magnesium, hydrolase; 2.70A {Sulfolobus
acidocaldarius} SCOP: b.40.5.1
Length = 173
Score = 85.4 bits (212), Expect = 1e-19
Identities = 45/170 (26%), Positives = 76/170 (44%), Gaps = 39/170 (22%)
Query: 169 DIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFP 223
+ N D + N++VEIP+ +N K E D ++G ++ Y + +P
Sbjct: 2 KLSPGKNAPD-VVNVLVEIPQGSNIKYEY-----------DDEEGVIKVDRVLYTSMNYP 49
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
NYG +P T E DGDP+DVL I G +I+V+ +G++ +
Sbjct: 50 F-----NYGFIPGTLE------------EDGDPLDVLVITNYQLYPGSVIEVRPIGILYM 92
Query: 284 IDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
DE D KI+A+ + DP+ + + D+ D+ +F+ YK
Sbjct: 93 KDEEGEDAKIVAVPKDKTDPSFSNIKDINDLPQAT---KNKIVHFFEHYK 139
>3d53_A Inorganic pyrophosphatase; seattle structural G center for
infectious disease, ssgcid, hydrolase, magnesium
binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A*
Length = 173
Score = 84.3 bits (209), Expect = 2e-19
Identities = 42/173 (24%), Positives = 67/173 (38%), Gaps = 41/173 (23%)
Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
I +N + N+++EIP + K E D + G L
Sbjct: 4 IKKIKAKAN--NNEINVIIEIPMNSGPIKYEF-----------DKESGALFVDRFMQTTM 50
Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
+P NYG +P T DGDP+DVL + G +I+ +A+GV
Sbjct: 51 SYPC-----NYGFIPDTLS------------NDGDPVDVLVVAHHPVVPGSVIKCRAIGV 93
Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
+ + DE D KIIA+ + D + ++ D+ K +F+ YK
Sbjct: 94 LMMEDESGLDEKIIAVPTSKLDITFDHIKELDDLCEML---KKRIVHFFEHYK 143
>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 = 83.8 bits (208), Expect = 3e-19
Identities = 27/153 (17%), Positives = 53/153 (34%), Gaps = 35/153 (22%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN------ADGKLKGCGFINYANKISAV 87
RL++ N+PF ITEE + F + + K F+ + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 88 KAILKSNKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDA 120
+A + + ++G+ + +++ KE +G +
Sbjct: 66 QA-MAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124
Query: 121 QLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
L+K++ G KG F Y + +AI N
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Score = 71.1 bits (175), Expect = 1e-14
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 21 KIERKKPDKTKRG--RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGF 77
KI R + G +LFI LP + +++ KE +G + L+K++ G KG F
Sbjct: 81 KIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 140
Query: 78 INYANKISAVKAILKSNKKPYKGK 101
Y + +AI N K
Sbjct: 141 CEYVDINVTDQAIAGLNGMQLGDK 164
>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 = 81.6 bits (202), Expect = 3e-19
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
E + K LF+ L + +EE+ F +G I + +L+ DG KGC F+ +++
Sbjct: 9 ESRGGRDRK---LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65
Query: 83 KISAVKAILKSNKK 96
A AI +
Sbjct: 66 HTEAQAAIHALHGS 79
Score = 62.7 bits (153), Expect = 1e-12
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
+ +EE+ F +G I + +L+ DG KGC F+ +++ A AI +
Sbjct: 26 QQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
>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 = 78.9 bits (195), Expect = 3e-18
Identities = 21/68 (30%), Positives = 38/68 (55%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+F+ NL +K+ ++ KE F G ++ A +L++ DGK +G G + + I AV+AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 94 NKKPYKGK 101
N + +
Sbjct: 77 NGQLLFDR 84
Score = 59.2 bits (144), Expect = 3e-11
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
K+ ++ KE F G ++ A +L++ DGK +G G + + I AV+AI N +
Sbjct: 26 KVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD 83
>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 = 78.8 bits (195), Expect = 4e-18
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 1/90 (1%)
Query: 12 KEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGK 71
K G + + K + L+I NLP + E+E + +G +I ++L+++ G
Sbjct: 6 SGLKASGVQA-QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64
Query: 72 LKGCGFINYANKISAVKAILKSNKKPYKGK 101
+G GF + I N K K
Sbjct: 65 SRGVGFARMESTEKCEAVIGHFNGKFIKTP 94
Score = 54.6 bits (132), Expect = 1e-09
Identities = 13/57 (22%), Positives = 25/57 (43%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E+E + +G +I ++L+++ G +G GF + I N K K
Sbjct: 37 MDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT 93
>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 = 81.2 bits (201), Expect = 6e-18
Identities = 30/155 (19%), Positives = 61/155 (39%), Gaps = 31/155 (20%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISA 86
L++ +L +TE E F G I+ ++ ++ + G ++N+ A
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 87 VKAILKSNKKPYKGK-----------------------------ITEEEFKEHFGQYGDI 117
+A+ N KGK I + + F +G+I
Sbjct: 71 ERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNI 130
Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
+ +++ + +G KG GF+++ + +A +AI K N
Sbjct: 131 LSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMN 164
Score = 66.5 bits (163), Expect = 7e-13
Identities = 25/117 (21%), Positives = 50/117 (42%), Gaps = 24/117 (20%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
K+ G +FIKNL I + + F +G+I+ +++ + +G KG GF+++ +
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQE 154
Query: 85 SAVKAILKSN----------------KKPYKGK-------ITEEEFKEHFGQYGDII 118
+A +AI K N +K + + + ++ G G I+
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGRIV 211
Score = 39.6 bits (93), Expect = 8e-04
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+TE E F G I+ ++ ++ + G ++N+ A +A+ N KG
Sbjct: 26 DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK 85
Query: 160 E 160
Sbjct: 86 P 86
>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 = 79.9 bits (198), Expect = 7e-18
Identities = 25/144 (17%), Positives = 54/144 (37%), Gaps = 30/144 (20%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L++ NL ITE+ K++F G I + +++ + + K F+ Y A A+ N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 95 KKPYKGK-----------------------------ITEEEFKEHFGQYGDIIDAQLLKN 125
K + + +E + F + + ++ +
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122
Query: 126 AD-GKLKGCGFINYANKISAVKAI 148
G +G GF+++ ++ A A+
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAM 146
Score = 60.2 bits (147), Expect = 4e-11
Identities = 11/68 (16%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
++ LF+ +L + +E + F + + ++ + G +G GF+++ +
Sbjct: 79 SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 83 KISAVKAI 90
+ A A+
Sbjct: 139 QDDAQNAM 146
Score = 44.4 bits (106), Expect = 1e-05
Identities = 14/59 (23%), Positives = 27/59 (45%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
ITE+ K++F G I + +++ + + K F+ Y A A+ N K + +
Sbjct: 12 ITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNI 70
>3tr4_A Inorganic pyrophosphatase; central intermediary metabolism,
hydrolase; HET: MSE; 2.00A {Coxiella burnetii}
Length = 178
Score = 79.7 bits (197), Expect = 1e-17
Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 39/161 (24%)
Query: 179 KIFNMVVEIP-RWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFPHHGYIWNYG 232
FN+++EIP K E D + G L + +P NYG
Sbjct: 15 DDFNVIIEIPANGGEVKYEY-----------DKELGFLTVDRFMPTSMRYPC-----NYG 58
Query: 233 ALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWK 292
+P T DGDP+DVL + + G +++V+ALG++ + DE D K
Sbjct: 59 FVPSTLA------------QDGDPLDVLVLTPVPVQPGVLMRVRALGIMKMEDEAGEDSK 106
Query: 293 IIAINVNDPNA--AKLNDVADIETHFPGYLKATNEWFKIYK 331
++A+ V + + DI + L A + +F+ YK
Sbjct: 107 VLAVPVVKACRAYEAIQSLKDISSLL---LDAISHFFERYK 144
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 77.3 bits (191), Expect = 1e-17
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 7/97 (7%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
+ + ++ + RLF++ P + E E E FG +G + + ++
Sbjct: 4 SHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63
Query: 65 LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
L G F+ + SA KAI + + K + +
Sbjct: 64 -------LNGFAFVEFEEAESAAKAIEEVHGKSFANQ 93
Score = 54.2 bits (131), Expect = 2e-09
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E E E FG +G + + ++ L G F+ + SA KAI + + K +
Sbjct: 43 VQESELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGKSFAN 92
>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 = 75.4 bits (186), Expect = 5e-17
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGC 75
G + P K ++ ++N+PF+ + E +E F +G++ +L K G +G
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 76 GFINYANKISAVKAI 90
GF+++ K A KA
Sbjct: 61 GFVDFITKQDAKKAF 75
Score = 51.5 bits (124), Expect = 1e-08
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAI 148
+ + E +E F +G++ +L K G +G GF+++ K A KA
Sbjct: 26 QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>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 = 75.4 bits (186), Expect = 5e-17
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
+ T+R RLF+ NLP ITEEE ++ F +YG + + K+ KG GFI +
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETR 61
Query: 84 ISAVKAILKSNKKPYKGK 101
A A ++ + P +GK
Sbjct: 62 TLAEIAKVELDNMPLRGK 79
Score = 56.1 bits (136), Expect = 3e-10
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
ITEEE ++ F +YG + + K+ KG GFI + A A ++ + P +G
Sbjct: 27 ITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRG 78
>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 = 77.8 bits (192), Expect = 8e-17
Identities = 27/169 (15%), Positives = 53/169 (31%), Gaps = 55/169 (32%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL------LKNADGKLKGCGFINYANKISAV 87
RL++ N+PF ITEE + F + L + K F+ + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 88 KAILKSNKKPYKGK---------------------------------------------- 101
+A+ + ++G+
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 102 -ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
+ +++ KE +G + L+K++ G KG F Y + +AI
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Score = 66.2 bits (162), Expect = 7e-13
Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 1/98 (1%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
+ +LFI LP + +++ KE +G + L
Sbjct: 87 DYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146
Query: 65 LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+K++ G KG F Y + +AI N K
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
>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 = 75.1 bits (185), Expect = 9e-17
Identities = 24/74 (32%), Positives = 35/74 (47%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
+ G+LFI L + E+ K FG++G I + L+K+ K +G FI + N A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 88 KAILKSNKKPYKGK 101
A N K GK
Sbjct: 63 NAAKDMNGKSLHGK 76
Score = 57.0 bits (138), Expect = 2e-10
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E+ K FG++G I + L+K+ K +G FI + N A A N K G
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG 75
>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 = 74.7 bits (184), Expect = 1e-16
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 1/87 (1%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
G D T+ +FI+NL F EE E Q+GD+ +++ + D KGC
Sbjct: 1 GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
Query: 77 FINYANKISAVKAILKSNKKPYKGKIT 103
F + + +A K + ++ + G +
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLK 87
Score = 52.7 bits (127), Expect = 6e-09
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKP 155
EE E Q+GD+ +++ + D KGC F + + +A K + ++ +
Sbjct: 27 SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA 81
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 74.2 bits (183), Expect = 1e-16
Identities = 24/79 (30%), Positives = 41/79 (51%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
+ ++ +LFI LPF T+EE +E +G + D +L+ N GK KG ++ Y N
Sbjct: 8 VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYEN 67
Query: 83 KISAVKAILKSNKKPYKGK 101
+ A +A++K + K
Sbjct: 68 ESQASQAVMKMDGMTIKEN 86
Score = 56.1 bits (136), Expect = 3e-10
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
P+ T+EE +E +G + D +L+ N GK KG ++ Y N+ A +A++K +
Sbjct: 26 PFS--CTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTI 83
Query: 157 KG 158
K
Sbjct: 84 KE 85
>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 = 73.4 bits (181), Expect = 2e-16
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
GRLF++NL + +EE+ ++ F YG + + ++ K KG F+ + AVKA
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 92 KSNKKPYKG 100
+ + + ++G
Sbjct: 69 EVDGQVFQG 77
Score = 54.9 bits (133), Expect = 7e-10
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+EE+ ++ F YG + + ++ K KG F+ + AVKA + + + ++G
Sbjct: 20 SSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG 77
>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 = 72.7 bits (179), Expect = 4e-16
Identities = 19/96 (19%), Positives = 45/96 (46%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
+ K++ +++ G+L + NL F +++ + +E F ++G + A +
Sbjct: 3 RPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62
Query: 66 KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ G+ G +++ K A+KA+ + N P G+
Sbjct: 63 YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 98
Score = 53.8 bits (130), Expect = 2e-09
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+++ + +E F ++G + A + + G+ G +++ K A+KA+ + N P G
Sbjct: 41 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG 97
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 72.7 bits (179), Expect = 4e-16
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+I N+P TE + F +G I+D + KGC FI Y A I+
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83
Query: 94 NKKPYKGK 101
P++G+
Sbjct: 84 ANFPFQGR 91
Score = 59.6 bits (145), Expect = 1e-11
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TE + F +G I+D + KGC FI Y A I+ P++G
Sbjct: 39 ATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVALANFPFQG 90
>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 = 72.3 bits (178), Expect = 6e-16
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK 88
K +F+ + ++ E E + F +YG + + +++ + G KG GF+++ N + K
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
Query: 89 AILKSNKKPYKGK 101
+ ++ + GK
Sbjct: 66 IV--ESQINFHGK 76
Score = 54.9 bits (133), Expect = 8e-10
Identities = 12/49 (24%), Positives = 26/49 (53%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
+ E E + F +YG + + +++ + G KG GF+++ N + K +
Sbjct: 21 MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 74.5 bits (183), Expect = 6e-16
Identities = 16/97 (16%), Positives = 43/97 (44%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
++ K + +++ +L + NL F +++ + +E F ++G + A +
Sbjct: 61 SRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120
Query: 65 LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ G+ G +++ + A+KA+ + P G+
Sbjct: 121 DYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 157
Score = 54.5 bits (131), Expect = 6e-09
