RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4086
(305 letters)
>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 = 181 bits (462), Expect = 2e-57
Identities = 53/167 (31%), Positives = 86/167 (51%), Gaps = 8/167 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SKTNL + L Q+ T ++ ++ G I S K + DK T + GYGFV++ A A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 117 VKALQDKGIHAQMARQQEQDP-------TNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+ L + + + P NLY++ LP + +LE L ++Y ++++RI
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
L D S+GVGF R + + + ++ I+ NG G+ EP+ VKFA
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 72.2 bits (178), Expect = 1e-15
Identities = 25/67 (37%), Positives = 39/67 (58%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
+ NLY+ GL + T K+L + SQYG II+++ ++D+ T RG GF+ F+ A
Sbjct: 84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143
Query: 114 LAAVKAL 120
A+K L
Sbjct: 144 EEAIKGL 150
>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 = 179 bits (457), Expect = 9e-57
Identities = 52/167 (31%), Positives = 78/167 (46%), Gaps = 8/167 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S TNL + L QD TD++L + GPI + + + D T GY FVDF S + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 VKALQDKGIHAQMARQQEQDP-------TNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+K L + + + P TNLY+ NLP + L+++ KY ++V I
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 170 LRDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
LRD +GV F R +++ + I N G +PL V+ A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 71.1 bits (175), Expect = 3e-15
Identities = 23/67 (34%), Positives = 33/67 (49%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + TNLY+ L + TD L + +YG I+ + DK T + RG FV + A
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 114 LAAVKAL 120
A+ AL
Sbjct: 145 QEAISAL 151
>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 = 168 bits (428), Expect = 3e-52
Identities = 38/172 (22%), Positives = 74/172 (43%), Gaps = 14/172 (8%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAA 116
+++ + + ++KDL + QYG + + D++ N + +G FV F + AL A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 117 VKALQDKGIHAQMA-----------RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVV 165
AL + + M + + L+I + E D+ + + + +
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 166 STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS-TLPGSKEPLLVKFAD 216
RILR + S+G F ++ I+ + + T+ G P++VKFAD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 65.7 bits (161), Expect = 3e-13
Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 7/101 (6%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD---NNNTSKGVGFARLESKDKCD 192
D +++ +P + E DL L +Y V +LRD N SKG F ++
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 193 QMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
+ + LPG P+ +K ADS ++
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR---KLF 99
>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 = 120 bits (304), Expect = 1e-34
Identities = 55/111 (49%), Positives = 75/111 (67%), Gaps = 6/111 (5%)
Query: 113 ALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD 172
+ L+ G+ AQMA+QQEQDPTNLYI+NLPL+ E +LE++L + V+STRILRD
Sbjct: 1 GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD 60
Query: 173 NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG------SKEPLLVKFADS 217
++ TS+GVGFAR+ES +KC+ +I FNG + EPLL KF+
Sbjct: 61 SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP 111
Score = 70.7 bits (174), Expect = 1e-15
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 1/88 (1%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
TNLYI L +++L NM +G +IST+ + D + RG GF ES A +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIG 84
Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLP 146
K I +P +
Sbjct: 85 HFNGKFIKTPPGVSAPTEPLLCKFSGPS 112
>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 = 124 bits (313), Expect = 6e-34
Identities = 31/170 (18%), Positives = 57/170 (33%), Gaps = 13/170 (7%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
+ L + L T + + +G + + + T + +GYGF ++ A A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 117 VKALQDKGIH--------AQM--ARQQEQDPTNLYIANLPLNFKECD-LESLLAKYVTVV 165
L K + L + LP F + D L L+ +
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213
Query: 166 STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
++ + KG E+ + ++ Q +G +L GS L V F
Sbjct: 214 FCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGS--HLRVSFC 261
Score = 113 bits (286), Expect = 5e-30
Identities = 41/178 (23%), Positives = 71/178 (39%), Gaps = 12/178 (6%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
++ + IRGL D T++++ ++ S Y + +K +G FV +G A AA
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAA 73
Query: 117 VKALQDKGIHAQMARQQEQDP-TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NN 174
+ A + + Q Q L +ANLP + + E L+ + ++ ++
Sbjct: 74 INAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERT 133
Query: 175 NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
SKG GFA KD + G L L V + D+G + A +
Sbjct: 134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR--TLYVHWTDAG-QLTPALLHSRCLC 188
Score = 66.2 bits (162), Expect = 1e-12
Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 2/77 (2%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKD-LINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
P L L + L D D L S + + + +G+ +++E+
Sbjct: 179 PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAE 237
Query: 112 YALAAVKALQDKGIHAQ 128
A A + +
Sbjct: 238 MAEEAQQQADGLSLGGS 254
Score = 46.1 bits (110), Expect = 5e-06
Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 10/101 (9%)
Query: 120 LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
L + I ++ + Q + + I LP + ++ LL+ Y + +
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY------ELKYCFVDKY 56
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
KG F L + ++ + I F+ S L L V+ +
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRER--ELSVQLQPTD 95
>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 = 122 bits (309), Expect = 1e-33
Identities = 37/211 (17%), Positives = 72/211 (34%), Gaps = 9/211 (4%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
P + L++ L D T++D + +YG D RG+GF+ ES
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67
Query: 110 GGYALAAVKALQDKGIHAQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTR 168
A A L + ++ R + L + NL LE +++ V
Sbjct: 68 RTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV 127
Query: 169 ILRDNNNTSKGVGFARLESKDKCDQMIQLFNGST--LPGSKEPLLVKFADSGLKKRGAGA 226
++ D+ + G GF +K + ++ L + P++V+ + + G
Sbjct: 128 VVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPE 187
Query: 227 GGPNIYRGPGAEVRLWGRDSADSQLAYEHPM 257
+ E R + +E+
Sbjct: 188 KLMQKTQQYHKEREQPPRFAQPGTFEFEYAS 218
>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 = 114 bits (287), Expect = 5e-30
Identities = 35/182 (19%), Positives = 64/182 (35%), Gaps = 17/182 (9%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
T + ++ L + + GPII K + ++F ALAA+
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAIT 99
Query: 119 ALQ----DKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDN 173
I + L++ N P ++ + ++ LL V +S R+
Sbjct: 100 KTHKVVGQNEIIVSHLTE-----CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR 154
Query: 174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK---RGAGAGGPN 230
NTS+ + + SK+ ++ NG + G L+ K ++ K A G
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLVTKVSNPLEKSKRTDSATLEGRE 212
Query: 231 IY 232
I
Sbjct: 213 IM 214
Score = 112 bits (283), Expect = 2e-29
Identities = 28/181 (15%), Positives = 59/181 (32%), Gaps = 20/181 (11%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
L++ L++ T +++ ++ + + + N R + ++D S A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Query: 114 LAAVKALQDKGIH--------AQMARQQEQDP------TNLYIANLPLNF-KECDLESLL 158
V+ L I + + ++ + I NL E L
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232
Query: 159 AKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
+ ++ I + F E+KD ++ +Q+ N S L + V AD
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNR--EISVSLAD 289
Query: 217 S 217
Sbjct: 290 K 290
Score = 48.8 bits (117), Expect = 6e-07
Identities = 12/105 (11%), Positives = 26/105 (24%), Gaps = 7/105 (6%)
Query: 100 RGYGFVDFESGGYALAAVKALQD----KGIHAQMARQQEQDPTNLYIANLPLNFKECDLE 155
YG L K + + R +E T + + NLP ++ + +
Sbjct: 2 MEYGHHARPDSKRPLDEGSPAAAGLTSKKANEALTRNREL--TTVLVKNLPKSYNQNKVY 59
Query: 156 SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG 200
++ + + D I +
Sbjct: 60 KYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAITKTHK 103
>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 = 108 bits (272), Expect = 5e-29
Identities = 32/187 (17%), Positives = 70/187 (37%), Gaps = 20/187 (10%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS + NL+I L + + +L S+ ++D T R +G+
Sbjct: 1 GSHMVEGSEST-TPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGY 58
Query: 105 VDFESGGYALAAVKA----LQDKGIHAQMARQQEQ----DPTNLYIANLPLNFKECDLES 156
VDFES A++ + I + + ++ L NL N E +L+
Sbjct: 59 VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKE 118
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
+ + + + SKG+ + +S+ ++ ++ G+ + G + + +
Sbjct: 119 VFEDALEIRL----VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR--SVSLYYT- 171
Query: 217 SGLKKRG 223
++G
Sbjct: 172 ---GEKG 175
Score = 61.5 bits (150), Expect = 8e-12
Identities = 15/102 (14%), Positives = 39/102 (38%), Gaps = 5/102 (4%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ P NL+I NL N +L+ +++ ++ T++ G+ ES +
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
++ ++L G + G+ + ++ + +
Sbjct: 67 LEKALEL-TGLKVFGN--EIKLEKPKG--RDSKKVRAARTLL 103
>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 = 106 bits (268), Expect = 4e-28
Identities = 41/179 (22%), Positives = 75/179 (41%), Gaps = 13/179 (7%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
P+ P +LY+ L D T+ L S GPI+S + D T + GY +V
Sbjct: 4 GSMNPSAPSY-PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 106 DFESGGYALAAVKA-----LQDKGIHAQMARQQEQ----DPTNLYIANLPLNFKECDLES 156
+F+ A A+ ++ K + +++ N++I NL + L
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
+ + ++S +++ D N SKG GF E+++ ++ I+ NG L + V
Sbjct: 123 TFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLND--RKVFVGRF 178
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 106 bits (267), Expect = 6e-28
Identities = 38/225 (16%), Positives = 72/225 (32%), Gaps = 28/225 (12%)
Query: 31 GGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA 90
G T Q + +Y+ + + + + + +GPI S
Sbjct: 1 GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60
Query: 91 ILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH------------------AQMARQ 132
D T K +G+ FV++E A A++ + + +
Sbjct: 61 SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE 120
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
+ + +Y+A++ + + D++S+ + + S + RD KG GF E
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
+ N L G + L V A P PG
Sbjct: 181 QDAVSSMNLFDLGG--QYLRVGKA----VTPPMPLLTPA---TPG 216
>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 = 101 bits (255), Expect = 1e-27
Identities = 47/74 (63%), Positives = 57/74 (77%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+ LYIRGL TTD+DL+ +C YG I+STKAILDKTTNKC+GYGFVDF+S A AV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 119 ALQDKGIHAQMARQ 132
AL+ G+ AQMA+Q
Sbjct: 66 ALKASGVQAQMAKQ 79
Score = 61.8 bits (151), Expect = 9e-13
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQM 194
+ LYI L + DL L Y +VST+ + D N KG GF +S +
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 195 IQLFNGSTLPG 205
+ S +
Sbjct: 64 VTALKASGVQA 74
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 100 bits (251), Expect = 6e-27
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 2/102 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
+ + + L++ L E D+ L + + +LR + +SKG F +
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64
Query: 187 SKDKCDQMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAG 227
S + I +GS T+PG+ L+VKFAD+ K+ G +G
Sbjct: 65 SHTEAQAAIHALHGSQTMPGASSSLVVKFADTD-KESGPSSG 105
Score = 72.3 bits (178), Expect = 3e-16
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 45 GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + + L++ L + +++D++ + +G I +L +G
Sbjct: 1 GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT-VLRGPDGSSKGCA 59
Query: 104 FVDFESGGYALAAVKALQDK 123
FV F S A AA+ AL
Sbjct: 60 FVKFSSHTEAQAAIHALHGS 79
>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 = 102 bits (257), Expect = 6e-27
Identities = 39/170 (22%), Positives = 77/170 (45%), Gaps = 11/170 (6%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
++ K ++I GL DTT+ +L +YG + K + D T + RG+GF+ FE
Sbjct: 1 KESCK--MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58
Query: 114 LAAVKA---LQDKGIHAQMA--RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTR 168
VK L K I + A R ++ +++ + + + + E +++ T++ +
Sbjct: 59 DEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 169 ILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