Identities = 11/57 (19%), Positives = 29/57 (50%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+++ + +E F ++G + A + + G+ G +++ + A+KA+ + P G
Sbjct: 100 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 156
>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 = 71.9 bits (177), Expect = 7e-16
Identities = 20/68 (29%), Positives = 32/68 (47%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+F+ NL ++ EE E F Q G + + K+ +GK K GF+ + + S AI
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77
Query: 94 NKKPYKGK 101
N G+
Sbjct: 78 NGIRLYGR 85
Score = 55.3 bits (134), Expect = 5e-10
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ EE E F Q G + + K+ +GK K GF+ + + S AI
Sbjct: 27 RVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI 74
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 71.8 bits (177), Expect = 7e-16
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
+ ++F++NLPF T + K+ F + G ++ A + +GK KGCG + + + A
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVA 61
Query: 87 VKAILKSNKKPYKGK 101
+A N G+
Sbjct: 62 ERACRMMNGMKLSGR 76
Score = 50.3 bits (121), Expect = 3e-08
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T + K+ F + G ++ A + +GK KGCG + + + A +A N G
Sbjct: 20 FTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSG 75
>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 = 71.6 bits (176), Expect = 2e-15
Identities = 15/79 (18%), Positives = 36/79 (45%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
+L + NL F +++ + +E F ++G + A + + G+ G +++
Sbjct: 26 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFER 85
Query: 83 KISAVKAILKSNKKPYKGK 101
+ A+KA+ + P G+
Sbjct: 86 RADALKAMKQYKGVPLDGR 104
Score = 53.1 bits (128), Expect = 6e-09
Identities = 11/57 (19%), Positives = 29/57 (50%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+++ + +E F ++G + A + + G+ G +++ + A+KA+ + P G
Sbjct: 47 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 103
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 71.9 bits (176), Expect = 2e-15
Identities = 19/128 (14%), Positives = 40/128 (31%), Gaps = 23/128 (17%)
Query: 4 LAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDI 59
+ + K E + + P + I N+ ++ +E+ + GDI
Sbjct: 1 MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 60 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKI----------------- 102
+D + + G +I +A + SA + P++G
Sbjct: 61 LDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDG 118
Query: 103 TEEEFKEH 110
+ E H
Sbjct: 119 SLEHHHHH 126
Score = 48.7 bits (116), Expect = 2e-07
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
++ +E+ + GDI+D + + G +I +A + SA + P+
Sbjct: 40 EVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYPF 97
Query: 157 KG 158
+G
Sbjct: 98 QG 99
>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 = 70.9 bits (174), Expect = 2e-15
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+I+NLP+KIT EE + FG+YG I ++ + +G ++ Y + A A+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 95 KKPYKGK 101
+
Sbjct: 69 GFNVSNR 75
Score = 53.5 bits (129), Expect = 3e-09
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
KIT EE + FG+YG I ++ + +G ++ Y + A A+ +
Sbjct: 19 KITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN 74
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 70.8 bits (174), Expect = 2e-15
Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 4/96 (4%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
+G +K++ RL + N+PF+ + + ++ FGQ+G I+D +++
Sbjct: 6 HHHHHSSGLVPRGSHM---NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62
Query: 66 KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
N G KG GF+ + N A +A K + +G+
Sbjct: 63 FNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 97
Score = 51.9 bits (125), Expect = 1e-08
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ + ++ FGQ+G I+D +++ N G KG GF+ + N A +A K + +G
Sbjct: 41 FRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEG 96
>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 = 69.9 bits (172), Expect = 3e-15
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
P+ ++I NL KI ++E K+ F ++G I+D + + K++G F+ +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKE 60
Query: 83 KISAVKAILKSNKKPYKGK 101
SA A+ P+ K
Sbjct: 61 VSSATNALRSMQGFPFYDK 79
Score = 51.5 bits (124), Expect = 1e-08
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
KI ++E K+ F ++G I+D + + K++G F+ + SA A+ P+
Sbjct: 19 KIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPF 76
Query: 157 KG 158
Sbjct: 77 YD 78
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 69.8 bits (171), Expect = 4e-15
Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 5/92 (5%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
G+ ++ +++ ++IK P T ++ KE G +++ Q+ + KG F
Sbjct: 1 GRWILKNDVKNRS----VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF 56
Query: 78 INYANKISAVKAILKSNKKPYKGKITEEEFKE 109
+ + + SA K +++ + YK FK+
Sbjct: 57 VVFDSIESAKKF-VETPGQKYKETDLLILFKD 87
Score = 54.0 bits (130), Expect = 2e-09
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
T ++ KE G +++ Q+ + KG F+ + + SA K +++ + YK ++
Sbjct: 23 ATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VETPGQKYKETD 80
>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 = 70.5 bits (173), Expect = 5e-15
Identities = 20/102 (19%), Positives = 46/102 (45%), Gaps = 3/102 (2%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
M+ K + + +K + KR +++ N+ + T ++ + HF G I
Sbjct: 6 MQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKR-SVYVGNVDYGSTAQDLEAHFSSCGSIN 64
Query: 61 DAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+L + G KG +I +A + ++V A + ++ ++G+
Sbjct: 65 RITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDETVFRGR 105
Score = 50.5 bits (121), Expect = 4e-08
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T ++ + HF G I +L + G KG +I +A + ++V A + ++ ++G
Sbjct: 48 STAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDETVFRG 104
>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 = 69.1 bits (170), Expect = 5e-15
Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
L+I+ L T+++ + YG I+ + + + K KG GF+++ + +A KA+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 92 KSNKKPYKGK 101
+ +
Sbjct: 66 ALKASGVQAQ 75
Score = 51.0 bits (123), Expect = 1e-08
Identities = 12/58 (20%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+++ + YG I+ + + + K KG GF+++ + +A KA+ +
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA 74
>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 = 71.0 bits (174), Expect = 5e-15
Identities = 27/107 (25%), Positives = 49/107 (45%), Gaps = 11/107 (10%)
Query: 2 EKLAKKKKVKKEFKK-KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
+L K + ++E + + E +P+ +++KNL + E++ K FG+Y D
Sbjct: 18 RELEKGRISREEMETLSVFRSYEPGEPNCR----IYVKNLAKHVQEKDLKYIFGRYVDFS 73
Query: 61 DAQLLKNAD------GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
D G++KG FI N+ +A KA+ ++N GK
Sbjct: 74 SETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK 120
>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 = 69.3 bits (170), Expect = 6e-15
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKIS 85
K + ++N+PF ++ +E + F Y I + L N G G + + ++
Sbjct: 10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 86 AVKAILKSNKKPYKG 100
A A++ N +P
Sbjct: 70 ATAAVIDLNDRPIGS 84
Score = 52.3 bits (126), Expect = 6e-09
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
P+ ++ +E + F Y I + L N G G + + ++ A A++ N +P
Sbjct: 24 PFT--VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP 81
Query: 156 YKG 158
Sbjct: 82 IGS 84
>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 = 69.2 bits (170), Expect = 6e-15
Identities = 23/73 (31%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVK 88
LFIKNL F TEE K F + G I + K + G GF+ Y A K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 89 AILKSNKKPYKGK 101
A+ + G
Sbjct: 66 ALKQLQGHTVDGH 78
Score = 49.2 bits (118), Expect = 8e-08
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAILKSNKKPYK 157
TEE K F + G I + K + G GF+ Y A KA+ +
Sbjct: 17 TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD 76
Query: 158 G 158
G
Sbjct: 77 G 77
>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 = 69.7 bits (171), Expect = 6e-15
Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
+LFI +P + E++ K F ++G I + +LK+ G KGC F+ Y + SA+KA
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Score = 56.2 bits (136), Expect = 4e-10
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
+ E++ K F ++G I + +LK+ G KGC F+ Y + SA+KA
Sbjct: 25 LDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 69.7 bits (171), Expect = 7e-15
Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 1/70 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+ L + E K+ +YG++ + ++L + K G + + + A + +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 93 SNKKPYKGKI 102
+ G I
Sbjct: 68 LHLTSVMGNI 77
Score = 54.3 bits (131), Expect = 1e-09
Identities = 9/58 (15%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E K+ +YG++ + ++L + K G + + + A + + + G
Sbjct: 18 VRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG 75
>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 = 68.5 bits (168), Expect = 1e-14
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKIS 85
K + ++N+PF ++ +E + F Y I + L N G G + + ++
Sbjct: 10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69
Query: 86 AVKAILKSNKKPYKG 100
A A++ N +P
Sbjct: 70 ATAAVIDLNDRPIGS 84
Score = 52.3 bits (126), Expect = 7e-09
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
P+ ++ +E + F Y I + L N G G + + ++ A A++ N +P
Sbjct: 24 PFT--VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP 81
Query: 156 YKG 158
Sbjct: 82 IGS 84
>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 = 68.9 bits (169), Expect = 1e-14
Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++ + +T++ ++ F +G I++ ++ KG F+ ++ SA AI+
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81
Query: 94 NKKPYKGK 101
N +G
Sbjct: 82 NGTTIEGH 89
Score = 56.6 bits (137), Expect = 3e-10
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+T++ ++ F +G I++ ++ KG F+ ++ SA AI+ N +G
Sbjct: 37 LTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG 88
>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 = 69.1 bits (169), Expect = 2e-14
Identities = 20/108 (18%), Positives = 42/108 (38%), Gaps = 8/108 (7%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLK 73
K +K R + +++K LPF+ + + F + + D+ + +GK
Sbjct: 8 KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67
Query: 74 GCGFINYANKISAVKAILKSNKKPYKG------KITEEEFKEHFGQYG 115
G GF+ + N+ A+ + +K+ IT++ E
Sbjct: 68 GEGFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIR 114
Score = 46.0 bits (109), Expect = 2e-06
Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P++ + + F + + D+ + +GK G GF+ + N+ A+ + +
Sbjct: 34 PFE--AENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQY 90
>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 = 68.1 bits (167), Expect = 2e-14
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
LF++NL +TEE ++ F Q+G + + KLK FI++ + AVKA+ +
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 94 NKKPYKGK 101
N K +G+
Sbjct: 66 NGKDLEGE 73
Score = 52.3 bits (126), Expect = 6e-09
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TEE ++ F Q+G + + KLK FI++ + AVKA+ + N K +G
Sbjct: 23 VTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGKDLEGEN 74
>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 = 68.5 bits (168), Expect = 2e-14
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L++KNL ++TE + F ++ + + G+++G FI + NK A +A+
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 93 SNKKPYKGK 101
N GK
Sbjct: 87 VNGYKLYGK 95
Score = 50.4 bits (121), Expect = 4e-08
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
++TE + F ++ + + G+++G FI + NK A +A+ N G
Sbjct: 36 RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG 94
>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 = 66.9 bits (164), Expect = 3e-14
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
DKT L++ L ITE + + HF Q+G+I +++ + C FI +A + +A
Sbjct: 9 DKTIT-TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAE 62
Query: 88 KAILKS-NKKPYKGK 101
A KS NK G+
Sbjct: 63 VAAEKSFNKLIVNGR 77
Score = 56.1 bits (136), Expect = 2e-10
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS-NKKPYKGS 159
ITE + + HF Q+G+I +++ + C FI +A + +A A KS NK G
Sbjct: 23 TITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGR 77
Query: 160 E 160
Sbjct: 78 R 78
>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 = 67.7 bits (166), Expect = 3e-14
Identities = 13/92 (14%), Positives = 34/92 (36%), Gaps = 6/92 (6%)
Query: 15 KKKGKKKIERKKPDKTKRGR----LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD- 69
GK + + + R +F L +I + ++ F G + D +++ + +
Sbjct: 4 GSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63
Query: 70 GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ KG ++ + +V + + G
Sbjct: 64 RRSKGIAYVEFCEI-QSVPLAIGLTGQRLLGV 94
Score = 49.2 bits (118), Expect = 9e-08
Identities = 8/59 (13%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+I + ++ F G + D +++ + + + KG ++ + +V + + G
Sbjct: 36 RIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAIGLTGQRLLG 93
>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 = 67.3 bits (165), Expect = 4e-14
Identities = 18/94 (19%), Positives = 51/94 (54%), Gaps = 4/94 (4%)
Query: 12 KEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-G 70
++ + + ++++ ++ ++ LFI L F+ TEE + ++ Q+G + D ++++
Sbjct: 9 EKTLETVPLERKKREKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK 66
Query: 71 KLKGCGFINYANKISAVKAILKSNKKPYKGKITE 104
+ +G GF+ +++ + V A + + G++ E
Sbjct: 67 RSRGFGFVTFSSM-AEVDAAMAARPHSIDGRVVE 99
Score = 48.0 bits (115), Expect = 2e-07
Identities = 10/53 (18%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
TEE + ++ Q+G + D ++++ + +G GF+ +++ A+
Sbjct: 40 TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHS 92
>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 = 66.6 bits (163), Expect = 9e-14
Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
G +++ P+ LFI +LP + +++ + F +G+++ A++ + K G
Sbjct: 14 GAAGSQKEGPEGAN---LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70
Query: 77 FINYANKISAVKAILKSNKKPYKGK 101
F++Y N +SA AI N K
Sbjct: 71 FVSYDNPVSAQAAIQSMNGFQIGMK 95
Score = 48.5 bits (116), Expect = 2e-07
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+++ + F +G+++ A++ + K GF++Y N +SA AI N
Sbjct: 37 FGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM 94
>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 = 66.1 bits (162), Expect = 9e-14
Identities = 17/88 (19%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
+ R + ++FI L ++ T+E +E+FGQ+G++ + ++++ + +G G
Sbjct: 11 SSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 77 FINYANKISAVKAILKSNKKPYKGKITE 104
F+ + ++ + V +L ++ K +