++ D + S+G GF +S D D++ Q + +K A+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDR--KIEIKRAEP 165
Score = 66.0 bits (162), Expect = 2e-13
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
EQ +++ G+ D K+ SQ+G II + +LDK T + RG+GFV ++S
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS--- 138
Query: 113 ALAAVKALQDKGI 125
A A + Q+K I
Sbjct: 139 ADAVDRVCQNKFI 151
>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 = 97.4 bits (243), Expect = 1e-24
Identities = 48/198 (24%), Positives = 85/198 (42%), Gaps = 20/198 (10%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 6 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDPTN------LYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123
Query: 157 LLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
+Y + I+ D + +G F + D D+++ T+ G V+ A
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHN--CEVRKA 180
Query: 216 DSGLKKRGAGAGGPNIYR 233
S K+ A A R
Sbjct: 181 LS--KQEMASASSSQRGR 196
>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 = 95.3 bits (238), Expect = 3e-24
Identities = 44/165 (26%), Positives = 73/165 (44%), Gaps = 13/165 (7%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
LY+ L + T+ L GPI + K ++DK NK Y FV++ A A++ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 QDKGIH--------AQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
K I A ++Q D T NL++ +L +N + L + + + +S ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 172 D-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
D +S+G GF S+D + G L G PL + +A
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164
Score = 58.7 bits (143), Expect = 7e-11
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
NL++ L + D+ L N + +S + D T RGYGFV F S A A+ +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 120 LQ 121
+Q
Sbjct: 149 MQ 150
Score = 51.0 bits (123), Expect = 5e-08
Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 4/93 (4%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
LY+ NL E L+ + + +I+ D NN + F + +Q N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
G + + + + +A + N++
Sbjct: 63 GKQIENN--IVKINWAFQSQQSSSDDTF--NLF 91
>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 = 93.4 bits (233), Expect = 2e-23
Identities = 35/171 (20%), Positives = 66/171 (38%), Gaps = 14/171 (8%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA-----ILDKTTNKCRGYGFVDFESGG 111
S LY+ + T++ +++ + + +L N+ + + F++F S
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 112 YALAAVKA----LQDKGIHAQMA--RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVV 165
A+ Q + + + Q L+I LP + ++ LL + +
Sbjct: 63 ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLK 122
Query: 166 STRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
+ +++D SKG F + DQ I NG L G K LLV+ A
Sbjct: 123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDK-KLLVQRA 171
Score = 63.0 bits (154), Expect = 3e-12
Identities = 14/68 (20%), Positives = 26/68 (38%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
L+I GL D + + + +GP+ + + D T +GY F ++
Sbjct: 89 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 148
Query: 113 ALAAVKAL 120
A+ L
Sbjct: 149 TDQAIAGL 156
>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 = 88.9 bits (221), Expect = 2e-21
Identities = 35/192 (18%), Positives = 67/192 (34%), Gaps = 34/192 (17%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIIS-----TKAILDKTTNKCRGYGFVDFESGGYALA 115
LY+ + T++ +++ + + +L N+ + + F++F S
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 116 AVKA----LQDKGIHAQMARQQEQ----------------------DPTNLYIANLPLNF 149
A+ Q + + + + L+I LP
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL 126
Query: 150 KECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE 208
+ ++ LL + + + +++D SKG F + DQ I NG L G K
Sbjct: 127 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDK- 184
Query: 209 PLLVKFADSGLK 220
LLV+ A G K
Sbjct: 185 KLLVQRASVGAK 196
Score = 64.3 bits (157), Expect = 1e-12
Identities = 17/75 (22%), Positives = 30/75 (40%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
PG + S L+I GL D + + + +GP+ + + D T +GY F
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Query: 106 DFESGGYALAAVKAL 120
++ A+ L
Sbjct: 162 EYVDINVTDQAIAGL 176
>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 = 86.1 bits (214), Expect = 3e-21
Identities = 30/115 (26%), Positives = 50/115 (43%), Gaps = 19/115 (16%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
GP N++I+ L + +K L + S +G I+S K + D N +GYGFV FE+
Sbjct: 1 GPL--GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQE 56
Query: 112 YALAAVKA-----LQDKGIHAQMAR----------QQEQDPTNLYIANLPLNFKE 151
A A++ L D+ + + + ++ TN+YI N
Sbjct: 57 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111
Score = 55.3 bits (134), Expect = 4e-10
Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 7/103 (6%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
N++I NL + L + + ++S +++ D N SKG GF E+++ ++ I
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAI 62
Query: 196 QLFNGSTLPGSKEPLLVKFA----DSGLKKRGAGAGGPNIYRG 234
+ NG L + V + + N+Y
Sbjct: 63 EKMNGMLLNDR--KVFVGRFKSRKEREAELGARAKEFTNVYIK 103
>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 = 83.1 bits (206), Expect = 3e-20
Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 5/109 (4%)
Query: 37 TTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT 96
++ + + E NL+I L Q+ D+DL+ M +G ++S K +DK T
Sbjct: 4 GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63
Query: 97 NKCRGYGFVDFESGGYALAAVKAL-----QDKGIHAQMARQQEQDPTNL 140
N + +GFV +++ A AA++++ K + Q+ R + +
Sbjct: 64 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGP 112
Score = 60.4 bits (147), Expect = 7e-12
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 3/111 (2%)
Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTS 177
L + I A ++++ + NL+I +LP F + DL + + VVS ++ D N S
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
K GF ++ IQ NG + G K L V+ S + + G
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNGFQI-GMK-RLKVQLKRSKNDSKSGPSSG 115
>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 = 83.3 bits (206), Expect = 6e-20
Identities = 34/119 (28%), Positives = 48/119 (40%), Gaps = 13/119 (10%)
Query: 37 TTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT 96
Q P T PE NL + + + L + +YGPI S K + D+ T
Sbjct: 21 QLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRET 80
Query: 97 NKCRGYGFVDFESGGYALAAVKAL-----QDKGIHAQMARQQEQDP--------TNLYI 142
+ RGYGFV F+SG A A+ L +K + +A Q P N Y+
Sbjct: 81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 59.4 bits (144), Expect = 3e-11
Identities = 30/123 (24%), Positives = 47/123 (38%), Gaps = 5/123 (4%)
Query: 113 ALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD 172
L ++ Q + I + NL + +P E L L +Y + S +I+ D
Sbjct: 18 QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77
Query: 173 -NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK--RGAGAGGP 229
S+G GF + +S Q I NG + + L V A SG ++ G
Sbjct: 78 RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN--KRLKVALAASGHQRPGIAGAVGDG 135
Query: 230 NIY 232
N Y
Sbjct: 136 NGY 138
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 81.6 bits (202), Expect = 1e-19
Identities = 27/94 (28%), Positives = 45/94 (47%)
Query: 27 GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
+ T P+ + + + E NL+I L Q+ TD DL + +G +I
Sbjct: 9 SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68
Query: 87 STKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
S K +DK T+ + +GFV F++ A A+KA+
Sbjct: 69 SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Score = 59.3 bits (144), Expect = 2e-11
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 3/99 (3%)
Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNT 176
AL A + + + NL+I +LP F + DL S + V+S ++ D +
Sbjct: 21 VALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80
Query: 177 SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
SK GF ++ D I+ NG + G+K L V+
Sbjct: 81 SKCFGFVSFDNPDSAQVAIKAMNGFQV-GTK-RLKVQLK 117
>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 = 76.6 bits (189), Expect = 7e-18
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ + L+I + ++ +KDL + ++G I + D+ T +G F
Sbjct: 1 GSSGSSGMKDH-DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
Query: 105 VDFESGGYALAAVKALQDKGIHAQMARQ 132
+ + AL A AL ++ M R
Sbjct: 60 LTYCERESALKAQSALHEQKTLPGMNRP 87
Score = 75.4 bits (186), Expect = 2e-17
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 2/99 (2%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
++ D L+I +P N E DL+ L ++ + +L+D KG F ++
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 191 CDQMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ + TLPG P+ VK ADS + + G
Sbjct: 68 ALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 76.3 bits (188), Expect = 1e-17
Identities = 17/71 (23%), Positives = 26/71 (36%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
+ L + + L +MC +YG + + +L T K G V F S A V
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 118 KALQDKGIHAQ 128
K L +
Sbjct: 66 KNLHLTSVMGN 76
Score = 57.4 bits (139), Expect = 8e-11
Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 3/87 (3%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
+ A L N +E L+ + KY V IL G+ S + +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKR 222
+ + +++ G+ + + G ++
Sbjct: 66 KNLHLTSVMGN--IIHAQLDIKGQQRM 90
>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 = 74.2 bits (183), Expect = 4e-17
Identities = 21/80 (26%), Positives = 37/80 (46%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+ +G SK+ +Y+ L T+ DL + S+YG ++ + DK T K +G
Sbjct: 2 SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61
Query: 104 FVDFESGGYALAAVKALQDK 123
F+ F A +A+ +K
Sbjct: 62 FILFLDKDSAQNCTRAINNK 81
Score = 56.1 bits (136), Expect = 1e-10
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLES 187
M+ + +Y++NLP + DL + +KY VV I++D + SKGV F
Sbjct: 8 MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
Query: 188 KDKCDQMIQLFNGSTLPG 205
KD + N L G
Sbjct: 68 KDSAQNCTRAINNKQLFG 85
>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 = 4e-17
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 2/79 (2%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G P+ + ++IR L+ D+ ++ L + Q+G + + +L T +G F
Sbjct: 4 GSSGLPSDVTEGKT--VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 105 VDFESGGYALAAVKALQDK 123
F + A + A +
Sbjct: 62 AQFMTQEAAQKCLAAASLE 80
Score = 48.1 bits (115), Expect = 2e-07
Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 9/103 (8%)
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKC 191
+ ++I NL + +E L +L ++ + R++ + SKG FA+ +++
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 192 DQMIQLFNGSTLPGSKE----PLLVKFADSGLKKRGAGAGGPN 230
+ + + G + L V A R A GP+
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLA----VTRDEAASGPS 109
>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 = 76.0 bits (187), Expect = 6e-17
Identities = 18/82 (21%), Positives = 35/82 (42%)
Query: 42 QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
+ P + L++ + ++ + ++ YG I + LD+ T +G
Sbjct: 56 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 115
Query: 102 YGFVDFESGGYALAAVKALQDK 123
Y V++E+ ALAA +AL
Sbjct: 116 YALVEYETHKQALAAKEALNGA 137
Score = 46.7 bits (111), Expect = 1e-06
Identities = 17/117 (14%), Positives = 44/117 (37%), Gaps = 4/117 (3%)
Query: 100 RGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLA 159
RG+G D + + + + + Q+ + L++ ++ +E +++
Sbjct: 36 RGFG-SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFC 94
Query: 160 KYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
Y + + + D SKG E+ + + NG+ + G + + V +
Sbjct: 95 DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 149
>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 = 73.4 bits (181), Expect = 9e-17
Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 6/98 (6%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ GP+ L + LT T+ L + +YG + + T RG+ F
Sbjct: 1 GSSGSS-GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 105 VDFESGGYALAAVKALQDKG-----IHAQMARQQEQDP 137
V F A A A+ + Q+AR +D
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL 97
Score = 49.5 bits (119), Expect = 3e-08
Identities = 20/97 (20%), Positives = 31/97 (31%), Gaps = 3/97 (3%)
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
L + NL L + KY V I R+ + +G F R +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+G+ L G L V+ A G + + G
Sbjct: 69 QDAEAAMDGAELDG--RELRVQVARYGRRDLSGPSSG 103
>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 = 73.0 bits (180), Expect = 1e-16
Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 7/99 (7%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G + + + L++DT + DL + +G I DKTT + +G+
Sbjct: 3 SGSSGPNRRAD--DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 104 FVDFESGGYALAAVKALQDKG-----IHAQMARQQEQDP 137
F+ F A A+ + G ++ + A+
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99
Score = 52.2 bits (126), Expect = 4e-09
Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 1/80 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
+ ++ D + + NL + +E DL+ L + ++ + +D SKG F
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 186 ESKDKCDQMIQLFNGSTLPG 205
++ + I +G
Sbjct: 65 HRREDAARAIAGVSGFGYDH 84