Sbjct: 71 FVTFMDQ-AGVDKVLAQSRHELDSKTID 97
Score = 48.0 bits (115), Expect = 2e-07
Identities = 11/47 (23%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
T+E +E+FGQ+G++ + ++++ + +G GF+ + ++ K +
Sbjct: 38 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 65.8 bits (161), Expect = 1e-13
Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+++NL +EE ++ F ++ K++ F++++N+ AV+A+ N
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALN 72
Query: 95 KKPYKGK 101
K G
Sbjct: 73 GKVLDGS 79
Score = 50.7 bits (122), Expect = 2e-08
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+EE ++ F ++ K++ F++++N+ AV+A+ N K GS
Sbjct: 27 TSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALNGKVLDGS 79
>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 = 65.3 bits (160), Expect = 2e-13
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKIS 85
P K+ +++ NLPF +T + F +YG ++ ++K+ D K KG FI + +K S
Sbjct: 14 PSKST---VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 86 AVKAILKSNKKPYKGK 101
A N K G+
Sbjct: 71 AQNCTRAINNKQLFGR 86
Score = 51.1 bits (123), Expect = 1e-08
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+T + F +YG ++ ++K+ D K KG FI + +K SA N K G
Sbjct: 28 LTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG 85
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 65.9 bits (161), Expect = 2e-13
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
K+ + + LFI +LP + T+ + F +G++I A++ + K GF+++ N
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP 92
Query: 84 ISAVKAILKSNKKPYKGK 101
SA AI N K
Sbjct: 93 DSAQVAIKAMNGFQVGTK 110
Score = 47.7 bits (114), Expect = 3e-07
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
T+ + F +G++I A++ + K GF+++ N SA AI
Sbjct: 52 FTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 65.0 bits (159), Expect = 2e-13
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
K+ RL + N+PF+ + + ++ FGQ+G I+D +++ N G KG GF+ + N A
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADA 68
Query: 87 VKAILKSNKKPYKGK 101
+A K + +G+
Sbjct: 69 DRAREKLHGTVVEGR 83
Score = 47.7 bits (114), Expect = 3e-07
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ + ++ FGQ+G I+D +++ N G KG GF+ + N A +A K + +G
Sbjct: 27 FRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEG 82
>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 = 64.9 bits (159), Expect = 3e-13
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
G + + + L++KNL I +E ++ F +G I A+++ G+ KG GF
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGF 59
Query: 78 INYANKISAVKAILKSNKKPYKGK 101
+ +++ A KA+ + N + K
Sbjct: 60 VCFSSPEEATKAVTEMNGRIVATK 83
Score = 46.1 bits (110), Expect = 1e-06
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
I +E ++ F +G I A+++ G+ KG GF+ +++ A KA+ + N +
Sbjct: 27 IDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT 82
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 64.4 bits (157), Expect = 3e-13
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
P + + +L I+N+P + E QYG + + + + Y++K A
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQA 67
Query: 87 VKAILKSNKKPYKGKI 102
+A+ K N +
Sbjct: 68 RQALDKLNGFQLENFT 83
Score = 43.6 bits (103), Expect = 7e-06
Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E QYG + + + + Y++K A +A+ K N +
Sbjct: 27 LQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQARQALDKLNGFQLEN 81
>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 = 63.8 bits (156), Expect = 4e-13
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
R PD L + L TE + +E F +YG I D ++ + + +G F+ + N
Sbjct: 9 RANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 83 KISAVKAILKSNKKPYKGK 101
A +A ++N G+
Sbjct: 67 VDDAKEAKERANGMELDGR 85
Score = 48.7 bits (117), Expect = 9e-08
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TE + +E F +YG I D ++ + + +G F+ + N A +A ++N G
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 84
>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 = 64.1 bits (157), Expect = 4e-13
Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
K+ + +F+ +P E E +E+F ++G + + ++ +A+ + +G GFI + ++
Sbjct: 5 SSGSKSNK--IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 84 ISAVKAILKSNKKPYKGKITE 104
+V + + GK E
Sbjct: 63 -QSVDQAVNMHFHDIMGKKVE 82
Score = 49.1 bits (118), Expect = 9e-08
Identities = 12/48 (25%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
E E +E+F ++G + + ++ +A+ + +G GFI + ++ S +A+
Sbjct: 22 CGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 64.9 bits (158), Expect = 5e-13
Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANK 83
D G + ++ LPF T+EE + F + + L + +GK+ G F+ +A++
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94
Query: 84 ISAVKAILKSNKKPYKG------KITEEEFKEH 110
A KA+ K +K+ K ++EE + +
Sbjct: 95 ELAEKALGK-HKERIGHRYIEVFKSSQEEVRSY 126
Score = 46.4 bits (110), Expect = 2e-06
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P+ T+EE + F + + L + +GK+ G F+ +A++ A KA+ K ++
Sbjct: 51 PFG--CTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKER 107
>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 = 64.2 bits (157), Expect = 5e-13
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 1/78 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
PD L + NL ++ + + + F +YG + D + + +G F+ + +
Sbjct: 5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 83 KISAVKAILKSNKKPYKG 100
+ A A + G
Sbjct: 65 RRDAQDAEAAMDGAELDG 82
Score = 48.0 bits (115), Expect = 2e-07
Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ + + F +YG + D + + +G F+ + ++ A A + G
Sbjct: 25 TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG 82
>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 = 64.0 bits (156), Expect = 5e-13
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCG 76
G PD G + ++ LPF ++EE + F + + L + G+ G
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 77 FINYANKISAVKAILKSNKK 96
F+ +A++ A KA+ K ++
Sbjct: 61 FVQFASQEIAEKALKKHKER 80
Score = 45.1 bits (107), Expect = 2e-06
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P+ ++EE + F + + L + G+ G F+ +A++ A KA+ K ++
Sbjct: 24 PFG--CSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER 80
>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 = 63.8 bits (156), Expect = 5e-13
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
G+LF+ L F E+ ++ F +YG I + ++K+ + + +G GF+ + N A A++
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 92 KSNKKPYKGK 101
N K G+
Sbjct: 73 AMNGKSVDGR 82
Score = 48.0 bits (115), Expect = 2e-07
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E+ ++ F +YG I + ++K+ + + +G GF+ + N A A++ N K G
Sbjct: 25 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG 81
>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 = 64.0 bits (156), Expect = 7e-13
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKS 93
I N+PF IT+ + + +A +L + +G+ G + + N+ A K+
Sbjct: 18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL- 76
Query: 94 NKKPYKG------KITEEEFKE 109
++K G +T E+ +E
Sbjct: 77 HRKKLNGREAFVHVVTLEDMRE 98
Score = 46.7 bits (111), Expect = 8e-07
Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
P+ IT+ + + +A +L + +G+ G + + N+ A K+ ++K
Sbjct: 24 PFS--ITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKK 80
Query: 156 YKG 158
G
Sbjct: 81 LNG 83
>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 = 63.4 bits (155), Expect = 7e-13
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+L+I NL +T ++ ++ FG + Q+ G F++Y ++ A++AI
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 64
Query: 94 NKK 96
+ K
Sbjct: 65 SGK 67
Score = 48.4 bits (116), Expect = 1e-07
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
+T ++ ++ FG + Q+ G F++Y ++ A++AI + K
Sbjct: 20 VTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSGK 67
>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 = 64.4 bits (157), Expect = 7e-13
Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 3/98 (3%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
++ + + R PD L + L TE + +E F +YG I D +
Sbjct: 21 MASMTGGQQMGRGSRHVGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSI 78
Query: 65 LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ + + +G F+ + N A +A ++N G+
Sbjct: 79 VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 116
Score = 48.6 bits (116), Expect = 2e-07
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TE + +E F +YG I D ++ + + +G F+ + N A +A ++N G
Sbjct: 57 YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 115
>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 = 65.2 bits (159), Expect = 8e-13
Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 5/98 (5%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
+ + F+ +++ + K T L++ NL F TEE+ E F + GDI +
Sbjct: 17 LSQYRDQHFRGDNEEQEKLLKKSCT----LYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72
Query: 66 KNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
+ G F+ Y ++ A A+ N +I
Sbjct: 73 LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110
Score = 49.0 bits (117), Expect = 2e-07
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE+ E F + GDI + + G F+ Y ++ A A+ N
Sbjct: 52 TEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 108
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 64.4 bits (157), Expect = 8e-13
Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 1/85 (1%)
Query: 17 KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGC 75
+G R PD L + NL ++ + + + F +YG + D + ++ + +G
Sbjct: 32 RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91
Query: 76 GFINYANKISAVKAILKSNKKPYKG 100
F+ + +K A A+ + G
Sbjct: 92 AFVRFHDKRDAEDAMDAMDGAVLDG 116
Score = 47.8 bits (114), Expect = 5e-07
Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ + + F +YG + D + ++ + +G F+ + +K A A+ + G
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116
>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 = 63.7 bits (155), Expect = 8e-13
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 29 KTKRGR--LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
+ R + + KNLP E +E F ++G + L + + + + A
Sbjct: 5 SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEA 59
Query: 87 VKAILKSNKKPYKGKI 102
KA +
Sbjct: 60 RKAFRHLAYSKFHHVP 75
Score = 46.7 bits (111), Expect = 8e-07
Identities = 8/59 (13%), Positives = 17/59 (28%), Gaps = 5/59 (8%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
E +E F ++G + L + + + + A KA +
Sbjct: 21 GTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSKFHHV 74
>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 = 63.0 bits (154), Expect = 9e-13
Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L++ +L F ITE+ + F +G I + L+K++D G+ KG GFI +++ A +A+ +
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 93 SNKKPYKG 100
N G
Sbjct: 67 LNGFELAG 74
Score = 49.1 bits (118), Expect = 8e-08
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
ITE+ + F +G I + L+K++D G+ KG GFI +++ A +A+ + N G
Sbjct: 17 ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG 74
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 62.7 bits (153), Expect = 1e-12
Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 6/81 (7%)
Query: 22 IERKKPDKTKRG--RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFIN 79
+E K R L KNL F ITE+E KE F +I + DGK KG +I
Sbjct: 4 LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIE 59
Query: 80 YANKISAVKAILKSNKKPYKG 100
+ ++ A K + + G
Sbjct: 60 FKSEADAEKNLEEKQGAEIDG 80
Score = 43.8 bits (104), Expect = 6e-06
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
ITE+E KE F +I + DGK KG +I + ++ A K + + G
Sbjct: 28 ITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 80
>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 = 63.1 bits (154), Expect = 1e-12
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
RL++ +L F ITE+ + F +G I QL+ +++ G+ KG GFI +++ A KA+ +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 93 SNKKPYKG 100
N G
Sbjct: 88 LNGFELAG 95
Score = 48.1 bits (115), Expect = 2e-07
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
ITE+ + F +G I QL+ +++ G+ KG GFI +++ A KA+ + N G
Sbjct: 38 ITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 61.7 bits (151), Expect = 1e-12
Identities = 16/72 (22%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++FI L ++ T+E +E+FGQ+G++ + ++++ + +G GF+ + ++ + V +L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 60
Query: 93 SNKKPYKGKITE 104
++ K +
Sbjct: 61 QSRHELDSKTID 72
Score = 49.0 bits (118), Expect = 5e-08
Identities = 12/53 (22%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
T+E +E+FGQ+G++ + ++++ + +G GF+ + ++ K + +S +
Sbjct: 13 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHE 65
>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 = 62.6 bits (153), Expect = 2e-12
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
K K L + LP+K TE++ KE+F +G+++ Q+ K+ G KG GF+ +
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Query: 85 SAVKAILKSNK 95
+ VK + + +
Sbjct: 69 TQVKVMSQRHM 79
Score = 49.9 bits (120), Expect = 5e-08
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 153
K TE++ KE+F +G+++ Q+ K+ G KG GF+ + + VK + + +
Sbjct: 26 KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM 79
>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 = 62.6 bits (153), Expect = 2e-12
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+ + NL E + +E F +G I L K+ G+ KG FI++ + A +AI
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 93 SNKKPYKGKI 102
+ Y I
Sbjct: 77 VSGFGYDHLI 86
Score = 49.1 bits (118), Expect = 9e-08
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E + +E F +G I L K+ G+ KG FI++ + A +AI + Y
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH 84
>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 = 62.1 bits (152), Expect = 2e-12
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+++ N+ + T EE + HF G + +L + G KG +I +++K +V+ L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 93 SNKKPYKG 100
++ ++G
Sbjct: 67 LDESLFRG 74
Score = 48.7 bits (117), Expect = 9e-08
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T EE + HF G + +L + G KG +I +++K +V+ L ++ ++G
Sbjct: 17 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLALDESLFRG 74
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+++ ++P+ TEE+ + G +I+ +++ + G+ KG FI + + S+ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 93 SNKKPYKG 100
N
Sbjct: 64 LNGYQLGS 71
Score = 49.5 bits (119), Expect = 5e-08
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE+ + G +I+ +++ + G+ KG FI + + S+ A+ N
Sbjct: 14 QTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 71
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 21/68 (30%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+F+ N+P++ TEE+ K+ F + G ++ +L+ + + GK KG GF Y ++ +A+ A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 93 SNKKPYKG 100
N + + G
Sbjct: 70 LNGREFSG 77
Score = 50.3 bits (121), Expect = 3e-08
Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 89 AILKSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKIS 143
A+ +S + + G + TEE+ K+ F + G ++ +L+ + + GK KG GF Y ++ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 144 AVKAILKSNKKPYKG 158
A+ A+ N + + G
Sbjct: 63 ALSAMRNLNGREFSG 77
>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 = 61.8 bits (151), Expect = 2e-12
Identities = 14/72 (19%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
++ G++F+ L + ++++ K++F ++G+++D + + + G+ +G GFI + +
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64
Query: 85 SAVKAILKSNKK 96
S K + + +
Sbjct: 65 SVEKVLDQKEHR 76
Score = 48.3 bits (116), Expect = 1e-07
Identities = 11/55 (20%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
++++ K++F ++G+++D + + + G+ +G GFI + + S K + + +
Sbjct: 22 DTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHR 76
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 7/81 (8%)
Query: 21 KIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY 80
KI K + T R L++ L + F ++G I +K +I Y
Sbjct: 8 KIGYGKANPTTR--LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQY 60
Query: 81 ANKISAVKAILKSNKKPYKGK 101
+ +A A K P G
Sbjct: 61 ESLDAAQAACAKMRGFPLGGP 81
Score = 50.3 bits (121), Expect = 3e-08
Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 5/60 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSEN 161
+ F ++G I +K +I Y + +A A K P G +
Sbjct: 29 TSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDR 83
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
+ G+LF+ L + T+E + +F QYG+++D ++K+ + +G GF+ + +
Sbjct: 8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Query: 83 KISAVKAILKSNKKPYKGKITE 104
+ V +L S G+ +
Sbjct: 68 P-NCVGTVLASRPHTLDGRNID 88
Score = 48.8 bits (117), Expect = 1e-07
Identities = 11/47 (23%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
T+E + +F QYG+++D ++K+ + +G GF+ + + +
Sbjct: 29 TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
>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 = 62.5 bits (152), Expect = 3e-12
Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
+ ++ + L++ +T + F +G+IID + +
Sbjct: 23 PFRRSDSFPERRAPRKGN-TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RN 74
Query: 75 CGFINYANKISAVKAILKSNKKPYKGK 101
C F+ Y SA +A+ + N +
Sbjct: 75 CAFVTYEKMESADQAVAELNGTQVESV 101
Score = 57.5 bits (139), Expect = 1e-10
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+T + F +G+IID + + C F+ Y SA +A+ + N +
Sbjct: 49 MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESV 101
>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 = 61.9 bits (151), Expect = 3e-12
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 9/86 (10%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ--------LLKNAD-GKLKGC 75
+ +F++ L +T E ++F Q G I + L + + GKLKG
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 76 GFINYANKISAVKAILKSNKKPYKGK 101
+++ + SA AI + K + G
Sbjct: 66 ATVSFDDPPSAKAAIDWFDGKEFSGN 91
Score = 46.1 bits (110), Expect = 1e-06
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 102 ITEEEFKEHFGQYGDIIDAQ--------LLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
+T E ++F Q G I + L + + GKLKG +++ + SA AI +
Sbjct: 25 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD 84
Query: 153 KKPYKGSE 160
K + G+
Sbjct: 85 GKEFSGNP 92
>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 = 62.3 bits (152), Expect = 3e-12
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVK 88
T ++F+ LP+ T+ +++F +GDI +A ++ + GK +G GF+ A++ +A +
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 89 AILKSNKK 96
A N
Sbjct: 75 ACKDPNPI 82
Score = 50.4 bits (121), Expect = 5e-08
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
T+ +++F +GDI +A ++ + GK +G GF+ A++ +A +A N
Sbjct: 30 TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI 82
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 61.4 bits (150), Expect = 3e-12
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAIL 91
++ I L +T++ E F YG I + KG ++ + N A KA+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 92 KSNKKPYKGK 101
+ G+
Sbjct: 66 HMDGGQIDGQ 75
Score = 46.0 bits (110), Expect = 6e-07
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+T++ E F YG I + KG ++ + N A KA+ + G
Sbjct: 16 VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
>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 = 62.8 bits (153), Expect = 3e-12
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L + +P + E + ++ F +YG I +++ + + + +G GF+ + + SA +AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 93 SNKKPYKGK 101
N K
Sbjct: 104 LNGFNILNK 112
Score = 47.0 bits (112), Expect = 1e-06
Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E + ++ F +YG I +++ + + + +G GF+ + + SA +AI N
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111
>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 = 63.3 bits (154), Expect = 3e-12
Identities = 19/101 (18%), Positives = 41/101 (40%), Gaps = 4/101 (3%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKR---GRLFIKNLPFKITEEEFKEHFGQYGDIID 61
+ ++ +++ + + +P + LF+ ++ + E+E +E F YG+I +
Sbjct: 42 SNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN 101
Query: 62 AQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
L + G KG + Y A+ A N G+
Sbjct: 102 IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 142
Score = 49.1 bits (117), Expect = 3e-07
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E+E +E F YG+I + L + G KG + Y A+ A N G
Sbjct: 84 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 141
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 62.2 bits (151), Expect = 4e-12
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 4/83 (4%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA----QLLKNADGKLK 73
G + K + + ++ LPF T EE FGQ+ I + DG+
Sbjct: 9 GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68
Query: 74 GCGFINYANKISAVKAILKSNKK 96
G F+ +A + A A+ K
Sbjct: 69 GDAFVLFACEEYAQNALRKHKDL 91
Score = 45.3 bits (107), Expect = 3e-06
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA----QLLKNADGKLKGCGFINYANKISAVKAILKSN 152
P+ T EE FGQ+ I + DG+ G F+ +A + A A+ K
Sbjct: 32 PFT--ATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHK 89
Query: 153 KK 154
Sbjct: 90 DL 91
>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 = 61.7 bits (150), Expect = 4e-12
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ + LP + ++ K+H + GD+ A + + G G + + K A+ K
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKL 70
Query: 94 NKKPYKGKITEEEF 107
+ ++ E +
Sbjct: 71 DNTKFRSHEGETAY 84
Score = 45.2 bits (107), Expect = 2e-06
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ ++ K+H + GD+ A + + G G + + K A+ K + ++ E
Sbjct: 27 GSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHE 79
>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 = 61.2 bits (149), Expect = 4e-12
Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+ ++ PF +TE+ E + ++++NA G G F++++N+ +A+ +
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNR 71
Query: 95 KK 96
+
Sbjct: 72 EY 73
Score = 45.4 bits (108), Expect = 1e-06
Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P+ +TE+ E + ++++NA G G F++++N+ +A+ + +
Sbjct: 19 PFN--VTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREY 73
>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 = 61.7 bits (150), Expect = 4e-12
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNAD--GKLKGCGFINYANKISAVKAI 90
RLFI +P EE E + + + D + +A K +G F+ Y + +A A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 91 LKSNKKPYK 99
K +
Sbjct: 70 RKLMPGRIQ 78
Score = 45.2 bits (107), Expect = 3e-06
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 102 ITEEEFKEHFGQYGDII-DAQLLKNAD--GKLKGCGFINYANKISAVKAILKSNKKPYK 157
EE E + + + D + +A K +G F+ Y + +A A K +
Sbjct: 20 KKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQ 78
>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 = 61.3 bits (149), Expect = 5e-12
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 1/79 (1%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
G T + ++ LP++ TE + F + + DG++ G
Sbjct: 1 GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEAD 59
Query: 78 INYANKISAVKAILKSNKK 96
+ +A AV A+ K
Sbjct: 60 VEFATHEDAVAAMAKDKAN 78
Score = 45.1 bits (107), Expect = 2e-06
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
PY+ TE + F + + DG++ G + +A AV A+ K
Sbjct: 24 PYR--ATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKAN 78
>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 = 61.5 bits (150), Expect = 5e-12
Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)
Query: 8 KKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN 67
++V+ E + + +R LF+ ++ + E+E +E F YG+I + L +
Sbjct: 6 ERVRNEDDDELEPGPQRSVEGWI----LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61
Query: 68 AD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
G KG + Y A+ A N G+
Sbjct: 62 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 96
Score = 48.4 bits (116), Expect = 2e-07
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E+E +E F YG+I + L + G KG + Y A+ A N G
Sbjct: 38 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 95
>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 = 61.5 bits (150), Expect = 5e-12
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
G +FIKNL I + + F +G+I+ +++ + +G KG GF+++ + +A +AI K
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEK 64
Query: 93 SNKKPYKGK 101
N +
Sbjct: 65 MNGMLLNDR 73
Score = 43.0 bits (102), Expect = 1e-05
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
I + + F +G+I+ +++ + +G KG GF+++ + +A +AI K N
Sbjct: 17 IDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMNGMLLND 72
Score = 29.9 bits (68), Expect = 0.58
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 13 EFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEF 49
+ +K+ + ++ + + T ++IKN T
Sbjct: 81 KSRKEREAELGARAKEFT---NVYIKNFGPGSTRAAA 114
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 61.6 bits (150), Expect = 5e-12
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 12/100 (12%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFI 78
D + +F++ L +T E ++F Q G I L + + GKLKG +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 79 NYANKISAVKAILKSNKKPYKG---KITEEEFKEHFGQYG 115
++ + SA AI + K + G K++ + F + G
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGG 102
Score = 43.5 bits (103), Expect = 1e-05
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 102 ITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
+T E ++F Q G I L + + GKLKG +++ + SA AI +
Sbjct: 19 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD 78
Query: 153 KKPYKG 158
K + G
Sbjct: 79 GKEFSG 84
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 61.3 bits (149), Expect = 6e-12
Identities = 17/104 (16%), Positives = 41/104 (39%), Gaps = 12/104 (11%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI--------IDAQLLKNAD 69
G + + ++++ L +T ++ + F Q G + + + +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 70 -GKLKGCGFINYANKISAVKAILKSNKKPYKG---KITEEEFKE 109
GK KG ++Y + +A A+ + K ++G K++ K
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
Score = 44.7 bits (106), Expect = 4e-06
Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 102 ITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
+T ++ + F Q G + + + + GK KG ++Y + +A A+ +
Sbjct: 27 VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD 86
Query: 153 KKPYKG 158
K ++G
Sbjct: 87 GKDFQG 92
>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 = 60.2 bits (147), Expect = 6e-12
Identities = 12/69 (17%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
LF+ +L + +E + F + + ++ + G +G GF+++ ++ A A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 93 SNKKPYKGK 101
+ G+
Sbjct: 63 MQGQDLNGR 71
Score = 46.0 bits (110), Expect = 6e-07
Identities = 8/48 (16%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
+ +E + F + + ++ + G +G GF+++ ++ A A+
Sbjct: 13 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 61.1 bits (149), Expect = 6e-12
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 27 PDKTKRG-RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
P ++ G LF+ + + TEE+ + F +YG+I + L + G LKG + Y
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
Query: 85 SAVKAI 90
A A+
Sbjct: 77 EAQAAM 82
Score = 48.4 bits (116), Expect = 2e-07
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
TEE+ + F +YG+I + L + G LKG + Y A A+
Sbjct: 35 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
>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 = 60.3 bits (147), Expect = 7e-12
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+LFI NLP + TE+E + F QYG +++ + +K GF++ +K +A AI
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAIRNL 62
Query: 94 NKKPYKGK 101
+ G
Sbjct: 63 HHYKLHGV 70
Score = 45.3 bits (108), Expect = 2e-06
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
TE+E + F QYG +++ + +K GF++ +K +A AI + G
Sbjct: 20 ATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70
>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 = 60.8 bits (148), Expect = 7e-12
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 8/76 (10%)
Query: 27 PDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
++G L++ +T + F +G+IID + + C F+ Y S
Sbjct: 9 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMES 61
Query: 86 AVKAILKSNKKPYKGK 101
A +A+ + N +
Sbjct: 62 ADQAVAELNGTQVESV 77
Score = 55.0 bits (133), Expect = 6e-10
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+T + F +G+IID + + C F+ Y SA +A+ + N +
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVES 76
>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 = 64.9 bits (157), Expect = 7e-12
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
P+ ++I NL KI ++E K+ F Q+G I+D + ++ K++G F+ +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKE 61
Query: 83 KISAVKAILKSNKKPYKGK 101
SA A+ P+ K
Sbjct: 62 VSSATNALRSMQGFPFYDK 80
Score = 47.2 bits (111), Expect = 5e-06
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
KI ++E K+ F Q+G I+D + ++ K++G F+ + SA A+ P+
Sbjct: 20 KIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFPF 77
Query: 157 KGSE 160
Sbjct: 78 YDKP 81
Score = 44.9 bits (105), Expect = 2e-05
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
F+ NLP + E F Q+ + +L+ F+ + N++ A A
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAAR 261
Score = 38.7 bits (89), Expect = 0.002
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
E F Q+ + +L+ F+ + N++ A A
Sbjct: 219 TNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAAR 261
>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 = 61.8 bits (150), Expect = 7e-12
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 1/82 (1%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
+ T + ++ LP+K TE + F + + DG++ G
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTG 87
Query: 75 CGFINYANKISAVKAILKSNKK 96
+ +A AV A+ K
Sbjct: 88 EADVEFATHEEAVAAMSKDRAN 109