>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 = 75.5 bits (185), Expect = 2e-16
Identities = 30/205 (14%), Positives = 55/205 (26%), Gaps = 53/205 (25%)
Query: 59 TNLYIRGLTQDTTDKD-LINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
L + GL Q + D + N+ YG + K + K G V+ G A+
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59
Query: 118 KALQDKGIHAQ-----MARQQEQDP----------------------------------- 137
L + + Q +++Q P
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI 119
Query: 138 ----TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCD 192
L+ N PL E + + + T + + + G +SK
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
Query: 193 QMIQLFNGSTLPGS--KEPLLVKFA 215
+ + N + P +K
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTLKLC 204
Score = 62.4 bits (151), Expect = 8e-12
Identities = 16/119 (13%), Positives = 36/119 (30%)
Query: 8 RVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLT 67
V + PA S + N + + Q L+
Sbjct: 73 NVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAP 132
Query: 68 QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
+ T+++ +C + G T + ++ G ++++S AL + L +
Sbjct: 133 LEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMK 191
>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 = 72.8 bits (179), Expect = 3e-16
Identities = 27/111 (24%), Positives = 45/111 (40%)
Query: 16 ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
++ H SS + +T GS L + GL+ TT++DL
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDL 63
Query: 76 INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
+ S+YGPI + D+ + + RG+ FV FE+ A A + +
Sbjct: 64 REVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 114
Score = 49.0 bits (117), Expect = 1e-07
Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 1/86 (1%)
Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKG 179
+G R L + L L E DL + +KY + I+ D S+G
Sbjct: 30 MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 89
Query: 180 VGFARLESKDKCDQMIQLFNGSTLPG 205
F E+ D + + NG L G
Sbjct: 90 FAFVYFENVDDAKEAKERANGMELDG 115
>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 = 74.5 bits (183), Expect = 3e-16
Identities = 32/207 (15%), Positives = 65/207 (31%), Gaps = 52/207 (25%)
Query: 56 LSKTNLYIRGLTQDT-TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
+ + L + L + T + L + YG + K + +K + V G A
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQ 55
Query: 115 AAVKALQ-----DKGIHAQMARQQEQDP-------------------------------- 137
A+ L K I +++ Q
Sbjct: 56 LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 115
Query: 138 -----TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD 192
L+++N+P + E DL+ L + VV + + + ++ S ++
Sbjct: 116 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAV 172
Query: 193 QMIQLFNGSTLPGSKEPLLVKFADSGL 219
Q + + L + L V F+ S +
Sbjct: 173 QALIDLHNHDLGENH-HLRVSFSKSTI 198
Score = 59.9 bits (145), Expect = 5e-11
Identities = 16/115 (13%), Positives = 39/115 (33%), Gaps = 6/115 (5%)
Query: 14 SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN--LYIRGLTQDTT 71
+ + + G ++ G N+ H + + + L++ + +
Sbjct: 74 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS 133
Query: 72 DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
++DL + S G ++ K K R + S A+ A+ L + +
Sbjct: 134 EEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 184
>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 = 71.6 bits (176), Expect = 6e-16
Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 7/100 (7%)
Query: 27 GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
GS I + + +PG P LY++ L+ T++DL+++ +++
Sbjct: 1 GSSGSSGEEIRKIPMFSSYNPGEPN-------KVLYLKNLSPRVTERDLVSLFARFQEKK 53
Query: 87 STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
T + RG F+ F + A A+ + ++
Sbjct: 54 GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY 93
Score = 48.8 bits (117), Expect = 9e-08
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 4/89 (4%)
Query: 129 MARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLE 186
+ +P LY+ NL E DL SL A++ I +G F
Sbjct: 16 FSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP 75
Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
+K+ Q + L NG L G + L+++F
Sbjct: 76 NKEIAWQALHLVNGYKLYG--KILVIEFG 102
>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 = 71.1 bits (175), Expect = 7e-16
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 52 GPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG 110
G S + L++R L+ ++++DL + S YGP+ +D T K +G+ FV F
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 111 GYALAAVKAL-----QDKGIHAQMARQQEQDP 137
+A+ A + Q + +H + +++
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92
Score = 46.1 bits (110), Expect = 6e-07
Identities = 15/75 (20%), Positives = 23/75 (30%), Gaps = 1/75 (1%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
L++ NL E DLE L + Y + D+ KG F +
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 191 CDQMIQLFNGSTLPG 205
+ +G G
Sbjct: 63 AVKAYAEVDGQVFQG 77
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 70.8 bits (174), Expect = 7e-16
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 3/73 (4%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESG 110
T + +R + T ++ S Y + + + I DK T + RG+ FV S
Sbjct: 5 HHHHMDT-IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63
Query: 111 GYALAAVKALQDK 123
A ++ LQ
Sbjct: 64 MDASQLLQILQSL 76
Score = 53.1 bits (128), Expect = 2e-09
Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 5/95 (5%)
Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGFARL 185
M + + N+ + + + L+ Y + V + R+++D ++G F +L
Sbjct: 1 MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL 60
Query: 186 ESKDKCDQMIQLFNGSTLPGSKE--PLLVKFADSG 218
S Q++Q+ P + + V FA S
Sbjct: 61 SSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 72.1 bits (177), Expect = 8e-16
Identities = 24/77 (31%), Positives = 35/77 (45%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+G +K LY+ GL ++ DK L +G I + LD T K RG+
Sbjct: 49 GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108
Query: 104 FVDFESGGYALAAVKAL 120
FV+FE A AA+ +
Sbjct: 109 FVEFELAEDAAAAIDNM 125
Score = 44.4 bits (105), Expect = 6e-06
Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 1/77 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESK 188
+ LY+ L + L + + + +I D +G F E
Sbjct: 56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 115
Query: 189 DKCDQMIQLFNGSTLPG 205
+ I N S L G
Sbjct: 116 EDAAAAIDNMNESELFG 132
>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 = 70.3 bits (173), Expect = 1e-15
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G ++ S L + GL TT++DL S +G ++ + D T +G+G
Sbjct: 3 SGSSGVKRAVQKTSD--LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 104 FVDFESGGYALAAVKALQDK 123
FV F VK + +
Sbjct: 61 FVRFTE---YETQVKVMSQR 77
Score = 29.5 bits (67), Expect = 0.38
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESK 188
++ Q ++L + LP E DL+ + + V+ ++ +D SKG GF R
Sbjct: 8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
Query: 189 DKCDQMIQ 196
+ +++
Sbjct: 68 ETQVKVMS 75
>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 = 69.5 bits (171), Expect = 2e-15
Identities = 24/72 (33%), Positives = 35/72 (48%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
G +K LY+ GL ++ DK L +G I + LD T K RG+ FV+FE
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 112 YALAAVKALQDK 123
A AA+ + +
Sbjct: 61 DAAAAIDNMNES 72
Score = 43.3 bits (103), Expect = 4e-06
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 5/78 (6%)
Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLES 187
MA + LY+ L + L + + + +I D +G F E
Sbjct: 3 MATTK----RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58
Query: 188 KDKCDQMIQLFNGSTLPG 205
+ I N S L G
Sbjct: 59 AEDAAAAIDNMNESELFG 76
>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 = 70.4 bits (173), Expect = 2e-15
Identities = 25/77 (32%), Positives = 33/77 (42%)
Query: 43 HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
+GS G + + T +++ GL TTD L +G I I D+ T K RGY
Sbjct: 2 SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61
Query: 103 GFVDFESGGYALAAVKA 119
GFV A A K
Sbjct: 62 GFVTMADRAAAERACKD 78
Score = 32.7 bits (75), Expect = 0.043
Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 12/111 (10%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGF---ARLES 187
Q++ T +++ LP + + L + + ++ D S+G GF A +
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 188 KDK-CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGA 237
++ C + +G V A G K R G GP +
Sbjct: 72 AERACKDPNPIIDGRKAN-------VNLAYLGAKPRSLQTGFAIGVSGPSS 115
>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 = 69.9 bits (172), Expect = 2e-15
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 50 PTGPEQLS--KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
+G ++ K LY+ GL ++ DK L +G I + LD T K RG+ FV+F
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 108 ESGGYALAAVKALQDK 123
E A AA+ + +
Sbjct: 62 ELAEDAAAAIDNMNES 77
Score = 46.8 bits (112), Expect = 3e-07
Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 7/99 (7%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
LY+ L + L + + + +I D +G F E +
Sbjct: 7 GMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 66
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
I N S L G + V A K GP
Sbjct: 67 AAAAIDNMNESELFG--RTIRVNLA----KPMRIKESGP 99
>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 = 69.6 bits (171), Expect = 2e-15
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-TNKCRGYGF 104
S + P++ + + + +R + +++ + S +G + + + T T RG+GF
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 105 VDFESGGYALAAVKALQD 122
VDF + A A AL
Sbjct: 63 VDFITKQDAKKAFNALCH 80
Score = 56.2 bits (136), Expect = 2e-10
Identities = 18/101 (17%), Positives = 45/101 (44%), Gaps = 5/101 (4%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESK 188
++Q + + + N+P + ++ L + + + + R+ + T +G GF +K
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 189 DKCDQMIQ-LFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ L + + L G L++++ADS + + + G
Sbjct: 69 QDAKKAFNALCHSTHLYGR--RLVLEWADSEVTVQSGPSSG 107
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 45 GSPGTPTGPEQLS-KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ G + + ++ L++ L D T++++ + +YG DK G+G
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFG 54
Query: 104 FVDFESGGYALAAVKALQDKGIHAQMAR 131
F+ E+ A A L + + + R
Sbjct: 55 FIRLETRTLAEIAKVELDNMPLRGKQLR 82
Score = 54.6 bits (132), Expect = 5e-10
Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 7/98 (7%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ + L++ NLP + E ++ L KY I +D KG GF RLE++
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTL 63
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ + L G L V+FA + G
Sbjct: 64 AEIAKVELDNMPLRGK--QLRVRFACHSASLTSGPSSG 99
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 70.5 bits (173), Expect = 3e-15
Identities = 29/138 (21%), Positives = 48/138 (34%), Gaps = 17/138 (12%)
Query: 7 HRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGL 66
H S+ P +H +S + G P+ T+L + L
Sbjct: 8 HHHSSGLVPRGSHMASMTGGQQMGRG------------SMSYGRPPPDVEGMTSLKVDNL 55
Query: 67 TQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-- 124
T T+ L + +YG + D+ T + RG+ FV F A A+ A+
Sbjct: 56 TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 115
Query: 125 ---IHAQMARQQEQDPTN 139
+ QMAR ++
Sbjct: 116 GRELRVQMARYGRPPDSH 133
Score = 47.4 bits (113), Expect = 4e-07
Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 1/80 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
+ T+L + NL L + KY V I RD S+G F R
Sbjct: 37 YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96
Query: 186 ESKDKCDQMIQLFNGSTLPG 205
K + + +G+ L G
Sbjct: 97 HDKRDAEDAMDAMDGAVLDG 116
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 18/67 (26%), Positives = 42/67 (62%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S ++++ + + T++ L ++ S+ GP++S + + D+ T K +GYGF +++ AL+A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 117 VKALQDK 123
++ L +
Sbjct: 67 MRNLNGR 73
Score = 55.3 bits (134), Expect = 3e-10
Identities = 25/103 (24%), Positives = 44/103 (42%), Gaps = 6/103 (5%)
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
++ ++++ N+P E L+ + ++ VVS R++ D KG GF + ++
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKK---RGAGAGGPNI 231
++ NG G L V A S K + G G P I
Sbjct: 64 LSAMRNLNGREFSG--RALRVDNAASEKNKEELKSLGTGAPVI 104
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 29/100 (29%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 45 GSPGTPTGP--EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G +GP E+ +Y+ GL + ++ L + Q GP+++T D+ T + +GY
Sbjct: 1 GSSG-SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59
Query: 103 GFVDFESGGYALAAVKALQD-----KGIHAQMARQQEQDP 137
GFV+F S A A+K + K I A ++
Sbjct: 60 GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99
Score = 45.7 bits (109), Expect = 8e-07
Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 5/103 (4%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
+ ++ QD T +Y+ L E L L + VV+T + +D +G GF
Sbjct: 6 SGPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64
Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
S++ D I++ + L G +P+ V A S K +G
Sbjct: 65 LSEEDADYAIKIMDMIKLYG--KPIRVNKA-SAHNKNLSGPSS 104
>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 = 68.4 bits (168), Expect = 5e-15
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G P+ L + GL+ TT++DL + S+YGPI + D+ + + RG+
Sbjct: 3 SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVDFESGGYALAAVKALQDK 123
FV FE+ A A +
Sbjct: 61 FVYFENVDDAKEAKERANGM 80
Score = 51.8 bits (125), Expect = 5e-09
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 3/93 (3%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
+ R L + L L E DL + +KY + I+ D + S+G F
Sbjct: 5 SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
E+ D + + NG L G + V SG
Sbjct: 65 ENVDDAKEAKERANGMELDG--RRIRVSGPSSG 95
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 68.4 bits (168), Expect = 6e-15
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 45 GSPGTPTGPEQ-LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
G GP++ + L++ G+ ++ T++D+ + ++YG I + LD+ T +GY
Sbjct: 9 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68
Query: 104 FVDFESGGYALAAVKALQDK 123
V++E+ A AA++ L +
Sbjct: 69 LVEYETYKEAQAAMEGLNGQ 88
Score = 43.0 bits (102), Expect = 7e-06
Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 3/85 (3%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
Q+ + L++ + E D+ A+Y + + + D KG E+ +
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA 215
++ NG L G +P+ V +
Sbjct: 78 AQAAMEGLNGQDLMG--QPISVDWC 100
>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 = 68.0 bits (167), Expect = 6e-15
Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 3/84 (3%)
Query: 45 GSPGTPTGP--EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ ++ + +++ L ++ L + Q GP+ D+ K + +
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSF 59
Query: 103 GFVDFESGGYALAAVKALQDKGIH 126
GFV F+ A+ L ++
Sbjct: 60 GFVCFKHPESVSYAIALLNGIRLY 83
Score = 63.4 bits (155), Expect = 4e-13
Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 2/92 (2%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
+ M QE+ +++ NL +E L L + + I +D K GF +
Sbjct: 6 SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFK 65
Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
+ I L NG L G P+ V SG
Sbjct: 66 HPESVSYAIALLNGIRLYGR--PINVSGPSSG 95
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 68.5 bits (168), Expect = 7e-15
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G L K L+I GL T ++L +C +G + + + ++ K +G
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 104 FVDFESGGYALAAVKAL 120
+V++E+ A AV +
Sbjct: 62 YVEYENESQASQAVMKM 78
Score = 58.8 bits (143), Expect = 2e-11
Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 3/101 (2%)
Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
G + L+I+ LP + + +LE + + TV R++ + KG+ +
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAY 62
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
E++ + Q + +G T+ + V ++SG G
Sbjct: 63 VEYENESQASQAVMKMDGMTIKE--NIIKVAISNSG-PSSG 100
>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 = 71.6 bits (175), Expect = 7e-15
Identities = 34/233 (14%), Positives = 70/233 (30%), Gaps = 56/233 (24%)
Query: 30 NGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDT-TDKDLINMCSQYGPIIST 88
+ +++ PG + L + L + T + L + YG +
Sbjct: 10 HSSGLVPRGSHMGRIAIPGLAGAG----NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV 65
Query: 89 KAILDKTTNKCRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQDP------ 137
K + +K + V G A A+ L K I +++ Q
Sbjct: 66 KILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE 120
Query: 138 -------------------------------TNLYIANLPLNFKECDLESLLAKYVTVVS 166
L+++N+P + E DL+ L + VV
Sbjct: 121 DQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 180
Query: 167 TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGL 219
+ + + ++ S ++ Q + + L + L V F+ S +
Sbjct: 181 GFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGENH-HLRVSFSKSTI 229
Score = 56.5 bits (136), Expect = 1e-09
Identities = 16/115 (13%), Positives = 39/115 (33%), Gaps = 6/115 (5%)
Query: 14 SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN--LYIRGLTQDTT 71
+ + + G ++ G N+ H + + + L++ + +
Sbjct: 105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS 164
Query: 72 DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
++DL + S G ++ K K R + S A+ A+ L + +
Sbjct: 165 EEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 215
Score = 40.4 bits (94), Expect = 3e-04
Identities = 17/136 (12%), Positives = 38/136 (27%), Gaps = 5/136 (3%)
Query: 126 HAQMARQQEQDPTNLYIANL-PLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFAR 184
+ + L ++NL P L L Y V +IL + K +
Sbjct: 23 RIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQ 78
Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGR 244
+ ++ + NG L G + + + R + + + +
Sbjct: 79 MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138
Query: 245 DSADSQLAYEHPMTPI 260
+ + P +
Sbjct: 139 PGSKNFQNIFPPSATL 154
>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 = 68.1 bits (167), Expect = 7e-15
Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 15/104 (14%)
Query: 45 GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + +S LY+R L T+++ + + P + K R Y
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYA 54
Query: 104 FVDFESGGYALAAVKALQDKGIH--------AQMARQQEQDPTN 139
FV F + A+ A+KAL K + A+ + P++
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98
Score = 49.6 bits (119), Expect = 4e-08
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 7/91 (7%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
LY+ NL L+ E +E R+ + + F +++ + ++
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKA 70
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
NG L GS P+ V A K + G
Sbjct: 71 LNGKVLDGS--PIEVTLAKPVDKDSSGPSSG 99
>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 = 68.0 bits (167), Expect = 9e-15
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ K L++ GL+ DT ++ L + S+YG I + D+ T + RG+GF
Sbjct: 1 GSSGSSGMASDEGK--LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGF 58
Query: 105 VDFESGGYALAAVKALQDK 123
V FE+ A A+ A+ K
Sbjct: 59 VTFENIDDAKDAMMAMNGK 77
Score = 53.0 bits (128), Expect = 2e-09
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 7/101 (6%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKD 189
D L++ L + E LE + +KY + +++D S+G GF E+ D
Sbjct: 6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65
Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
+ NG ++ G + V A K GP+
Sbjct: 66 DAKDAMMAMNGKSVDG--RQIRVDQA----GKSSDNRSGPS 100
>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 = 68.6 bits (168), Expect = 9e-15
Identities = 19/80 (23%), Positives = 40/80 (50%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
P + L++ G+ ++ T++D+ + ++YG I + LD+ T +GY
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
Query: 104 FVDFESGGYALAAVKALQDK 123
V++E+ A AA++ L +
Sbjct: 68 LVEYETYKEAQAAMEGLNGQ 87
Score = 48.9 bits (117), Expect = 1e-07
Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 3/106 (2%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
Q+ + L++ + E D+ A+Y + + + D KG E+ +
Sbjct: 17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
++ NG L G +P+ V + +G GG R P
Sbjct: 77 AQAAMEGLNGQDLMG--QPISVDWCFVRGPPKGKRRGGRRRSRSPD 120
>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 = 67.6 bits (166), Expect = 9e-15
Identities = 18/62 (29%), Positives = 37/62 (59%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+Y+ + D T++ ++++CS GP+I+ K + D T + +GY F++F + +AV+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 119 AL 120
L
Sbjct: 63 NL 64
Score = 48.0 bits (115), Expect = 1e-07
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 1/69 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
+Y+ ++P + E + L + V++ +++ D SKG F + ++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 197 LFNGSTLPG 205
NG L
Sbjct: 63 NLNGYQLGS 71
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 18/82 (21%), Positives = 35/82 (42%)
Query: 42 QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
+ P + L++ + ++ + ++ YG I + LD+ T +G
Sbjct: 10 NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69
Query: 102 YGFVDFESGGYALAAVKALQDK 123
Y V++E+ ALAA +AL
Sbjct: 70 YALVEYETHKQALAAKEALNGA 91
Score = 43.0 bits (102), Expect = 9e-06
Identities = 13/99 (13%), Positives = 37/99 (37%), Gaps = 3/99 (3%)
Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNT 176
+ + + Q+ + L++ ++ +E +++ Y + + + D
Sbjct: 7 RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 66
Query: 177 SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
SKG E+ + + NG+ + G + + V +
Sbjct: 67 SKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 103
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
S +G +++ K L++ GL TT + L + SQYG ++ + DKTTN+ RG+G
Sbjct: 4 GSSGMNNSGADEIGK--LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 104 FVDFESGGYALAAVKALQDKG 124
FV F+ L +
Sbjct: 62 FVKFKD---PNCVGTVLASRP 79
>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 = 66.4 bits (163), Expect = 2e-14
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
E K +++ GL+ DT+ KDL + +++G ++ +D T + RG+GF+ F+
Sbjct: 5 SKNEEDAGK--MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62
Query: 110 GGYALAAVKA 119
+
Sbjct: 63 AASVEKVLDQ 72
Score = 29.5 bits (67), Expect = 0.32
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGF---ARL 185
A + E+D +++ L + + DL+ K+ VV I D N S+G GF
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63
Query: 186 ESKDK-CDQMIQLFNG 200
S +K DQ +G
Sbjct: 64 ASVEKVLDQKEHRLDG 79
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 68.4 bits (167), Expect = 3e-14
Identities = 20/123 (16%), Positives = 42/123 (34%), Gaps = 7/123 (5%)
Query: 16 ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLS-----KTNLYIRGLTQDT 70
++ + N Q+ P + TP S + +Y+ + T
Sbjct: 8 SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWT 67
Query: 71 TDKDLINMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ 128
TD+ LI + G ++ K ++ + +GY V S ++ L K ++ +
Sbjct: 68 TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE 127
Query: 129 MAR 131
Sbjct: 128 KVD 130
Score = 48.0 bits (114), Expect = 3e-07
Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 6/114 (5%)
Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGF 182
+Y+ + + L ++ VV + + N SKG
Sbjct: 44 ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS-GLKKRGAGAGGPNIYRGP 235
+ S++ ++++L G L G E + V+ A L + A A R P
Sbjct: 104 VVVASENSVHKLLELLPGKVLNG--EKVDVRPATRQNLSQFEAQARKRECVRVP 155
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 66.6 bits (163), Expect = 3e-14
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 8/84 (9%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS +LS T L++R D + +L + +GP+ K + G+ F
Sbjct: 18 GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAF 69
Query: 105 VDFESGGYALAAVKALQDKGIHAQ 128
V+FE A A++ + K Q
Sbjct: 70 VEFEEAESAAKAIEEVHGKSFANQ 93
Score = 53.5 bits (129), Expect = 2e-09
Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 9/100 (9%)
Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
+G H ++ E T L++ PL+ +E +L + + + +IL G F
Sbjct: 17 RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAF 69
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
E + + I+ +G + +PL V ++ K+
Sbjct: 70 VEFEEAESAAKAIEEVHGKSFAN--QPLEVVYSKLPAKRY 107
>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 = 66.1 bits (162), Expect = 3e-14
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 7/87 (8%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALA 115
+ LYI LT TTD+DL G I+ K ++ + +G+ V S +
Sbjct: 1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
Query: 116 AVKALQDKGIHAQ-----MARQQEQDP 137
+ L + +H Q + + E
Sbjct: 61 LMDLLPKRELHGQNPVVTPSNKLEHHH 87
Score = 51.4 bits (124), Expect = 6e-09
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 5/80 (6%)
Query: 139 NLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
LYI NL + DL + ++ + + N SKG + S+ +++
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 196 QLFNGSTLPGSKEPLLVKFA 215
L L G + +V +
Sbjct: 63 DLLPKRELHG--QNPVVTPS 80
>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 = 66.4 bits (163), Expect = 3e-14
Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS + + +K +++ G+ + + +L ++G + I D + RG+GF
Sbjct: 1 GSS--GSSGSKSNK--IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGF 56
Query: 105 VDFESGGYALAAVKALQDKG 124
+ FE + +A+
Sbjct: 57 ITFEDEQ---SVDQAVNMHF 73
Score = 29.5 bits (67), Expect = 0.41
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQLF 198
+++ +P N E +L K+ V ++ D +G GF E + DQ + +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM- 71
Query: 199 NGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ + G K + VK A+ K + G
Sbjct: 72 HFHDIMGKK--VEVKRAEPRDSKSSGPSSG 99
>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 = 66.6 bits (163), Expect = 4e-14
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
L+I GL ++T +K L + ++GPI I D+ T+K RG+ F+ FE+ A A K
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66
Query: 119 ALQDK 123
+ K
Sbjct: 67 DMNGK 71
Score = 53.9 bits (130), Expect = 2e-09
Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 2/101 (1%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
P L+I L E L+++ K+ + +++D + S+G F E+