Score = 46.0 bits (109), Expect = 2e-06
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
PYK TE + F + + DG++ G + +A AV A+ K
Sbjct: 55 PYK--ATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRAN 109
>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 = 60.9 bits (148), Expect = 8e-12
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 8/95 (8%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
+ P + + +PF E + ++ F + LLK+ G+ G G + + +
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSP 66
Query: 84 ISAVKAILKSNKKPYKG------KITEEEFKEHFG 112
+A LK N+ TE ++ G
Sbjct: 67 QDTFEA-LKRNRMLMIQRYVEVSPATERQWVAAGG 100
Score = 42.8 bits (101), Expect = 2e-05
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P+ E + ++ F + LLK+ G+ G G + + + +A+ ++
Sbjct: 25 PFS--AMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRML 79
>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 = 60.3 bits (147), Expect = 8e-12
Identities = 13/66 (19%), Positives = 26/66 (39%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
+ + T LFI NL + E K + D ++ G + G++++ +
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69
Query: 85 SAVKAI 90
KA+
Sbjct: 70 DLEKAL 75
Score = 44.9 bits (107), Expect = 2e-06
Identities = 7/47 (14%), Positives = 18/47 (38%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+ E K + D ++ G + G++++ + KA+
Sbjct: 29 KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
>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 = 60.8 bits (148), Expect = 9e-12
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 2/78 (2%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
+ P R+++ NLP I ++ ++ F +YG I D L F+ + +
Sbjct: 14 IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDP 71
Query: 84 ISAVKAILKSNKKPYKGK 101
A A+ + Y G
Sbjct: 72 RDAEDAVYGRDGYDYDGY 89
Score = 45.0 bits (107), Expect = 3e-06
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
I ++ ++ F +YG I D L F+ + + A A+ + Y G
Sbjct: 34 IRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR 90
>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 = 60.3 bits (147), Expect = 1e-11
Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 1/76 (1%)
Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
D + L++ NL +TE + F Q G +++ F+ +
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRD 67
Query: 86 AVKAILKSNKKPYKGK 101
A A+ N + GK
Sbjct: 68 AAAALAAMNGRKILGK 83
Score = 46.9 bits (112), Expect = 5e-07
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TE + F Q G +++ F+ + A A+ N + G E
Sbjct: 26 DVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGKE 84
>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 = 59.7 bits (145), Expect = 1e-11
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 6/70 (8%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
+ +KNLP +E + Y L + K F+ N A AI
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 92 KSNKKPYKGK 101
++ ++GK
Sbjct: 59 MFHQYSFRGK 68
Score = 41.2 bits (97), Expect = 4e-05
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 6/59 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+E + Y L + K F+ N A AI ++ ++G +
Sbjct: 17 SNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD 69
>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 = 60.4 bits (147), Expect = 1e-11
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
+K D + +F+ +L +IT E+ K F +G I DA+++K+ GK KG GF+++ N
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 83 KISAVKAILKSNKKPYKGK 101
K A AI + + G+
Sbjct: 67 KWDAENAIQQMGGQWLGGR 85
Score = 46.6 bits (111), Expect = 8e-07
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
IT E+ K F +G I DA+++K+ GK KG GF+++ NK A AI + + G
Sbjct: 27 ITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 84
>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 = 59.9 bits (146), Expect = 1e-11
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L++ L ++ ++ F +GDI D Q+ + + K +G F+ + A AI
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 93 SNKKPYKGK 101
N+ G+
Sbjct: 74 MNESELFGR 82
Score = 46.4 bits (111), Expect = 8e-07
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
++ ++ F +GDI D Q+ + + K +G F+ + A AI
Sbjct: 23 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
>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 = 59.1 bits (144), Expect = 2e-11
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++F+ N+ T +E + F + G +I+ + +K F++ + A AI +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDV-------VKDYAFVHMEKEADAKAAIAQL 63
Query: 94 NKKPYKGK 101
N K KGK
Sbjct: 64 NGKEVKGK 71
Score = 44.1 bits (105), Expect = 4e-06
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T +E + F + G +I+ + +K F++ + A AI + N K KG
Sbjct: 21 CTSQELRSLFERRGRVIECDV-------VKDYAFVHMEKEADAKAAIAQLNGKEVKG 70
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 58.6 bits (143), Expect = 2e-11
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++F+ L T E+ K +F Q+G + DA L+ + + +G GF+ + ++ V+ + +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCE 59
Query: 93 SNKKPYKGKITE 104
+ K+ E
Sbjct: 60 IHFHEINNKMVE 71
Score = 47.5 bits (114), Expect = 2e-07
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
T E+ K +F Q+G + DA L+ + + +G GF+ + ++ K
Sbjct: 12 TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58
>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 = 58.7 bits (143), Expect = 3e-11
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
L++ L ++ ++ F +GDI D Q+ + + K +G F+ + A AI
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Score = 46.4 bits (111), Expect = 5e-07
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
++ ++ F +GDI D Q+ + + K +G F+ + A AI
Sbjct: 18 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 60.2 bits (146), Expect = 3e-11
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 1/74 (1%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
G T + L++ L ++ ++ F +GDI D Q+ + + K +G
Sbjct: 49 GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108
Query: 77 FINYANKISAVKAI 90
F+ + A AI
Sbjct: 109 FVEFELAEDAAAAI 122
Score = 47.1 bits (112), Expect = 1e-06
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
++ ++ F +GDI D Q+ + + K +G F+ + A AI
Sbjct: 74 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
L + NL + TEE +E F + I ++ +N +GK KG FI +A+ A +A+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 94 NKKPYKGK 101
NK+ +G+
Sbjct: 74 NKREIEGR 81
Score = 43.0 bits (102), Expect = 1e-05
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE +E F + I ++ +N +GK KG FI +A+ A +A+ NK+ +G
Sbjct: 27 ATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG 80
>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 = 60.2 bits (146), Expect = 4e-11
Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYA 81
D L + NL ++ + + + F +YG + D + ++ + +G F+ +
Sbjct: 61 HHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 120
Query: 82 NKISAVKAI 90
+K A A+
Sbjct: 121 DKRDAEDAM 129
Score = 45.6 bits (108), Expect = 4e-06
Identities = 9/48 (18%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
+ + + F +YG + D + ++ + +G F+ + +K A A+
Sbjct: 82 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
>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 = 59.1 bits (143), Expect = 4e-11
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
P + R+ + LP + ++ K+H + GD+ A + + G G + + K
Sbjct: 8 YGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRK 61
Query: 84 ISAVKAILKSNKKPYKGKITEEEF 107
A+ K + ++ E +
Sbjct: 62 EDMTYAVRKLDNTKFRSHEGETAY 85
Score = 42.5 bits (100), Expect = 3e-05
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ ++ K+H + GD+ A + + G G + + K A+ K + ++ E
Sbjct: 28 GSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHE 80
>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 = 59.3 bits (144), Expect = 4e-11
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
LF+ + + TEE+ + F +YG+I + L + G LKG + Y A A+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Score = 46.6 bits (111), Expect = 1e-06
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
TEE+ + F +YG+I + L + G LKG + Y A A+
Sbjct: 34 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 59.9 bits (145), Expect = 5e-11
Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYAN 82
+ +R +++ + + T+++ + G D+++ + +N G+ KG + A+
Sbjct: 49 SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108
Query: 83 KISAVKAILKSNKKPYKGK 101
+ S K + K G+
Sbjct: 109 ENSVHKLLELLPGKVLNGE 127
Score = 44.5 bits (105), Expect = 9e-06
Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+++ + G D+++ + +N G+ KG + A++ S K + K G
Sbjct: 67 TTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG 126
>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 = 58.4 bits (142), Expect = 5e-11
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGC 75
G + K+ F+ NLP+ +TEE KE F I +L + +LKG
Sbjct: 1 GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59
Query: 76 GFINYANKISAVKAI 90
G+ + + S + A+
Sbjct: 60 GYAEFEDLDSLLSAL 74
Score = 39.9 bits (94), Expect = 2e-04
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAI 148
PY +TEE KE F I +L + +LKG G+ + + S + A+
Sbjct: 24 PYD--VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
>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 = 58.0 bits (141), Expect = 5e-11
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+L + N+ T +E + F +YG +I+ + +K F++ AV+AI
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEAIRGL 64
Query: 94 NKKPYKGK 101
+ ++GK
Sbjct: 65 DNTEFQGK 72
Score = 43.4 bits (103), Expect = 6e-06
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 11/72 (15%)
Query: 92 KSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
K++ K + G T +E + F +YG +I+ + +K F++ AV+A
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEA 60
Query: 148 ILKSNKKPYKGS 159
I + ++G
Sbjct: 61 IRGLDNTEFQGK 72
>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 = 57.6 bits (140), Expect = 6e-11
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
+ +F+ +TE+E +E F QYGD++D + K + F+ +A+ A
Sbjct: 3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSL 58
Query: 90 I 90
Sbjct: 59 C 59
Score = 46.4 bits (111), Expect = 5e-07
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+TE+E +E F QYGD++D + K + F+ +A+ A
Sbjct: 17 MTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLC 59
>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 = 58.2 bits (141), Expect = 7e-11
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 16 KKGKKKIERKKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
K + K K+ R+FI NL + + + + F +YG + + K G
Sbjct: 11 KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK-------G 63
Query: 75 CGFINYANKISAVKAILKSNKKPYKGK 101
F+ Y+N+ A A+L N + G+
Sbjct: 64 YAFVQYSNERHARAAVLGENGRVLAGQ 90
Score = 44.7 bits (106), Expect = 4e-06
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+ + + + F +YG + + K G F+ Y+N+ A A+L N + G
Sbjct: 39 LVKKSDVETIFSKYGRVAGCSVHK-------GYAFVQYSNERHARAAVLGENGRVLAGQ 90
>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 = 57.2 bits (139), Expect = 8e-11
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 4/69 (5%)
Query: 22 IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYA 81
+ ++F+ +T EE ++ F QYG+++D + K + F+ +A
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFA 56
Query: 82 NKISAVKAI 90
+ A
Sbjct: 57 DDKVAQSLC 65
Score = 46.4 bits (111), Expect = 6e-07
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+T EE ++ F QYG+++D + K + F+ +A+ A
Sbjct: 23 MTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFADDKVAQSLC 65
>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 = 57.6 bits (140), Expect = 8e-11
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGC 75
R + K+ F+ NLP+ +TEE KE F I +L + +LKG
Sbjct: 5 HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63
Query: 76 GFINYANKISAVKAILKSNKK 96
G+ + + S + A+ + +
Sbjct: 64 GYAEFEDLDSLLSALSLNEES 84
Score = 41.1 bits (97), Expect = 6e-05
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKK 154
PY +TEE KE F I +L + +LKG G+ + + S + A+ + +
Sbjct: 28 PYD--VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES 84
>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 = 56.8 bits (138), Expect = 1e-10
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVK 88
R L+I NL + T+E+ E G DI++ + +N G+ KG + ++ S+ K
Sbjct: 1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
Query: 89 AILKSNKKPYKGK 101
+ K+ G+
Sbjct: 61 LMDLLPKRELHGQ 73
Score = 44.1 bits (105), Expect = 3e-06
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+E+ E G DI++ + +N G+ KG + ++ S+ K + K+ G
Sbjct: 13 TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 72
>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 = 56.4 bits (137), Expect = 1e-10
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++F+ L EE+ +E+FG +G++ +L + K +G FI + + VK I++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIME 59
Query: 93 SNKKPYKGKITE 104
E
Sbjct: 60 KKYHNVGLSKCE 71
Score = 47.9 bits (115), Expect = 1e-07
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 150
EE+ +E+FG +G++ +L + K +G FI + + K + K
Sbjct: 11 TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 60.1 bits (145), Expect = 1e-10
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYA 81
KR L+I NL + T+E+ E G DI++ + +N A+G+ KG +
Sbjct: 61 VYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG 120
Query: 82 NKISAVKAILKSNKKPYKGK 101
++ S+ K + K+ G+
Sbjct: 121 SEASSKKLMDLLPKRELHGQ 140
Score = 43.9 bits (103), Expect = 4e-05
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+E+ E G DI++ + +N A+G+ KG + ++ S+ K + K+ G
Sbjct: 80 TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 139
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 57.1 bits (138), Expect = 1e-10
Identities = 9/88 (10%), Positives = 25/88 (28%), Gaps = 9/88 (10%)
Query: 11 KKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG 70
+ + + I+ L + E + E ++G I ++
Sbjct: 4 HHHHHMENYDDPHKTPASPV----VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--- 56
Query: 71 KLKGCGFINYANKISAVKAILKSNKKPY 98
K + + + + A A+ +
Sbjct: 57 --KRQALVEFEDVLGACNAVNYAADNQI 82
Score = 41.3 bits (97), Expect = 4e-05
Identities = 7/56 (12%), Positives = 19/56 (33%), Gaps = 5/56 (8%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
+ E + E ++G I ++ K + + + + A A+ +
Sbjct: 32 GVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQI 82
>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 = 57.3 bits (139), Expect = 1e-10
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 22 IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINY 80
I + D T +++ L K++E E F Q G +++ + K+ G+ +G GF+ +
Sbjct: 9 ISERNQDAT----VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64
Query: 81 ANKISAVKAILKSNKKPYKGK 101
++ A AI + GK
Sbjct: 65 LSEEDADYAIKIMDMIKLYGK 85
Score = 44.6 bits (106), Expect = 4e-06
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