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
+ NG +L G + + V+ A + G P R
Sbjct: 66 KDMNGKSLHG--KAIKVEQAKKPSFQSGGRRRPPASSRNRS 104
>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 = 66.6 bits (163), Expect = 4e-14
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
LYIR L T +++ ++ +YGPI I T + RG +V +E A AV
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVD 65
Query: 119 ALQ-----DKGIHAQMARQQEQDP 137
L ++ +
Sbjct: 66 HLSGFNVSNRYLVVLYYNANRAFQ 89
Score = 48.1 bits (115), Expect = 2e-07
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
LYI NLP ++ + KY + R+ ++G + E +
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDH 66
Query: 198 FNGSTLPGSKEPLLVKFA 215
+G + L+V +
Sbjct: 67 LSGFNVSN--RYLVVLYY 82
>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 = 65.7 bits (161), Expect = 5e-14
Identities = 17/65 (26%), Positives = 30/65 (46%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+ LY+ L + T+ L + +G I + + D T + +GYGF+ F A A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 119 ALQDK 123
L
Sbjct: 66 QLNGF 70
Score = 52.6 bits (127), Expect = 2e-09
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 7/96 (7%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQM 194
+ LY+ +L N E L + + + + +++D + SKG GF + +
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
++ NG L G P+ V +R G GP+
Sbjct: 64 LEQLNGFELAG--RPMRVGHV----TERLDGGSGPS 93
>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 = 65.2 bits (160), Expect = 5e-14
Identities = 20/65 (30%), Positives = 31/65 (47%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
NL++ L + D+ L N + +S + D T RGYGFV F S A A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 119 ALQDK 123
++Q +
Sbjct: 62 SMQGQ 66
Score = 48.6 bits (117), Expect = 5e-08
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
NL++ +L +N + L + + + +S ++ D +S+G GF S+D +
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 197 LFNGSTLPG 205
G L G
Sbjct: 62 SMQGQDLNG 70
>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 = 66.2 bits (162), Expect = 5e-14
Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 38 TNNVQHNGSPGTPTGPEQLSK--TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
++ + + ++ S LY+ L + T+ L + +G I S + ++D
Sbjct: 4 HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE 63
Query: 96 TNKCRGYGFVDFESGGYALAAVKALQDK 123
T + +GYGF+ F A A++ L
Sbjct: 64 TGRSKGYGFITFSDSECAKKALEQLNGF 91
Score = 52.3 bits (126), Expect = 4e-09
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 1/80 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
A ++ P LY+ +L N E L + + + S +++ D SKG GF
Sbjct: 16 ANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 186 ESKDKCDQMIQLFNGSTLPG 205
+ + ++ NG L G
Sbjct: 76 SDSECAKKALEQLNGFELAG 95
>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 = 65.7 bits (161), Expect = 5e-14
Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 11/104 (10%)
Query: 45 GSPGTPT-GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + LY+ L++D T+ ++ + SQ GP S K I + T+N Y
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYC 58
Query: 104 FVDFESGGYALAAVKALQDKGIH--------AQMARQQEQDPTN 139
FV+F A AA+ A+ + I A Q+ P++
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
Score = 44.2 bits (105), Expect = 3e-06
Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 4/98 (4%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ + P LY+ NL + E + L ++ S +++ + + ++ F
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRD 67
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA-DSGLKKRGAGAG 227
+ NG + G + V +A +K G +G
Sbjct: 68 AAAALAAMNGRKILGK--EVKVNWATTPSSQKSGPSSG 103
>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 = 67.1 bits (164), Expect = 6e-14
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 1/84 (1%)
Query: 42 QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
G + S T LY+ L+ TT++ + + S+ G I LDK G
Sbjct: 24 HFRGDNEEQEKLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 102 YGFVDFESGGYALAAVKALQDKGI 125
+ FV++ S A A++ + +
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRL 106
Score = 43.3 bits (102), Expect = 2e-05
Identities = 24/137 (17%), Positives = 48/137 (35%), Gaps = 11/137 (8%)
Query: 121 QDKGIHAQMARQQEQDP--TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTS 177
+D+ Q++ LY+ NL E + L +K + + D T+
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA--DSGLKKRGAGAGGPNI---Y 232
G F S+ + ++ NG+ L + + ++ G G G + Y
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRLDD--RIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138
Query: 233 RGPGAEVRL-WGRDSAD 248
R R +G+ + +
Sbjct: 139 RQDYDAGRGGYGKLAQN 155
>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 = 64.9 bits (159), Expect = 7e-14
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGGYALA 115
T ++I LT++ T ++ + S YG I +++ + +GY +V+FE+ A
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 116 AVKAL 120
A+K +
Sbjct: 63 ALKHM 67
Score = 48.3 bits (116), Expect = 6e-08
Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQM 194
PT ++I L N + + + + Y + + + + SKG + E+ D+ ++
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 195 IQLFNGSTLPGSKEPLLVKFA 215
++ +G + G +
Sbjct: 64 LKHMDGGQIDGQ--EITATAV 82
>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 = 65.4 bits (160), Expect = 1e-13
Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 1/81 (1%)
Query: 40 NVQHNGSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK 98
+ H+ S P G S ++I GL+ TT + L Q+G + + D T +
Sbjct: 6 HHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR 65
Query: 99 CRGYGFVDFESGGYALAAVKA 119
RG+GFV F +
Sbjct: 66 SRGFGFVTFMDQAGVDKVLAQ 86
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 64.0 bits (157), Expect = 1e-13
Identities = 20/59 (33%), Positives = 34/59 (57%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
+++ GL+ +TT +D+ + Q+G + + DKTTN+ RG+GFV FES +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 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 = 67.8 bits (165), Expect = 1e-13
Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 2/113 (1%)
Query: 16 ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
+ + ++ + T P T + G+ + LYI LT TTD+DL
Sbjct: 26 SPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDL 85
Query: 76 INMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
G I+ K ++ + +G+ V S + + L + +H
Sbjct: 86 TEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH 138
Score = 50.1 bits (119), Expect = 2e-07
Identities = 26/189 (13%), Positives = 43/189 (22%), Gaps = 11/189 (5%)
Query: 115 AAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD 172
V KG + LYI NL + DL + ++ + +
Sbjct: 46 PTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN 105
Query: 173 -NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNI 231
N SKG + S+ +++ L L G + +V + +
Sbjct: 106 RANGQSKGFALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPVNKQFLSQFEMQSRKTT 163
Query: 232 YRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQY 291
G + RF G P P P
Sbjct: 164 QSGQM------SGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPP 217
Query: 292 VMPAPHMSQ 300
Sbjct: 218 FPAGQTHHH 226
>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 = 66.4 bits (162), Expect = 1e-13
Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 5/101 (4%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS + T+L + LT T+ L + +YG + D+ T + RG+
Sbjct: 56 EGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115
Query: 104 FVDFESGGYALAAVKALQDK-----GIHAQMARQQEQDPTN 139
FV F A A+ A+ + QMAR ++
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156
Score = 52.9 bits (127), Expect = 8e-09
Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 1/92 (1%)
Query: 115 AAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN 174
A +G H + T+L + NL L + KY V I RD
Sbjct: 48 ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107
Query: 175 -NTSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
S+G F R K + + +G+ L G
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G L++ + D DL M Q+G I+ + I ++ + +G+G
Sbjct: 3 SGSSGNSESKST--PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFG 58
Query: 104 FVDFESGGYALAAVKAL 120
FV FE+ A A + L
Sbjct: 59 FVTFENSADADRAREKL 75
Score = 60.4 bits (147), Expect = 5e-12
Identities = 20/98 (20%), Positives = 45/98 (45%), Gaps = 3/98 (3%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ + P L+++N+P F++ DL + ++ ++ I+ + SKG GF E+
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSAD 67
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
D+ + +G+ + G + V A + + + G
Sbjct: 68 ADRAREKLHGTVVEG--RKIEVNNATARVMTNSGPSSG 103
>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 = 64.2 bits (157), Expect = 2e-13
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC---RGYGFVDFESGGYALA 115
+ L+I+ L TT++ L + S+ G I S K G+GFV+++ A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 116 AVKALQDK 123
A+K LQ
Sbjct: 66 ALKQLQGH 73
Score = 59.2 bits (144), Expect = 1e-11
Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN----NTSKGVGFARLESKDKC 191
+ L+I NL + E L+ + +K + S I + N S G GF + ++
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ ++ G T+ G L V+ ++ K + G
Sbjct: 64 QKALKQLQGHTVDGH--KLEVRISERATKPASGPSSG 98
>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 = 64.2 bits (157), Expect = 2e-13
Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 51 TGPE-QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
+ PE ++ +++ G+ + ++ + ++YG + K I D+ T +GYGFV F +
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN 59
Query: 110 GGYALAAVKALQD 122
V++ +
Sbjct: 60 DVDVQKIVESQIN 72
Score = 49.9 bits (120), Expect = 3e-08
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
P +++ + + E ++ S A+Y +V +I+ D SKG GF + ++++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 197 LFNGSTLPGSKEPLLVKFA 215
+ G K L + A
Sbjct: 69 --SQINFHGKK--LKLGPA 83
>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 = 64.3 bits (157), Expect = 3e-13
Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 7/102 (6%)
Query: 45 GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + + +++ L K L + S G ++ + DK K RG G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59
Query: 104 FVDFESGGYALAAVKA-----LQDKGIHAQMARQQEQDPTNL 140
V FE A+ A+ L D+ +H +M +
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFF 101
Score = 62.3 bits (152), Expect = 1e-12
Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 2/108 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKD 189
A Q + + +++ANL L+ + + VV IL D + S+G+G E
Sbjct: 8 ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSI 67
Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGA 237
+ Q I +FNG L P+ VK + L K GP +
Sbjct: 68 EAVQAISMFNGQLLFD--RPMHVKMDERALPKGDFFPPERPQQSGPSS 113
>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 = 63.3 bits (155), Expect = 3e-13
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
N+Y+ L T + + + SQ+G + + K I D+ T K +G+GFV+ + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 120 LQDK 123
L +
Sbjct: 62 LDNT 65
Score = 47.2 bits (113), Expect = 2e-07
Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
N+Y+ NL + ++ L +++ V + +++ D KG GF ++ + + I
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 198 FNGSTLPGSKEPLLVKFA 215
+ + G + V A
Sbjct: 62 LDNTDFMGR--TIRVTEA 77
>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 = 63.3 bits (155), Expect = 3e-13
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
P G ++++ L+ + T + + +G I + + D T K +GYGFV F +
Sbjct: 2 PLGSH----FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
Query: 110 GGYALAAVKALQDK 123
A A++ + +
Sbjct: 58 KWDAENAIQQMGGQ 71
Score = 41.4 bits (98), Expect = 2e-05
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQL 197
++++ +L + + A + + R+++D SKG GF +K + IQ
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 198 FNGSTLPG 205
G L G
Sbjct: 68 MGGQWLGG 75
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 63.6 bits (155), Expect = 3e-13
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
S + + P++ L IR + + L ++ QYG + S + + + V
Sbjct: 3 SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNV 59
Query: 106 DFESGGYALAAVKAL 120
+ S A A+ L
Sbjct: 60 TYSSKDQARQALDKL 74
Score = 54.8 bits (132), Expect = 5e-10
Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 6/93 (6%)
Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFAR 184
+ + + Q L I N+P + + L+SLL +Y V S + ++ T V ++
Sbjct: 4 GSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSS 63
Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
+ + + NG L L V +
Sbjct: 64 KDQARQA---LDKLNGFQLENF--TLKVAYIPD 91
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 62.9 bits (154), Expect = 4e-13
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
++I GL+ TT + L Q+G + + D T + RG+GFV F +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>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 = 64.3 bits (157), Expect = 4e-13
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 42 QHNGSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCR 100
QH+ G E + L + L +D D+ + +++G + D+ + +
Sbjct: 18 QHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSL 76
Query: 101 GYGFVDFESGGYALAAVKAL 120
G V FE AL A+K
Sbjct: 77 GTADVHFERRADALKAMKQY 96
Score = 57.0 bits (138), Expect = 1e-10
Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 2/100 (2%)
Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
K D + + L ++NL + D++ L A++ T+ + D + S
Sbjct: 16 KWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 75
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
G E + + ++ + G L G P+ ++ S
Sbjct: 76 LGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQLVAS 113
>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 = 63.1 bits (154), Expect = 5e-13
Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+ + ++T L + L+ + T+ +L + I L K +G +++F+
Sbjct: 8 CTSKKVRAART-LLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFK 61
Query: 109 SGGYALAAVKALQDK 123
S A ++ Q
Sbjct: 62 SEADAEKNLEEKQGA 76
Score = 45.7 bits (109), Expect = 6e-07
Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
++ + L NL N E +L+ + + + + SKG+ + +S+
Sbjct: 11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADA 66
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
++ ++ G+ + G + + + RG
Sbjct: 67 EKNLEEKQGAEIDGR--SVSLYYTGEKGGTRG 96
>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 = 63.1 bits (154), Expect = 5e-13
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 7/80 (8%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
S + E SKT L + L+ T++ L + + I + K +GY
Sbjct: 4 GSSGNSTWSGE--SKT-LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYA 56
Query: 104 FVDFESGGYALAAVKALQDK 123
F++F S A A+ + +
Sbjct: 57 FIEFASFEDAKEALNSCNKR 76
Score = 46.9 bits (112), Expect = 3e-07
Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 9/99 (9%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ L ++NL + E L+ + K + ++ ++ N SKG F S +
Sbjct: 9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFED 65
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
+ + N + G + ++ RG+ GP
Sbjct: 66 AKEALNSCNKREIEG--RAIRLELQ----GPRGSPNSGP 98
>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 = 63.5 bits (155), Expect = 5e-13
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
EQ K L+I GL+ +TT++ L N Q+G + + D + + RG+GFV F
Sbjct: 20 KKREKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Query: 109 SGGYALAAVKA 119
S AA+ A
Sbjct: 78 SMAEVDAAMAA 88
>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 = 63.0 bits (154), Expect = 5e-13
Identities = 26/101 (25%), Positives = 50/101 (49%), Gaps = 15/101 (14%)
Query: 43 HNGSPGTPTGPEQLSK---TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC 99
+GS G +++++ NLY++ L D+ L S +G I S K +++ +
Sbjct: 2 SSGSSG-----DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRS 54
Query: 100 RGYGFVDFESGGYALAAVKALQD-----KGIHAQMARQQEQ 135
+G+GFV F S A AV + K ++ +A+++E+
Sbjct: 55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Score = 56.8 bits (138), Expect = 1e-10
Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 4/106 (3%)
Query: 124 GIHAQMARQQEQDP-TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
G + + NLY+ NL + L + + T+ S +++ + SKG GF
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR-SKGFGF 59
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
S ++ + + NG + +K PL V A +++ + G
Sbjct: 60 VCFSSPEEATKAVTEMNGRIV-ATK-PLYVALAQRKEERQSGPSSG 103
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 63.1 bits (154), Expect = 7e-13
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
+ M + + P L+++N+P F++ DL + ++ ++ I+ + SKG GF E
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFE 77
Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
+ D+ + +G+ + G + V A
Sbjct: 78 NSADADRAREKLHGTVVEG--RKIEVNNA 104
Score = 61.6 bits (150), Expect = 2e-12
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
L++ + D DL M Q+G I+ + I ++ +G+GFV FE+ A A +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87
Query: 119 AL 120
L
Sbjct: 88 KL 89
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 62.2 bits (152), Expect = 8e-13
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 13/95 (13%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ +++R L D T K L + ++ G ++ ++ K +G G
Sbjct: 1 GSSGSSGA------CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGV 52
Query: 105 VDFESGGYALAAVKA-----LQDKGIHAQMARQQE 134
V FES A A + L + I ++ R
Sbjct: 53 VKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS 87
Score = 56.4 bits (137), Expect = 1e-10
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 7/92 (7%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
+++ NLP +F L+ + V+ I +N SKG G + ES + ++ +
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-SKGCGVVKFESPEVAERACR 66
Query: 197 LFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ NG L G + V+ + + G
Sbjct: 67 MMNGMKLSG--REIDVRID----RNASGPSSG 92
>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 = 62.7 bits (153), Expect = 9e-13
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 3/78 (3%)
Query: 43 HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
+ G G E L + L +D D+ + +++G + D+ + + G
Sbjct: 16 FDSGFGGGAGVET--GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGT 72
Query: 103 GFVDFESGGYALAAVKAL 120
V FE AL A+K
Sbjct: 73 ADVHFERKADALKAMKQY 90
Score = 59.6 bits (145), Expect = 1e-11
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 2/97 (2%)
Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV 180
D + L ++NL + D++ L A++ T+ + D + S G
Sbjct: 13 HDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGT 72
Query: 181 GFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
E K + ++ +NG L G P+ ++ S
Sbjct: 73 ADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVTS 107
>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 = 61.4 bits (150), Expect = 1e-12
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
+++ GL+ DT ++ + +G + S + +D TNK RG+ F+ F+ K +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE---PVKKIM 58
Query: 121 QDK 123
+ K
Sbjct: 59 EKK 61
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
L++R L T++ L SQ+G + K + + Y F+ F+ A+ A++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAME 63
Query: 119 ALQDKGIHAQ 128
+ K + +
Sbjct: 64 EMNGKDLEGE 73
Score = 46.1 bits (110), Expect = 6e-07
Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 9/98 (9%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
L++ NL E LE +++ + + L+D F + +D + ++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEE 64
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
NG L G + + FA +KR GP
Sbjct: 65 MNGKDLEGE--NIEIVFAKPPDQKRKERKAQRQAASGP 100
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 1/83 (1%)
Query: 45 GSPGTP-TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + + T + ++ + + ++++ Y I + + G
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 104 FVDFESGGYALAAVKALQDKGIH 126
V FES A AAV L D+ I
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIG 83
Score = 44.2 bits (105), Expect = 2e-06
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 1/69 (1%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
PT + + N+P ++ Y V S + + G ES+D+
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 195 IQLFNGSTL 203
+ N +
Sbjct: 74 VIDLNDRPI 82
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 62.1 bits (151), Expect = 1e-12
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
+ ++YI+G D T D+ G +++ + + +G FV F+S
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDS---I 62
Query: 114 LAAVKALQDKGI 125
+A K ++ G
Sbjct: 63 ESAKKFVETPGQ 74
Score = 61.7 bits (150), Expect = 2e-12
Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 1/91 (1%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
+ + ++YI P + D++ L V++ ++ R + KG F +S +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
+ ++ G + +L K K
Sbjct: 66 KKFVET-PGQKYKETDLLILFKDDYFAKKNE 95
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 66.4 bits (161), Expect = 2e-12
Identities = 20/66 (30%), Positives = 30/66 (45%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ + DTT+ L YGPI + K + K RGY F+++E +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 QDKGIH 126
K I
Sbjct: 165 DGKKID 170
Score = 42.9 bits (100), Expect = 8e-05
Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 2/74 (2%)
Query: 136 DPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
D L++A + + E L Y + ++ + +G F E +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 194 MIQLFNGSTLPGSK 207
+ +G + G +
Sbjct: 160 AYKHADGKKIDGRR 173
>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 = 62.4 bits (152), Expect = 2e-12
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 4/91 (4%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
P + +++ K ++Y+ + +T +DL S G I + DK + +GY +
Sbjct: 23 PQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAY 82
Query: 105 VDFESGGYALAAV----KALQDKGIHAQMAR 131
++F AAV + + I R
Sbjct: 83 IEFAERNSVDAAVAMDETVFRGRTIKVLPKR 113
Score = 51.6 bits (124), Expect = 1e-08
Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 2/86 (2%)
Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKG 179
+ ++E D ++Y+ N+ DLE+ + ++ IL D + KG
Sbjct: 20 EGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
Query: 180 VGFARLESKDKCDQMIQLFNGSTLPG 205
+ ++ D + + + + G
Sbjct: 80 YAYIEFAERNSVDAAVAM-DETVFRG 104
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 24/97 (24%), Positives = 33/97 (34%), Gaps = 15/97 (15%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G P + LY+ G D T L S +G II +
Sbjct: 3 SGSSGERRAPRK--GNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCA 52
Query: 104 FVDFESGGYALAAVKALQDKGIHAQM-----ARQQEQ 135
FV +E A AV L + + AR+Q
Sbjct: 53 FVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 89
Score = 38.0 bits (89), Expect = 4e-04
Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 9/98 (9%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
R+ + LY+ + L + + ++ + + F E +
Sbjct: 9 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMES 61
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
DQ + NG+ + L V A + G
Sbjct: 62 ADQAVAELNGTQVESV--QLKVNIARKQPMLDSGPSSG 97
>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 = 62.1 bits (151), Expect = 2e-12
Identities = 23/111 (20%), Positives = 34/111 (30%), Gaps = 8/111 (7%)
Query: 21 SSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCS 80
SS + + G P ++ S P LY+ G D T L S
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFS 59
Query: 81 QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
+G II + FV +E A AV L + + +
Sbjct: 60 PFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVESVQLK 104
Score = 38.6 bits (90), Expect = 3e-04
Identities = 12/99 (12%), Positives = 29/99 (29%), Gaps = 7/99 (7%)
Query: 109 SGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTR 168
S G + + R+ + LY+ + L + + ++
Sbjct: 11 SSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS 68
Query: 169 ILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK 207
+ + F E + DQ + NG+ + +
Sbjct: 69 MDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQ 102
>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 = 61.6 bits (150), Expect = 3e-12
Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 15/106 (14%)
Query: 26 TGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPI 85
+ +G T + +V + SP +Y G+ TD+ + S +G I
Sbjct: 2 SSGSSGNTKQLRFEDVVNQSSP---------KNCTVYCGGIASGLTDQLMRQTFSPFGQI 52
Query: 86 ISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
+ + +K GY FV F + A A+ ++ I + +
Sbjct: 53 MEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVK 92
Score = 43.1 bits (102), Expect = 7e-06
Identities = 13/101 (12%), Positives = 31/101 (30%), Gaps = 7/101 (6%)
Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
+ Q +Y + + + + + ++ R+ + KG F R +
Sbjct: 16 DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFST 70
Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ I NG+T+ G + + + G
Sbjct: 71 HESAAHAIVSVNGTTIEGH--VVKCYWGKESPDMTSGPSSG 109
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 61.2 bits (149), Expect = 3e-12
Identities = 23/109 (21%), Positives = 41/109 (37%), Gaps = 19/109 (17%)
Query: 27 GSQNGGT----HPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY 82
GSQ G +P +++ + P T YI + T+ DLI + +
Sbjct: 1 GSQTIGLPPQVNPQAVDHIIRSAPP---------RVTTAYIGNIPHFATEADLIPLFQNF 51
Query: 83 GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
G I+ K +K G F+ +++ A + AL + + R
Sbjct: 52 GFILDFKHYPEK------GCCFIKYDTHEQAAVCIVALANFPFQGRNLR 94
Score = 44.6 bits (106), Expect = 2e-06
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 5/80 (6%)
Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
+ R T YI N+P E DL L + ++ + + KG F + ++
Sbjct: 18 HIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDT 72
Query: 188 KDKCDQMIQLFNGSTLPGSK 207
++ I G
Sbjct: 73 HEQAAVCIVALANFPFQGRN 92
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 45 GSPGTP-TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + T + ++ + + ++++ Y I + + G
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 104 FVDFESGGYALAAVKALQDKGIH 126
V FES A AAV L D+ I
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIG 83
Score = 45.4 bits (108), Expect = 1e-06
Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 1/75 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESK 188
A + PT + + N+P ++ Y V S + + G ES+
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 189 DKCDQMIQLFNGSTL 203