K++E E F Q G +++ + K+ G+ +G GF+ + ++ A AI
Sbjct: 26 KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
>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 = 56.7 bits (137), Expect = 2e-10
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 5/64 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+ ++ L + E + E ++G I ++ K + + N SA + + +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAA 72
Query: 95 KKPY 98
P
Sbjct: 73 DVPV 76
Score = 42.5 bits (100), Expect = 2e-05
Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
+ E + E ++G I ++ K + + N SA + + + P
Sbjct: 26 SVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPV 76
>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 = 57.2 bits (138), Expect = 2e-10
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 31 KRGRLFIKNLPFKITEEEF---KEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANK 83
++ +F+ L ++ + E E+FG++G I + + ++ Y
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 84 ISAVKAILKSNKKPYKGKI 102
A++AI N G+
Sbjct: 74 EDALRAIQCVNNVVVDGRT 92
Score = 45.2 bits (107), Expect = 2e-06
Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 101 KITEEEF---KEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAILKSNK 153
++ + E E+FG++G I + + ++ Y A++AI N
Sbjct: 26 RLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN 85
Query: 154 KPYKG 158
G
Sbjct: 86 VVVDG 90
>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 = 56.0 bits (136), Expect = 2e-10
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+F+ +L +IT F +G I DA+++K+ GK KG GF+++ NK A AI +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 93 SNKKPYKGK 101
+ G+
Sbjct: 68 MGGQWLGGR 76
Score = 45.2 bits (108), Expect = 1e-06
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
IT F +G I DA+++K+ GK KG GF+++ NK A AI + + G
Sbjct: 18 ITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 75
>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 = 58.9 bits (142), Expect = 2e-10
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 1/74 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
L N P ++TEE F E + G + + + + G + + +K A++ +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 94 NKKPYKGKITEEEF 107
N K +
Sbjct: 186 NHYQMKNPNGPYPY 199
Score = 49.7 bits (118), Expect = 4e-07
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 35 LFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
L + L K+ + F YG++ + +K+ G + A+ + +AI
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHL 62
Query: 94 NKKPYKGK 101
N G+
Sbjct: 63 NNNFMFGQ 70
Score = 48.2 bits (114), Expect = 1e-06
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 3/68 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TEE F E + G + + + + G + + +K A++ + N K
Sbjct: 135 VTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNP- 193
Query: 161 NGLISPFH 168
P+
Sbjct: 194 -NGPYPYT 200
Score = 39.3 bits (91), Expect = 0.001
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
K+ + F YG++ + +K+ G + A+ + +AI N
Sbjct: 16 KMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNF 66
>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 = 56.5 bits (136), Expect = 3e-10
Identities = 13/84 (15%), Positives = 25/84 (29%), Gaps = 5/84 (5%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
+ + + I+ LP +TE E +G + + +LK K
Sbjct: 14 LVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KN 68
Query: 75 CGFINYANKISAVKAILKSNKKPY 98
FI + +A +
Sbjct: 69 QAFIEMNTEEAANTMVNYYTSVTP 92
Score = 41.4 bits (97), Expect = 6e-05
Identities = 10/55 (18%), Positives = 18/55 (32%), Gaps = 5/55 (9%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
+TE E +G + + +LK K FI + +A +
Sbjct: 43 VTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTP 92
>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 = 55.6 bits (135), Expect = 4e-10
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+++ NL + T E+ KE F Q+G + + +L+ + + K KG GF+ + S +AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAK 61
Query: 93 SNKKPYKGK 101
+ + G+
Sbjct: 62 LDNTDFMGR 70
Score = 42.5 bits (101), Expect = 1e-05
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKP 155
Y T E+ KE F Q+G + + +L+ + + K KG GF+ + S +AI K +
Sbjct: 10 VYS--ATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAKLDNTD 66
Query: 156 YKG 158
+ G
Sbjct: 67 FMG 69
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 55.8 bits (135), Expect = 4e-10
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++++ NL + E + F YG + + +N G F+ + + A A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGL 57
Query: 94 NKKPYKGK 101
+ K G
Sbjct: 58 DGKVICGS 65
Score = 41.9 bits (99), Expect = 3e-05
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 4/59 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ E + F YG + + +N G F+ + + A A+ + K GS
Sbjct: 12 AGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 55.2 bits (133), Expect = 6e-10
Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 5/65 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+ I+ LP +TE E +G + + +LK K FI + +A +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73
Query: 95 KKPYK 99
Sbjct: 74 SVTPV 78
Score = 40.6 bits (95), Expect = 9e-05
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 5/56 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK 157
+TE E +G + + +LK K FI + +A +
Sbjct: 28 VTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPV 78
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 55.0 bits (133), Expect = 6e-10
Identities = 9/71 (12%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
+ ++N+ + Y + + +L+K+ + +G F+ ++ + A + +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 92 KSNKKPYKGKI 102
KI
Sbjct: 72 ILQSLHPPLKI 82
Score = 38.8 bits (91), Expect = 3e-04
Identities = 7/63 (11%), Positives = 22/63 (34%), Gaps = 3/63 (4%)
Query: 103 TEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+ Y + + +L+K+ + +G F+ ++ + A + +
Sbjct: 22 VVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLK 81
Query: 160 ENG 162
+G
Sbjct: 82 IDG 84
>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 = 54.4 bits (131), Expect = 1e-09
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 7/69 (10%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI--LK 92
L I+ LP ++TE E +G + + +LK K F+ A + +A+ +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72
Query: 93 SNKKPYKGK 101
+ + +
Sbjct: 73 AVTPHLRNQ 81
Score = 39.8 bits (93), Expect = 2e-04
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
++TE E +G + + +LK K F+ A + +A+ + +
Sbjct: 26 EVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTP 76
>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 = 53.9 bits (130), Expect = 1e-09
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 34 RLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
RLFI NLP +++E+ F YG I+ + GFI + N S AI
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEX 76
Query: 93 SNKKPYKGK 101
+++ GK
Sbjct: 77 ESQEMNFGK 85
Score = 42.3 bits (100), Expect = 2e-05
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+++E+ F YG I+ + GFI + N S AI +++ G
Sbjct: 34 NVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGK 85
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 54.4 bits (131), Expect = 2e-09
Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 2/78 (2%)
Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
KR R+ +KNLP + ++ K+ + + G G + + ++
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN--TRDFDGTGALEFPSE 77
Query: 84 ISAVKAILKSNKKPYKGK 101
V+A+ + N ++G
Sbjct: 78 EILVEALERLNNIEFRGS 95
Score = 36.7 bits (85), Expect = 0.002
Identities = 7/57 (12%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ ++ K+ + + G G + + ++ V+A+ + N ++G
Sbjct: 40 CSWQDLKDLARENSLETTFSSVN--TRDFDGTGALEFPSEEILVEALERLNNIEFRG 94
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 54.2 bits (131), Expect = 2e-09
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANK 83
LF+ +L + + E F + Y +++ + G KG GF+ + ++
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61
Query: 84 ISAVKAILKSNKKPYKG 100
+ +A+ + G
Sbjct: 62 LEQKRALTECQGAVGLG 78
Score = 40.7 bits (96), Expect = 8e-05
Identities = 11/59 (18%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 102 ITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+ + E F + Y +++ + G KG GF+ + +++ +A+ + GS
Sbjct: 21 VDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS 79
>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 = 56.4 bits (136), Expect = 2e-09
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 35 LFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
L + NL P ++T + FG YGD+ ++L N K + A+ A A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 61
Query: 94 NKKPYKGK 101
N GK
Sbjct: 62 NGHKLHGK 69
Score = 54.9 bits (132), Expect = 6e-09
Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 11/104 (10%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRG--------RLFIKNLPFKITEEEFKEHFGQY 56
+ ++ + K G + R K +K L + N+P ++EE+ K F
Sbjct: 85 REGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN 144
Query: 57 GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 100
G ++ D + I + AV+A++ +
Sbjct: 145 GGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGE 185
Score = 45.7 bits (108), Expect = 7e-06
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
++T + FG YGD+ ++L N K + A+ A A+ N G
Sbjct: 15 RVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHG 68
>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 = 54.2 bits (130), Expect = 2e-09
Identities = 9/77 (11%), Positives = 27/77 (35%), Gaps = 3/77 (3%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFIN 79
P+ + + ++ LP+ + E+ + + + +G+ G F+
Sbjct: 8 MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVE 67
Query: 80 YANKISAVKAILKSNKK 96
++ A+ K +
Sbjct: 68 LESEDDVKLALKKDRES 84
Score = 38.7 bits (90), Expect = 5e-04
Identities = 7/61 (11%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 97 PYKGKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
P+ + E+ + + + +G+ G F+ ++ A+ K +
Sbjct: 26 PWS--CSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRE 83
Query: 154 K 154
Sbjct: 84 S 84
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 53.0 bits (128), Expect = 3e-09
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 34 RLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
RLFI NLP K +++E+ F YG I+ + GFI + N S AI
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64
Query: 93 SNKKPYKGK 101
+++ GK
Sbjct: 65 ESQEMNFGK 73
Score = 41.8 bits (99), Expect = 3e-05
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+++E+ F YG I+ + GFI + N S AI +++ G
Sbjct: 22 NVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIECESQEMNFGK 73
>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 = 55.8 bits (134), Expect = 4e-09
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 5/85 (5%)
Query: 27 PDKTKRGRLFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
L + NL P ++T + FG YGD+ ++L N K + A+
Sbjct: 29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQ 84
Query: 86 AVKAILKSNKKPYKGKITEEEFKEH 110
A A+ N GK +H
Sbjct: 85 AQLAMSHLNGHKLHGKPIRITLSKH 109
Score = 55.4 bits (133), Expect = 6e-09
Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 11/103 (10%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGR--------LFIKNLPFKITEEEFKEHFGQYG 57
+ ++ + K G + R K +K + L + N+P ++EE+ K F G
Sbjct: 117 EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG 176
Query: 58 DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 100
++ D + I + AV+A++ +
Sbjct: 177 GVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGE 216
Score = 44.2 bits (104), Expect = 3e-05
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
++T + FG YGD+ ++L N K + A+ A A+ N G
Sbjct: 46 RVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGK 100
Score = 43.1 bits (101), Expect = 8e-05
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
++EE+ K F G ++ D + I + AV+A++ + +
Sbjct: 163 VSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGEN 217
>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 = 53.0 bits (128), Expect = 4e-09
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNAD-GKLKGCGFINYANKISAVKAI 90
+FI NL +I E+ + F +G I+ +++++ D G KG FIN+A+ ++ AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 91 LKSNKKPYKGK 101
N + +
Sbjct: 66 EAMNGQYLCNR 76
Score = 36.8 bits (86), Expect = 0.002
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 102 ITEEEFKEHFGQYGDIID-AQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
I E+ + F +G I+ +++++ D G KG FIN+A+ ++ AI N
Sbjct: 17 IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69
>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 = 55.2 bits (132), Expect = 5e-09
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++IK P T ++ KE G +++ Q+ + KG F+ + + SA K +
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170
Query: 94 NKKPYKGKITEEEFKE 109
+K YK FK+
Sbjct: 171 GQK-YKETDLLILFKD 185
Score = 47.5 bits (112), Expect = 2e-06
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
T ++ KE G +++ Q+ + KG F+ + + SA K + +K YK ++
Sbjct: 122 TLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETD 178
>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 = 53.1 bits (127), Expect = 9e-09
Identities = 9/80 (11%), Positives = 27/80 (33%), Gaps = 3/80 (3%)
Query: 20 KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCG 76
+ P+ + + ++ LP+ + E+ + + +G+ G
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 77 FINYANKISAVKAILKSNKK 96
F+ ++ A+ K +
Sbjct: 92 FVELGSEDDVKMALKKDRES 111
Score = 38.4 bits (89), Expect = 0.001
Identities = 7/61 (11%), Positives = 19/61 (31%), Gaps = 5/61 (8%)
Query: 97 PYKGKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
P+ + E+ + + +G+ G F+ ++ A+ K +
Sbjct: 53 PWS--CSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRE 110
Query: 154 K 154
Sbjct: 111 S 111
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 51.6 bits (124), Expect = 9e-09
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILK 92
+F+ P + + E+F +G + + K+ KG + + A +A+L
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV-GAREAVLS 63
Query: 93 SNKKPYKGK 101
++ G
Sbjct: 64 QSQHSLGGH 72
Score = 40.0 bits (94), Expect = 1e-04
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKG 158
+ + E+F +G + + K+ KG + + A +A+L ++ G
Sbjct: 20 VDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV-GAREAVLSQSQHSLGG 71
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 6/83 (7%)
Query: 20 KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFI 78
+ +K LF+K L TEE KE F + A+++ + + G KG GF+
Sbjct: 5 SSGPNARSQPSKT--LFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFV 59
Query: 79 NYANKISAVKAILKSNKKPYKGK 101
++ ++ A A G
Sbjct: 60 DFNSEEDAKAAKEAMEDGEIDGN 82
Score = 36.9 bits (86), Expect = 0.002
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE KE F + A+++ + + G KG GF+++ ++ A A G
Sbjct: 27 TTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG 81
>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 = 51.8 bits (124), Expect = 1e-08
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 3/74 (4%)
Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYAN 82
+ + + + LP+ T E+ F L N DGK +G I +
Sbjct: 5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMES 64
Query: 83 KISAVKAILKSNKK 96
+ KA+ K
Sbjct: 65 EQDVQKALEKHRMY 78
Score = 38.3 bits (89), Expect = 7e-04
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 97 PYKGKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
P+ T E+ F L N DGK +G I ++ KA+ K
Sbjct: 20 PWS--CTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRM 77
Query: 154 K 154
Sbjct: 78 Y 78
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 54.4 bits (130), Expect = 1e-08
Identities = 21/109 (19%), Positives = 37/109 (33%), Gaps = 6/109 (5%)
Query: 52 HFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI-LKSNKKPYKGKITEEEFKEH 110
+ D + + + G G NK V I N K K E +
Sbjct: 104 LRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFV 163
Query: 111 FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
F + GDI + +++ K CGF+ + + +A A + +
Sbjct: 164 FSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLLP 207
Score = 50.9 bits (121), Expect = 2e-07
Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 14/88 (15%)
Query: 35 LFIKNLPFKIT---------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
L++ + + E + F + GDI + +++ K CGF+ + + +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQAN 191
Query: 86 AVKAILKSNKKPYKGKITEEEFKEHFGQ 113
A A + + +E G
Sbjct: 192 AEFAKEAMSNQTLLLPSDKEWDDRREGT 219
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 51.1 bits (123), Expect = 2e-08
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
++ NLPF + + F I +L+++ D K KG ++ + S +A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Score = 36.5 bits (85), Expect = 0.002
Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
+ + F I +L+++ D K KG ++ + S +A+
Sbjct: 27 TVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>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 = 50.8 bits (122), Expect = 2e-08
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L++ +L + E F G ++ ++++N G G F+ +A+ +A K + K
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 93 SNKKPYKGKITEEEFK 108
N KP G + FK
Sbjct: 72 INGKPLPGATPAKRFK 87
Score = 40.0 bits (94), Expect = 1e-04
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+ E F G ++ ++++N G G F+ +A+ +A K + K N KP G+
Sbjct: 21 MDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA 80
Query: 160 E 160
Sbjct: 81 T 81
>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 = 50.7 bits (121), Expect = 3e-08
Identities = 9/58 (15%), Positives = 18/58 (31%), Gaps = 7/58 (12%)
Query: 35 LFIKN--LPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L + N L ++ + + G + + N K F Y + +A
Sbjct: 28 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAY 80
Score = 45.7 bits (108), Expect = 2e-06
Identities = 6/47 (12%), Positives = 14/47 (29%), Gaps = 5/47 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ + + G + + N K F Y + +A
Sbjct: 39 VSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAY 80
>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 = 54.1 bits (129), Expect = 4e-08
Identities = 23/114 (20%), Positives = 50/114 (43%), Gaps = 5/114 (4%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGR----LFIKNLPFKITEEEFKEHFGQY 56
ME+ ++K +++ + + + K+ D +G LF+ + + TE + + F Y
Sbjct: 67 MERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVY 126
Query: 57 GDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKE 109
G I ++ + GK +G FI Y ++ A ++ K G+ + +
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
Score = 38.7 bits (89), Expect = 0.004
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
TE + + F YG I ++ + GK +G FI Y ++ A ++ K G
Sbjct: 114 TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR 173
>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 = 51.0 bits (122), Expect = 5e-08
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++++ NL + E + FG YG + + +N G F+ + + A A+ +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVREL 130
Query: 94 NKKPYKG 100
+ + G
Sbjct: 131 DGRTLCG 137
Score = 38.3 bits (89), Expect = 0.001
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ E + FG YG + + +N G F+ + + A A+ + + + G
Sbjct: 85 GNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVRELDGRTLCGCR 139
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 50.4 bits (120), Expect = 5e-08
Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK---NADGKLKGCGFINYA 81
+++ +F+ LP I E+E F ++G ++ K + KG F+ +
Sbjct: 3 SGSSGSRK--VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 82 NKISAVKAILKS 93
+ S V+A++ +
Sbjct: 61 EESS-VQALIDA 71
Score = 41.1 bits (96), Expect = 7e-05
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLK---NADGKLKGCGFINYANKISAVKAILKS 151
I E+E F ++G ++ K + KG F+ + + S V+A++ +
Sbjct: 20 IDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESS-VQALIDA 71
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 49.0 bits (117), Expect = 1e-07
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 1/72 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
G I + + ++ F + G +++ + + A GK KG F+ + A K I
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 92 KSNKKPYKGKIT 103
+ K K
Sbjct: 73 SFHGKRLDLKHR 84
Score = 47.0 bits (112), Expect = 5e-07
Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 1/75 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+ ++ F + G +++ + + A GK KG F+ + A K I + K
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH 83
Query: 161 NGLISPFHDIPLYSN 175
+ D+ Y++
Sbjct: 84 RLFLYTMKDVERYNS 98
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 48.3 bits (115), Expect = 1e-07
Identities = 9/68 (13%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+++ NLP + K + G + + + F++Y + +A +A+
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCL 76
Query: 94 NKKPYKGK 101
Sbjct: 77 QGLRLGTD 84
Score = 36.3 bits (84), Expect = 0.003
Identities = 6/58 (10%), Positives = 17/58 (29%), Gaps = 4/58 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+ K + G + + + F++Y + +A +A+
Sbjct: 31 ARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCLQGLRLGTD 84
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 45.8 bits (109), Expect = 8e-07
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 9/76 (11%)
Query: 35 LFIKNLPFKITEEEF-------KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
+ + N+P ++ + + F ++G I + + DGK KG F+ YA+ AV
Sbjct: 4 IVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAV 61
Query: 88 KAILKSNKKPYKGKIT 103
A+ ++ + T
Sbjct: 62 DAVKNADGYKLDKQHT 77
Score = 39.7 bits (93), Expect = 1e-04
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 99 KGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
+ + + + F ++G I + + DGK KG F+ YA+ AV A+ ++
Sbjct: 16 RLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYK 71
>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 = 47.4 bits (112), Expect = 1e-06
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ ++NL + +T + + F ++G ++ + + YA+ +SA A L
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSL 104
Query: 94 NKKP 97
+ +
Sbjct: 105 DGQN 108
Score = 35.8 bits (82), Expect = 0.009
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
+T + + F ++G ++ + + YA+ +SA A L + +
Sbjct: 57 PVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQN 108
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 45.9 bits (109), Expect = 1e-06
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 34 RLFIKNLPFKITEEEF-------KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
+ + N+P ++ + + F ++G I + DGK KG F+ YA+ A
Sbjct: 17 VIVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHA 74
Query: 87 VKAILKSNKKPYKGKIT 103
V A+ ++ + T
Sbjct: 75 VDAVKNADGYKLDKQHT 91
Score = 41.6 bits (98), Expect = 5e-05
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 99 KGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ + + + F ++G I + DGK KG F+ YA+ AV A+ ++
Sbjct: 30 RLEKLKNVIHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88
Query: 159 SENGLISPFHDI 170
++ F D
Sbjct: 89 QHTFRVNLFTDF 100
>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 = 44.7 bits (106), Expect = 2e-06
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 7/70 (10%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN------ADGKLKGCGFINY 80
P + R RL++ N+PF ITEE + F + + K F+ +
Sbjct: 2 PLGSAR-RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
Query: 81 ANKISAVKAI 90
+ +A+
Sbjct: 61 RSVDETTQAM 70
Score = 27.8 bits (62), Expect = 2.3
Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 6/53 (11%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN------ADGKLKGCGFINYANKISAVKAI 148
ITEE + F + + K F+ + + +A+
Sbjct: 18 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 70
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.0 bits (106), Expect = 5e-06
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ ++NL + +T + + F ++G ++ + + YA+ +SA A L
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSL 86
Query: 94 NKKP 97
+ +
Sbjct: 87 DGQN 90
Score = 33.8 bits (77), Expect = 0.033
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
+T + + F ++G ++ + + YA+ +SA A L + +
Sbjct: 39 PVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQN 90
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 42.0 bits (98), Expect = 4e-05
Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 4/83 (4%)
Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
K+ + K L I+N + IT + G + + K +
Sbjct: 8 KRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK----RNGI 63
Query: 75 CGFINYANKISAVKAILKSNKKP 97
+ + + + A KA N
Sbjct: 64 QAMVEFESVLCAQKAKAALNGAD 86
Score = 33.5 bits (76), Expect = 0.039
Identities = 9/63 (14%), Positives = 17/63 (26%), Gaps = 4/63 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
IT + G + + K + + + + + A KA N
Sbjct: 36 PITVDVLYTVCNPVGKVQRIVIFK----RNGIQAMVEFESVLCAQKAKAALNGADIYAGC 91
Query: 161 NGL 163
L
Sbjct: 92 CTL 94
>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 = 39.2 bits (91), Expect = 2e-04
Identities = 12/71 (16%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 35 LFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+ + N+ ++++ +E ++ F ++G + +L + D +LK + N A+ A+
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLK--AVVQMENLQDAIGAV 69
Query: 91 LKSNKKPYKGK 101
++ K
Sbjct: 70 NSLHRYKIGSK 80
>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 = 39.5 bits (92), Expect = 3e-04
Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 19 KKKIERKKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
+K ++++ + + + NLP ++ + YG I + L++ K F
Sbjct: 16 QKFDQKQELGRV----IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAF 66
Query: 78 INYANKISAVKAILKSNKKP 97
I + A+ + KK
Sbjct: 67 IEMETREDAMAMVDHCLKKA 86
Score = 32.2 bits (73), Expect = 0.10
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 5/56 (8%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
++ + YG I + L++ K FI + A+ + KK
Sbjct: 36 SGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKA 86
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 38.5 bits (89), Expect = 4e-04
Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 5/73 (6%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L +KNL +I + Q+G ++ N +G Y + A KA + N
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-----QGIALCKYTTREEANKAQMALN 64
Query: 95 KKPYKGKITEEEF 107
E
Sbjct: 65 NCVLANTTIFAES 77
>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 = 36.4 bits (84), Expect = 0.002
Identities = 10/64 (15%), Positives = 18/64 (28%), Gaps = 6/64 (9%)
Query: 35 LFIKNLPFKI-TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+ I + + + +G I + +L FI A A A+
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYY 72
Query: 94 NKKP 97
P
Sbjct: 73 TTTP 76
Score = 32.1 bits (73), Expect = 0.078
Identities = 11/56 (19%), Positives = 17/56 (30%), Gaps = 5/56 (8%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
GK + + +G I + +L FI A A A+ P
Sbjct: 26 GKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTP 76
>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 = 38.3 bits (88), Expect = 0.006
Identities = 46/378 (12%), Positives = 105/378 (27%), Gaps = 86/378 (22%)
Query: 36 FIKNLPFKITEEEFKEHFG--QYGDIIDAQLLKNADGKLKGCGFINYANKI--SAVKAIL 91
F+ N K ++ K + II ++ + +L ++ ++ V+ +L
Sbjct: 29 FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT-LLSKQEEMVQKFVEEVL 87
Query: 92 KSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 151
+ N K I + E ++ I+ + D ++ ++ ++ L
Sbjct: 88 RINYKFLMSPI-KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146
Query: 152 -NKKPY------KGSENG---L-ISPFHDIPLYSNVKDKIF----------NMVVEIPRW 190
GS G + + + + KIF V+E+ +
Sbjct: 147 LRPAKNVLIDGVLGS--GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 191 TNAKMEINLNEPLN-----PIKQDIKKGNLRYVANVFPHHGY---------IWNYGALPQ 236
+++ N + ++ + LR + Y + N +
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELR---RLLKSKPYENCLLVLLNVQN----AK 257
Query: 237 TWE-------------NPDETDAHTGQKGDGDPIDVLEIG-------ERIAK-------- 268
W TD + +D + + K
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317
Query: 269 -RGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDV--ADIETHFPGYLKATNE 325
E++ + +I E D N N KL + + + P + +
Sbjct: 318 LPREVLTTNPR-RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 326 WFKIYKIPDGK--PENVL 341
++ P P +L
Sbjct: 377 RLSVF--PPSAHIPTILL 392
Score = 32.9 bits (74), Expect = 0.24
Identities = 28/182 (15%), Positives = 50/182 (27%), Gaps = 60/182 (32%)
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPD--------- 334
E Q +K I ++V + D D++ L E I D
Sbjct: 11 TGEHQYQYKDI-LSVFEDAFVDNFDCKDVQDMPKSILS-KEEIDHIIMSKDAVSGTLRLF 68
Query: 335 ----GKPENVLNTRVEG--ESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPF 388
K E ++ VE + F+ S ++T P
Sbjct: 69 WTLLSKQEEMVQKFVEEVLRINYKFL-----------MSPIKTEQ-----------RQPS 106
Query: 389 HDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQL-NLLQE 447
+Y +D+++N + +N+ YL+L L E
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAK--------------------YNVSRLQPYLKLRQALLE 146
Query: 448 QQ 449
+
Sbjct: 147 LR 148
Score = 29.1 bits (64), Expect = 4.4
Identities = 25/162 (15%), Positives = 51/162 (31%), Gaps = 42/162 (25%)
Query: 1 MEKLAKKKKVKKEFKK----------------KGKKKIERKKPDKTKRGRLFIKNLPFKI 44
+ KL K V+K+ K+ + + + R D + F +
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467
Query: 45 TEEE-FKEHFG-------QYGDI-------IDAQLLKNADGKLKGCGFINYANKISAVKA 89
++ F H G + +D + L+ K++ N ++
Sbjct: 468 YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ---KIRHDSTA--WNASGSILN 522
Query: 90 ILKSNKKPYKGKITEEEFKEHFGQY-GDIIDAQLLKNADGKL 130
L+ K YK I + + + + I+D L + L