D+ + N +
Sbjct: 68 DEATAAVIDLNDRPI 82
>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 = 60.7 bits (148), Expect = 4e-12
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
S + L+++GL++DTT++ L + + + + D+ T +G+GFV
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGFV 59
Query: 106 DFESGGYALAAVKALQDKGI 125
DF S A AA +A++D I
Sbjct: 60 DFNSEEDAKAAKEAMEDGEI 79
Score = 47.3 bits (113), Expect = 2e-07
Identities = 23/108 (21%), Positives = 39/108 (36%), Gaps = 11/108 (10%)
Query: 124 GIHAQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVG 181
G P+ L++ L + E L+ V RI+ D +SKG G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57
Query: 182 FARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
F S++ + + G+ + + +A K +G G GP
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGN--KVTLDWA----KPKGEGGSGP 99
>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 = 61.0 bits (148), Expect = 4e-12
Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL--DKTTNKCRGYGFVDFESGGYAL 114
L+I G+ + ++++ ++ + + K RG+ FV++ES A
Sbjct: 7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66
Query: 115 AAVKALQDKGIH 126
A + L I
Sbjct: 67 MARRKLMPGRIQ 78
Score = 47.5 bits (113), Expect = 3e-07
Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 3/85 (3%)
Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL---RDNNNTSKGVGFARLESKDKC 191
L+I +P K ++ +AK V I+ + ++G F ES
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFAD 216
+ + + V +A+
Sbjct: 66 AMARRKLMPGRIQLWGHQIAVDWAE 90
>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 = 60.8 bits (148), Expect = 5e-12
Identities = 14/73 (19%), Positives = 28/73 (38%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
P PE+ ++ L +DL + S G + + I D+ + + +G +V
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72
Query: 106 DFESGGYALAAVK 118
+F A+
Sbjct: 73 EFCEIQSVPLAIG 85
Score = 55.0 bits (133), Expect = 5e-10
Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
+E+D ++ L + DLE + V RI+ D N SKG+ +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
I L G L G P++V+ + + K R +G
Sbjct: 80 VPLAIGL-TGQRLLGV--PIIVQASQAE-KNRLSGPSS 113
>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 = 60.8 bits (148), Expect = 5e-12
Identities = 17/78 (21%), Positives = 38/78 (48%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
S + + + ++++ L+ + T +D+ + +G I + + D T K +GYGFV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 106 DFESGGYALAAVKALQDK 123
F + A A++ + +
Sbjct: 63 SFFNKWDAENAIQQMGGQ 80
Score = 45.0 bits (107), Expect = 2e-06
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKD 189
++ + ++++ +L D+++ A + + R+++D SKG GF +K
Sbjct: 9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 68
Query: 190 KCDQMIQLFNGSTLPG 205
+ IQ G L G
Sbjct: 69 DAENAIQQMGGQWLGG 84
>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 = 59.6 bits (145), Expect = 7e-12
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 9/88 (10%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ E + T LY+ GL T+ DL N Q+G I + + + F
Sbjct: 1 GSSGSS--GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAF 52
Query: 105 VDFESGGYA-LAAVKALQDKGIHAQMAR 131
+ F + A +AA K+ ++ +
Sbjct: 53 IQFATRQAAEVAAEKSFNKLIVNGRRLN 80
Score = 41.9 bits (99), Expect = 1e-05
Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 10/87 (11%)
Query: 132 QQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKD 189
+D T LY+ L E DL + ++ + + +++ + F + ++
Sbjct: 5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQ 59
Query: 190 KCDQ-MIQLFNGSTLPGSKEPLLVKFA 215
+ + FN + G L VK+
Sbjct: 60 AAEVAAEKSFNKLIVNG--RRLNVKWG 84
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 6/73 (8%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
T L++ GL +T+ L ++G I + + + ++ +ES A AA
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACA 71
Query: 119 ALQDKGIHAQMAR 131
++ + R
Sbjct: 72 KMRGFPLGGPDRR 84
Score = 47.6 bits (114), Expect = 2e-07
Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 6/83 (7%)
Query: 137 PTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
PT L++ L N L ++ ++ + ++ + + ES D
Sbjct: 16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAAC 70
Query: 196 QLFNGSTLPGSKEPLLVKFADSG 218
G L G L V FA SG
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSG 93
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 8/82 (9%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIIST--------KAILDKTTNKCRG 101
++++GL ++ T + + + Q G I + D+ T K +G
Sbjct: 5 HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64
Query: 102 YGFVDFESGGYALAAVKALQDK 123
V F+ A AA+ K
Sbjct: 65 EATVSFDDPPSAKAAIDWFDGK 86
Score = 43.4 bits (103), Expect = 5e-06
Identities = 14/98 (14%), Positives = 26/98 (26%), Gaps = 11/98 (11%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTS 177
D +++ L N + + + + + D
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
KG + I F+G G+ P+ V FA
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFA 98
>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 = 59.5 bits (144), Expect = 2e-11
Identities = 21/128 (16%), Positives = 47/128 (36%), Gaps = 28/128 (21%)
Query: 14 SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDK 73
++ H SS + +++ + S G P S+ ++IR L D T+
Sbjct: 2 GSSHHHHHHSSGLVPRG--------SHMGDSRSAGVP------SRV-IHIRKLPIDVTEG 46
Query: 74 DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-------IH 126
++I++ +G + + + K + F++ + A V I+
Sbjct: 47 EVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY 100
Query: 127 AQMARQQE 134
Q + +E
Sbjct: 101 IQFSNHKE 108
Score = 44.9 bits (106), Expect = 2e-06
Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 5/95 (5%)
Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
+G H +R ++I LP++ E ++ SL + V + +L+ K F
Sbjct: 17 RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAF 71
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
+ +++ + M+ + T +P+ ++F++
Sbjct: 72 IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 59.0 bits (143), Expect = 2e-11
Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 13/92 (14%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPI--------ISTKAILDKTTNKCRGYGFVDFESG 110
++++GL ++ T + + + Q G I D+ T K +G V F+
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 111 GYALAAVKALQDK-----GIHAQMARQQEQDP 137
A AA+ K I A ++
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99
Score = 45.5 bits (108), Expect = 1e-06
Identities = 17/114 (14%), Positives = 29/114 (25%), Gaps = 11/114 (9%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTSKGVGF 182
Q D +++ L N + + + + + D KG
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
+ I F+G G+ P+ V FA G G
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFATRRADFNRGGGNGRGGLEHHH 113
>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 = 59.8 bits (145), Expect = 2e-11
Identities = 20/102 (19%), Positives = 34/102 (33%), Gaps = 17/102 (16%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA-----ILDKTTNK 98
+ PG P +Y++ L + +KDL + +Y S I +
Sbjct: 38 SYEPGEPN-------CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR 90
Query: 99 CRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQ 135
+G F+ + A A+K K + Q AR
Sbjct: 91 MKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 132
Score = 47.1 bits (112), Expect = 6e-07
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTR------ILRDNNNTSKGVGFARLESKDKC 191
+Y+ NL + +E DL+ + +YV S I KG F L ++
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFA 215
+ ++ NG L G +P++V+FA
Sbjct: 106 AKALKEANGYVLFG--KPMVVQFA 127
>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 = 58.3 bits (142), Expect = 2e-11
Identities = 10/67 (14%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
G E +++ +Y+ + T ++L G + + DK + +G+ +++F
Sbjct: 1 GMEADARS-IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
Query: 112 YALAAVK 118
++
Sbjct: 60 SVRTSLA 66
Score = 51.4 bits (124), Expect = 6e-09
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCD 192
E D ++Y+ N+ +LE+ +V IL D + KG + K+
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 193 QMIQLFNGSTLPG 205
+ L + S G
Sbjct: 63 TSLAL-DESLFRG 74
>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 = 58.4 bits (142), Expect = 2e-11
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
PE +YI L + +L + S++G I+ + K RG FV F+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFK 59
Query: 109 SGGYALAAVKALQ-----DKGIHAQMARQQE 134
A A++++Q DK + Q A+
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90
Score = 36.4 bits (85), Expect = 0.001
Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 9/87 (10%)
Query: 134 EQDPTN-LYIANLPLNFKECDLESLL----AKYVTVVSTRILRDNNNTSKGVGFARLESK 188
E P + +YI NL K+ +L+ L +++ ++ + R +G F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEV 61
Query: 189 DKCDQMIQLFNGSTLPGSKEPLLVKFA 215
++ G P+ +++A
Sbjct: 62 SSATNALRSMQGFPFYDK--PMRIQYA 86
>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 = 58.6 bits (142), Expect = 3e-11
Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 14/104 (13%)
Query: 45 GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIIST--------KAILDKT 95
GS G+ P++ S + +Y++GL T DL + Q G + LDK
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 96 TNKCRGYGFVDFESGGYALAAVKALQDK-----GIHAQMARQQE 134
T K +G V +E A AAV+ K + +AR++
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
Score = 48.6 bits (116), Expect = 1e-07
Identities = 20/106 (18%), Positives = 31/106 (29%), Gaps = 11/106 (10%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTSKGVGF 182
++ D + +Y+ L + DL + V I D KG
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 69
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
E ++ F+G GSK L V A + G
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARKKPPMNSGPSSG 113
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
+G ++K LYI L+ T DL + L GY FVD+
Sbjct: 2 SSGSSGMNK--LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPD 53
Query: 110 GGYALAAVKALQDK 123
+A+ A++ L K
Sbjct: 54 QNWAIRAIETLSGK 67
Score = 44.2 bits (105), Expect = 3e-06
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 8/93 (8%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
LYI NL DL L ++ ++L G F ++ + I+
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIE 62
Query: 197 LFNGST-LPGSKEPLLVKFADSGLKKRGAGAGG 228
+G L G + + V ++ S + + G
Sbjct: 63 TLSGKVELHG--KIMEVDYSVSKKLRSSGPSSG 93
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 57.9 bits (140), Expect = 4e-11
Identities = 18/106 (16%), Positives = 41/106 (38%), Gaps = 20/106 (18%)
Query: 36 ITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
+ ++ H+ G P S+ ++IR L D T+ ++I++ +G + + +
Sbjct: 1 MRGSHHHHHHGSGVP------SRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLML---- 49
Query: 96 TNKCRGYGFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
K + F++ + A V I+ Q + +E
Sbjct: 50 --KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 93
Score = 46.8 bits (111), Expect = 4e-07
Identities = 16/95 (16%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
+G H ++I LP++ E ++ SL + V + +L+ K F
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAF 56
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
+ +++ + M+ + T +P+ ++F++
Sbjct: 57 IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 57.7 bits (140), Expect = 4e-11
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
+L++ L + + + G ++S K I ++ T GY FV+F A
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
Query: 116 AVKALQDKGIH 126
+ + K +
Sbjct: 68 CLHKINGKPLP 78
Score = 44.6 bits (106), Expect = 2e-06
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 2/80 (2%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRD-NNNTSKGVGFARLESKD 189
+L++ +L E + A TV+S +I+R+ G F
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 190 KCDQMIQLFNGSTLPGSKEP 209
++ + NG LPG+
Sbjct: 64 TAEKCLHKINGKPLPGATPA 83
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 58.8 bits (142), Expect = 4e-11
Identities = 18/103 (17%), Positives = 36/103 (34%), Gaps = 13/103 (12%)
Query: 42 QHNGSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTT 96
QH SP + P + + I + + + L + S G I+ I+ +
Sbjct: 12 QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLS 68
Query: 97 NKCRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQE 134
+ G ++ F + A A V+A Q + + +
Sbjct: 69 DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111
Score = 39.5 bits (92), Expect = 2e-04
Identities = 17/113 (15%), Positives = 44/113 (38%), Gaps = 13/113 (11%)
Query: 114 LAAVKALQDKGIHAQMARQQEQDP-----TNLYIANLPLNFKECDLESLL----AKYVTV 164
+ A + + H P + I N+ + L++LL + +
Sbjct: 1 MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
+ I+ D ++ + G + +++ ++ F G G+ PL++ F+++
Sbjct: 61 LD--IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN--PLVITFSET 109
>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 = 57.6 bits (140), Expect = 4e-11
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ L+I L ++ T++++ ++ QYG ++ I + YGF
Sbjct: 1 GSSGSS------GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGF 46
Query: 105 VDFESGGYALAAVKALQDK 123
V E A A++ L
Sbjct: 47 VHIEDKTAAEDAIRNLHHY 65
Score = 49.1 bits (118), Expect = 5e-08
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 9/91 (9%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