Sbjct: 523 TLQQLKF-YKPYICDND--PKYERLVNAILD--FLPKIEENL 559
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 36.3 bits (83), Expect = 0.008
Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 14/57 (24%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIE------RKKPDKTKRGRLFIKNLPFKITEEEFKEH 52
E A K +++E+++K KK +E ++ +K K N +I ++ F +
Sbjct: 100 ELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI-----NN---RIADKAFYQQ 148
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 34.5 bits (79), Expect = 0.014
Identities = 15/62 (24%), Positives = 29/62 (46%)
Query: 46 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEE 105
EE F E +YG++ + + N L G ++ + + A KA++ N + + G+
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 106 EF 107
E
Sbjct: 101 EL 102
Score = 32.5 bits (74), Expect = 0.060
Identities = 12/45 (26%), Positives = 22/45 (48%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
EE F E +YG++ + + N L G ++ + + A KA+
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAV 85
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.2 bits (77), Expect = 0.039
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 320 LKATNEWFKIYKIPDGKPENVLNTRVE 346
LK K+Y D P + +E
Sbjct: 22 LKKLQASLKLYA-DDSAPALAIKATME 47
Score = 29.9 bits (66), Expect = 0.94
Identities = 7/20 (35%), Positives = 11/20 (55%), Gaps = 3/20 (15%)
Query: 207 KQDIKK--GNLR-YVANVFP 223
KQ +KK +L+ Y + P
Sbjct: 19 KQALKKLQASLKLYADDSAP 38
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 32.8 bits (74), Expect = 0.042
Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
G +++ +YG++++ L K G + +A +A A+
Sbjct: 27 GGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAV 71
Score = 31.7 bits (71), Expect = 0.13
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 44 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+++ +YG++++ L K G + +A +A A+
Sbjct: 29 YSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAV 71
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 31.7 bits (72), Expect = 0.12
Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 9/73 (12%)
Query: 46 EEEFKEHFGQYGDIIDAQLLKNADG---KLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
E+ ++ +YG + ++ + DG G F+ + + KA+ + + ++
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88
Query: 103 ------TEEEFKE 109
+ +
Sbjct: 89 VVTKYCDPDSYHR 101
Score = 29.4 bits (66), Expect = 0.77
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNADG---KLKGCGFINYANKISAVKAI 148
E+ ++ +YG + ++ + DG G F+ + + KA+
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAM 76
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 30.7 bits (69), Expect = 0.26
Identities = 9/67 (13%), Positives = 25/67 (37%), Gaps = 12/67 (17%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQY-----GDIIDAQLLKNADGKLKGCGFINYANKISAV 87
+ ++ LP + +E +F G ++ Q +L G + + A
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-------RLGCGGVLTFREPADAE 61
Query: 88 KAILKSN 94
+ + +++
Sbjct: 62 RVLAQAD 68
>3mwu_A Calmodulin-domain protein kinase 1; serine/threonine protein
kinase, transferase, calcium-bindin binding, bumped
kinase inhibitor, BKI; HET: BK3; 1.98A {Cryptosporidium
parvum} PDB: 3igo_A* 3ncg_A*
Length = 486
Score = 31.6 bits (72), Expect = 0.58
Identities = 17/128 (13%), Positives = 38/128 (29%), Gaps = 34/128 (26%)
Query: 43 KITEEEFKEHFGQYGDIIDA------------------QLLKNADGKLKGCGFINYANKI 84
+ +E + ++ + L+ D + G G I Y+ I
Sbjct: 347 MLDRDELVRGYHEFMRLKGVDSNSLIQNEGSTIEDQIDSLMPLLD--MDGSGSIEYSEFI 404
Query: 85 SAVKAILKSNKKPY------------KGKITEEEFKEHFGQYGDIIDAQLLKN--ADGKL 130
++ + GKI+ +E + F Q I + L++
Sbjct: 405 ASAIDRTILLSRERMERAFKMFDKDGSGKISTKELFKLFSQADSSIQMEELESIIEQVDN 464
Query: 131 KGCGFINY 138
G +++
Sbjct: 465 NKDGEVDF 472
>1svj_A Potassium-transporting ATPase B chain; alpha-beta sandwich,
hydrolase; NMR {Escherichia coli} SCOP: d.220.1.1 PDB:
1u7q_A 2a00_A* 2a29_A*
Length = 156
Score = 29.4 bits (66), Expect = 1.2
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 240 NPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV-----KALGVIGLID 285
+ D H G P DV + +++A++G V + LGVI L D
Sbjct: 102 SVDAIRRHVEANGGHFPTDVDQKVDQVARQGATPLVVVEGSRVLGVIALKD 152
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 28.9 bits (64), Expect = 1.4
Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 17/90 (18%)
Query: 109 EHFGQYGDIIDAQLLKNADGKLKGCGF---------------INYANKISAVKAILKSNK 153
+F ++G I++ + + I Y N SAV A L N
Sbjct: 25 AYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDA-LLENG 83
Query: 154 KPYKGSENGLISPFHDIPLYSNVKDKIFNM 183
+ G G+I P+ + K K+ +
Sbjct: 84 AVFNGVLLGVI-PYTKDAVERLQKRKLTSS 112
Score = 27.0 bits (59), Expect = 7.1
Identities = 17/91 (18%), Positives = 27/91 (29%), Gaps = 24/91 (26%)
Query: 51 EHFGQYGDIIDAQLLKNADGKLKGCGF---------------INYANKISAVKAILKSNK 95
+F ++G I++ + + I Y N SAV A+L++
Sbjct: 25 AYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGA 84
Query: 96 ---------KPYKGKITEEEFKEHFGQYGDI 117
PY E K DI
Sbjct: 85 VFNGVLLGVIPYTKDAVERLQKRKLTSSEDI 115
>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 159
Score = 28.5 bits (63), Expect = 2.5
Identities = 13/42 (30%), Positives = 15/42 (35%), Gaps = 10/42 (23%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIER----------KKPDKTKR 32
K+ K K F+ GK KI R KK K K
Sbjct: 89 GYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKN 130
>3izc_e 60S ribosomal protein RPL7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_e
3o58_G 3o5h_G 3u5e_F 3u5i_F
Length = 244
Score = 29.0 bits (64), Expect = 3.0
Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 11/103 (10%)
Query: 2 EKLAKKKKVKKEFK-KKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
E KK K +++ + ++ RK +K KR + + KE+ +II
Sbjct: 10 ESQLKKSKAQQKTAEQVAAERAARKAANKEKR------AIILERNAAYQKEYETAERNII 63
Query: 61 DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKIT 103
A+ D K G ++ +K+ V I NK P K +
Sbjct: 64 QAK----RDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKV 102
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair,
helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF);
HET: 3DR; 2.28A {Schizosaccharomyces pombe}
Length = 228
Score = 28.5 bits (64), Expect = 3.3
Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 15/92 (16%)
Query: 107 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISP 166
FK ++ ++ CGF A KI ++K+I + + +GLI
Sbjct: 75 FKSISNNGQFPTPEEIRDMDFEIMRACGFS--ARKIDSLKSI-------AEATISGLIPT 125
Query: 167 FHDIPLYSNVKDKIFNMVVEIP---RWTNAKM 195
+ SN +++ + +I RWT +M
Sbjct: 126 KEEAERLSN--EELIERLTQIKGIGRWT-VEM 154
>3a4u_B Multiple coagulation factor deficiency protein 2; lectin, ergic,
ER, golgi, transport, disulfide bond, endopla reticulum,
ER-golgi transport; 1.84A {Homo sapiens} PDB: 2vrg_A
3lcp_C
Length = 143
Score = 28.0 bits (62), Expect = 3.8
Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 23/97 (23%)
Query: 43 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
+++ +E + H+ + D DG ++ +A+ + K +
Sbjct: 63 EMSPQELQLHYFKMHDY---------DGN----NLLDGLELSTAITHVHKEEGSEQAPLM 109
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYA 139
+E+E IID +L++ D G+I+YA
Sbjct: 110 SEDELIN-------IID-GVLRDDD--KNNDGYIDYA 136
>3v2d_8 50S ribosomal protein L35; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8
2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8
2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ...
Length = 65
Score = 26.4 bits (59), Expect = 4.0
Identities = 10/42 (23%), Positives = 13/42 (30%), Gaps = 10/42 (23%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIER----------KKPDKTKR 32
M K+ K KK K K+ +K K R
Sbjct: 1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIR 42
>3gms_A Putative NADPH:quinone reductase; structural genomics, putative
quinone oxidoreductase, unknown function, PSI-2; 1.76A
{Bacillus thuringiensis}
Length = 340
Score = 28.7 bits (65), Expect = 4.1
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 254 GDPIDVLEIGER---IAKRGEI-IQVKALGV 280
G+P DVL++ + K E+ +++ +
Sbjct: 14 GNPKDVLQVEYKNIEPLKDNEVFVRMLVRPI 44
>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3
3cf5_3* 3dll_3* 3pio_3* 3pip_3* 1nwy_3* 1nwx_3* 1xbp_3*
1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5
1vou_5 1vow_5 ...
Length = 66
Score = 26.1 bits (57), Expect = 5.0
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDK----TKRGRLFIKNL 40
M K+ K K+ K G K+ K K T + I+
Sbjct: 1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGK 44
>3ceg_A Baculoviral IAP repeat-containing protein 6; apoptosis, ligase,
protease inhibitor, thiol protease inhibitor, UBL
conjugation pathway; HET: MSE; 2.01A {Homo sapiens}
Length = 323
Score = 28.1 bits (62), Expect = 5.6
Identities = 11/54 (20%), Positives = 17/54 (31%)
Query: 41 PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
P +E +HF I AQ + + +S A LK +
Sbjct: 250 PSPCFKEVIHKHFYLKRVEIMAQCEEWIADIQQYSSDKRVGRTMSHHAAALKRH 303
>2dp9_A Hypothetical protein TTHA0113; jellyroll, structural genomics,
NPPSFA, national project on structural and functional
analyses; 1.90A {Thermus thermophilus} SCOP: b.122.1.5
PDB: 1wk2_A
Length = 124
Score = 27.0 bits (59), Expect = 5.8
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 3/86 (3%)
Query: 17 KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCG 76
G+K E ++ RG L I + I + + G +LL + + L
Sbjct: 23 DGRKVWEIRRRKTRHRGPLGIVSGGRLIGQADLVGVEGP---FSVEELLAHQEKHLAEEA 79
Query: 77 FINYANKISAVKAILKSNKKPYKGKI 102
F+ K + A + N Y+ +
Sbjct: 80 FLRAYAKDEPLYAWVLENAFRYEKPL 105
>1wlz_A DJBP, CAP-binding protein complex interacting protein 1 isoform A;
EF-hand like, unknown function; 1.60A {Homo sapiens}
SCOP: a.39.1.7
Length = 105
Score = 26.7 bits (59), Expect = 5.9
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 6/43 (13%)
Query: 100 GKITEEEFKEHFGQYGDIID----AQLLKNADGKLKGCGFINY 138
I+ EEF+ + I+ +L + G + Y
Sbjct: 39 NTISREEFRAICNRRVQILTDEQFDRLWNEMP--VNAKGRLKY 79
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure
initiative; NMR {Homo sapiens}
Length = 97
Score = 26.7 bits (59), Expect = 6.0
Identities = 6/37 (16%), Positives = 12/37 (32%), Gaps = 3/37 (8%)
Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI 59
+ I+ LP +T+E+ +E
Sbjct: 3 HHHHHHSHM---VVIRRLPPGLTKEQLEEQLRPLPAH 36
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_K
Length = 206
Score = 27.6 bits (61), Expect = 6.1
Identities = 23/135 (17%), Positives = 35/135 (25%), Gaps = 19/135 (14%)
Query: 19 KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
+ I P KT RG + L K E + +I L
Sbjct: 86 WRTIRGMIPHKTARGEAALARL--KAYEGVPPPYDRTKRMVIPDALKVLRLQP------- 136
Query: 79 NYANKISAVKAILKSNKKPYKGKIT--EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 136
++ + + K Y I EE+ KE + KL+
Sbjct: 137 --GHRYCLLGQLSKEVGWNYADTIRELEEKRKEKAKVS------YDRRKQLAKLRVKAEK 188
Query: 137 NYANKISAVKAILKS 151
K+ IL
Sbjct: 189 AAEEKLGTQLEILAP 203
>1pjz_A Thiopurine S-methyltransferase; polymorphism, S-adenosylmethionine,
drug metabolism; NMR {Pseudomonas syringae PV} SCOP:
c.66.1.36
Length = 203
Score = 27.8 bits (61), Expect = 6.3
Identities = 2/20 (10%), Positives = 6/20 (30%)
Query: 41 PFKITEEEFKEHFGQYGDII 60
PF + + ++
Sbjct: 152 PFSVPQTWLHRVMSGNWEVT 171
>3rpc_A Possible metal-dependent hydrolase; structural genomics,
PSI-biology, protein structure initiati midwest center
for structural genomics; 1.49A {Veillonella parvula}
Length = 264
Score = 27.8 bits (62), Expect = 7.0
Identities = 8/48 (16%), Positives = 13/48 (27%), Gaps = 5/48 (10%)
Query: 219 ANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERI 266
A + H + T + + + V E GE I
Sbjct: 220 AKIIAVH-----MDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETI 262
>2zkr_w 60S ribosomal protein L7; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 270
Score = 27.9 bits (61), Expect = 7.1
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 11/101 (10%)
Query: 2 EKLAKKKKVKKEFK-KKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
E L KK++ E K K+ +KK K K +R ++ K + KE+ Y I
Sbjct: 38 ETLKKKRRNFAELKVKRLRKKFALKTLRKARRKLIYEK------AKHYHKEYRQMYRTEI 91
Query: 61 DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ + G ++ K++ V I N K +
Sbjct: 92 RMARMA----RKAGNFYVPAEPKLAFVIRIRGINGVSPKVR 128
>1jba_A GCAP-2, protein (guanylate cyclase activating protein 2); EF-hand,
calcium-binding protein, guanylyl cyclase regulation,
lyase; NMR {Bos taurus} SCOP: a.39.1.5
Length = 204
Score = 27.5 bits (61), Expect = 7.2
Identities = 27/146 (18%), Positives = 45/146 (30%), Gaps = 31/146 (21%)
Query: 43 KITEEEFKEHFGQYGDIIDAQLLKN----ADGKLKGCGFINYANKISAVKAILKSNKKPY 98
+ EFK F + Q ++ D G I++ ++A+ +L+
Sbjct: 39 TLFMHEFKRFFKVPDNEEATQYVEAMFRAFD--TNGDNTIDFLEYVAALNLVLRGTL--- 93
Query: 99 KGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E + K F Y D G I+ + V++I K K
Sbjct: 94 -----EHKLKWTFKIY-D-------------KDRNGCIDRQELLDIVESIYKLKKACSVE 134
Query: 159 SENGLISPFHDIPLYSNVKDKIFNMV 184
E V D+IF +V
Sbjct: 135 VEAEQQGKLLTP---EEVVDRIFLLV 157
>3lij_A Calcium/calmodulin dependent protein kinase with A kinase domain
and 4 calmodulin...; transferase, calcium dependent
protein kinase; HET: ANP; 1.90A {Cryptosporidium parvum}
PDB: 3hzt_A* 3dxn_A 3l19_A*
Length = 494
Score = 27.7 bits (62), Expect = 8.8
Identities = 17/123 (13%), Positives = 37/123 (30%), Gaps = 32/123 (26%)
Query: 43 KITEEEFKEHFGQYGDIIDA------------QLLKNADGKLKGCGFINYANKISAVKAI 90
++ +E + + + A +L AD G+I+Y+ ++
Sbjct: 362 QLDRQELIDGYSKLSGEEVAVFDLPQIESEVDAILGAAD--FDRNGYIDYSEFVTVAMDR 419
Query: 91 LKSNKKPY------------KGKITEEEFKEHFGQYG---DIIDAQLLKNADGKLKGCGF 135
K GKI+ +E FG +++ D G
Sbjct: 420 KSLLSKDKLESAFQKFDQDGNGKISVDELASVFGLDHLESKTWK-EMISGID--SNNDGD 476
Query: 136 INY 138
+++
Sbjct: 477 VDF 479
>1ij5_A Plasmodial specific LAV1-2 protein; fourty kDa calcium binding
protein, CBP40, metal binding protein; 3.00A {Physarum
polycephalum} SCOP: a.39.1.9 PDB: 1ij6_A
Length = 323
Score = 27.5 bits (61), Expect = 9.0
Identities = 19/107 (17%), Positives = 39/107 (36%), Gaps = 13/107 (12%)
Query: 43 KITEEEFKEHFGQYGDIIDAQLLKN--ADGKLKGCGFINYANKISAVKAILKSNK----- 95
K + ++ K+ +Y D I LK + G ++Y ++ +
Sbjct: 138 KFSFQDLKQVLAKYADTIPEGPLKKLFVMVENDTKGRMSYITLVAVANDLAALVADFRKI 197
Query: 96 -KPYKGKITEEEFKEHFGQYGDIIDA---QLLKNADGKLKGCGFINY 138
G ++ +EF+EHF + G + L + AD + +
Sbjct: 198 DTNSNGTLSRKEFREHFVRLGFDKKSVQDALFRYAD--EDESDDVGF 242
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
0.316 0.137 0.406
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,192,910
Number of extensions: 456180
Number of successful extensions: 1947
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1581
Number of HSP's successfully gapped: 467
Length of query: 451
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 354
Effective length of database: 3,993,456
Effective search space: 1413683424
Effective search space used: 1413683424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 59 (26.4 bits)