L+I NLP E ++ SL +Y V+ I+ K GF +E K + I+
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRN 61
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ L G + V+ + + K + G
Sbjct: 62 LHHYKLHG--VNINVEASKNKSKASSGPSSG 90
>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 = 57.2 bits (139), Expect = 6e-11
Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 51 TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG 110
+G + T L++ ++ T+++L +YGP+I + + Y FV E
Sbjct: 3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERA 54
Query: 111 GYALAAVKALQDK---G--IHAQMARQQEQDP 137
A+ A++ L + G +H Q++ + +
Sbjct: 55 EDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA 86
Score = 49.5 bits (119), Expect = 3e-08
Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ T L++ N+ +L + +Y V+ I++ F +E +
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAED 56
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ I+ + + G + + V+ + S L+ + G
Sbjct: 57 AVEAIRGLDNTEFQG--KRMHVQLSTSRLRTASGPSSG 92
>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 = 60.7 bits (146), Expect = 7e-11
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 12/92 (13%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
PE +YI L + +L + SQ+G I+ IL + K RG FV F+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFK 60
Query: 109 SGGYALAAVKALQ-----DKGIHAQMARQQEQ 135
A A++++Q DK + Q A+
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 92
Score = 54.1 bits (129), Expect = 1e-08
Identities = 21/174 (12%), Positives = 53/174 (30%), Gaps = 8/174 (4%)
Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLL----AKYVTVVSTRILRDNNNTSKGVGFAR 184
MA + + +YI NL K+ +L+ L +++ ++ + R +G F
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVI 58
Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGR 244
+ ++ G P+ +++A + G + + +
Sbjct: 59 FKEVSSATNALRSMQGFPFYDK--PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQ 116
Query: 245 DSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHM 298
++ ++ A + P T + Y+ P +
Sbjct: 117 ETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMI 170
Score = 50.6 bits (120), Expect = 2e-07
Identities = 18/138 (13%), Positives = 40/138 (28%), Gaps = 11/138 (7%)
Query: 1 MTMQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN 60
++H + + P E
Sbjct: 150 APRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHI 209
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ L ++T + L + +Q+ + + + FV+F++ A AA AL
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDAL 264
Query: 121 Q------DKGIHAQMARQ 132
Q + + A++
Sbjct: 265 QGFKITQNNAMKISFAKK 282
>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 = 56.8 bits (138), Expect = 8e-11
Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVK 118
++I L + +K L + S +G I+ T K + D T +GY F++F S + AA++
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 119 ALQ-----DKGIHAQMARQQEQDPT 138
A+ ++ I A +++ +
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSKGS 91
Score = 39.9 bits (94), Expect = 8e-05
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 7/97 (7%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRD-NNNTSKGVGFARLESKDKCDQ 193
+ ++I NL E L + + ++ T +I+RD + SKG F S D D
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
I+ NG L P+ V +A KK G+G +
Sbjct: 64 AIEAMNGQYLCNR--PITVSYA---FKKDSKGSGPSS 95
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
GP + +Y+ L D KD+ ++ +YG I I K + FV+FE
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---IDLKNRRGGPPFAFVEFEDPR 72
Query: 112 YALAAVKAL 120
A AV
Sbjct: 73 DAEDAVYGR 81
Score = 50.8 bits (122), Expect = 1e-08
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 4/93 (4%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
+ +Y+ NLP + + D+E + KY + + F E + +
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAV 78
Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+G G + L V+F SG + G
Sbjct: 79 YGRDGYDYDGYR--LRVEFPRSGRGTGSGPSSG 109
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 58.3 bits (141), Expect = 2e-10
Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 3/109 (2%)
Query: 13 TSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTD 72
PA + P + + G G E L + L +D
Sbjct: 45 NRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVET--GAKLLVSNLDFGVSD 102
Query: 73 KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ 121
D+ + +++G + D+ + + G V FE AL A+K +
Sbjct: 103 ADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYK 150
Score = 56.8 bits (137), Expect = 5e-10
Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 2/100 (2%)
Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
K D + + L ++NL + D++ L A++ T+ + D + S
Sbjct: 69 KWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 128
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
G E + + ++ + G L G P+ ++ S
Sbjct: 129 LGTADVHFERRADALKAMKQYKGVPLDGR--PMDIQLVAS 166
>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 = 55.6 bits (134), Expect = 3e-10
Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 16/99 (16%)
Query: 45 GSPGTPTGPEQL--SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ S+ L+IR L + T+ ++I + +G + + K +
Sbjct: 1 GSSGSSGDKMDGAPSRV-LHIRKLPGEVTETEVIALGLPFGKVTNIL------MLKGKNQ 53
Query: 103 GFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
F++ + A+ V I+ Q + +E
Sbjct: 54 AFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92
Score = 44.0 bits (104), Expect = 4e-06
Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 6/93 (6%)
Query: 124 GIHAQMARQQEQDPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
G + + P+ L+I LP E ++ +L + V + +L+ K F
Sbjct: 1 GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAF 55
Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
L +++ M+ ++ T +P+ ++++
Sbjct: 56 LELATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88
>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 = 55.2 bits (133), Expect = 5e-10
Identities = 17/99 (17%), Positives = 33/99 (33%), Gaps = 16/99 (16%)
Query: 45 GSPGTPTGPEQL--SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ ++ S +++RGL + + DL+ ++G I +
Sbjct: 1 GSSGSSGSHHKVSVSPV-VHVRGLCESVVEADLVEALEKFGTICYVM------MMPFKRQ 53
Query: 103 GFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
V+FE+ A V D + +
Sbjct: 54 ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92
Score = 41.3 bits (97), Expect = 3e-05
Identities = 11/87 (12%), Positives = 29/87 (33%), Gaps = 6/87 (6%)
Query: 132 QQEQDPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ + +++ L + E DL L K+ T+ ++ K E+ D
Sbjct: 9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDS 63
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADS 217
+ + + + + ++ S
Sbjct: 64 AKECVTFAADVPVYIAGQQAFFNYSTS 90
>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 = 54.5 bits (132), Expect = 5e-10
Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 18/98 (18%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ +++ ++ T ++L ++ + G +I + + Y F
Sbjct: 1 GSSGSSGNT-----WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAF 47
Query: 105 VDFESGGYALAAVKALQDK---G--IHAQMARQQEQDP 137
V E A AA+ L K G I+ +++ + ++
Sbjct: 48 VHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85
Score = 50.3 bits (121), Expect = 1e-08
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ +++ N+ +L SL + V+ ++ K F +E +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEAD 55
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAG 227
I NG + G + + V+ + G KK G +G
Sbjct: 56 AKAAIAQLNGKEVKG--KRINVELSTKGQKKSGPSSG 90
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 54.4 bits (131), Expect = 6e-10
Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 14/85 (16%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S ++IRGL + DL+ ++GPI + + V+FE A A
Sbjct: 21 SPV-VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNA 73
Query: 117 VKALQDKG-------IHAQMARQQE 134
V D + Q+
Sbjct: 74 VNYAADNQIYIAGHPAFVNYSTSQK 98
Score = 40.9 bits (96), Expect = 4e-05
Identities = 15/100 (15%), Positives = 29/100 (29%), Gaps = 11/100 (11%)
Query: 124 GIHAQMARQQEQDPTN------LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
G H + DP ++I L E DL L ++ + ++
Sbjct: 2 GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----K 56
Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
K E + + + + P V ++ S
Sbjct: 57 KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96
>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 = 54.2 bits (131), Expect = 9e-10
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
NL+I L + + +L S+ ++D T R +G+VDFES A++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKALE 76
Score = 53.4 bits (129), Expect = 2e-09
Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 3/93 (3%)
Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
+ P NL+I NL N +L+ +++ ++ T++ G+ ES +
Sbjct: 11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 70
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
++ ++L G + G+ + ++ RG
Sbjct: 71 LEKALEL-TGLKVFGN--EIKLEKPKGRDGTRG 100
>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 = 53.8 bits (130), Expect = 9e-10
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 7/71 (9%)
Query: 48 GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
G+ SK +++ T+D T ++L QYG + + K R + FV F
Sbjct: 3 GSHHHHHHGSK--VFVGRCTEDMTAEELQQFFCQYGEV--VDVFIPK---PFRAFAFVTF 55
Query: 108 ESGGYALAAVK 118
A +
Sbjct: 56 ADDKVAQSLCG 66
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 53.2 bits (128), Expect = 2e-09
Identities = 14/59 (23%), Positives = 28/59 (47%)
Query: 62 YIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
I K L ++ S+ G +++ + +D+ T K +G+ FV+ S A +K+
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSF 74
Score = 38.9 bits (91), Expect = 2e-04
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 1/77 (1%)
Query: 141 YIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFN 199
I + + + L SL +K VV+ D +KG F S + ++I+ F+
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 200 GSTLPGSKEPLLVKFAD 216
G L L D
Sbjct: 76 GKRLDLKHRLFLYTMKD 92
>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 = 54.5 bits (131), Expect = 2e-09
Identities = 23/105 (21%), Positives = 37/105 (35%), Gaps = 8/105 (7%)
Query: 16 ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
AN + T T +T + H+ + P +Y+ L + +L
Sbjct: 34 ANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCP---LDCKVYVGNLGNNGNKTEL 90
Query: 76 INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
YGP+ S + G+ FV+FE A AV+ L
Sbjct: 91 ERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130
Score = 48.0 bits (114), Expect = 4e-07
Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 6/90 (6%)
Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARL 185
H M R +Y+ NL N + +LE Y + S + R+ G F
Sbjct: 62 HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEF 117
Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
E ++ +G TL G + V+ +
Sbjct: 118 EDPRDAADAVRELDGRTLCG--CRVRVELS 145
>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 = 52.4 bits (126), Expect = 2e-09
Identities = 9/70 (12%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
+ + ++ L QD+ +++ ++ Y + ++ + FV +G A A
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA 56
Query: 117 VKALQDKGIH 126
++
Sbjct: 57 IQMFHQYSFR 66
Score = 47.0 bits (112), Expect = 2e-07
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 8/91 (8%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
+ + + NLP + ++ LL Y + + R +K F L + ++ IQ+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQNAIQM 59
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
F+ + G L+V+ + + G
Sbjct: 60 FHQYSFRGK--DLIVQLQPTDALLCSGPSSG 88
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 52.1 bits (125), Expect = 5e-09
Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 10/94 (10%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
PG+P G ++Y+ L +D DL + G + L T R F+
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFL 61
Query: 106 DFESGGYALAAVKALQD-----KGIHAQMARQQE 134
+ A AV LQ + +ARQQ
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95
Score = 44.4 bits (105), Expect = 2e-06
Identities = 20/96 (20%), Positives = 31/96 (32%), Gaps = 8/96 (8%)
Query: 122 DKGIHAQMARQQEQDP--TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKG 179
G + E P ++Y+ NLP + + DL+ L + +V LR +
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGPRR 57
Query: 180 VGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
F Q + G L L V A
Sbjct: 58 RAFLHYPDSAAAQQAVSCLQGLRLGTD--TLRVALA 91
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 52.3 bits (126), Expect = 5e-09
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 43 HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
+GS G P + T Y+ L +T D+ + I S + + DK T+K +G+
Sbjct: 2 SSGSSGKEL-PTEPPYT-AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGF 58
Query: 103 GFVDFESGGYALAAVK 118
+V+F+ A+
Sbjct: 59 CYVEFDEVDSLKEALT 74
Score = 47.3 bits (113), Expect = 3e-07
Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 5/95 (5%)
Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
+ P Y+ NLP N + D++++ ++ S R++RD + + KG + + D +
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ +G+ L L V A+ + + + G
Sbjct: 72 ALTY-DGALLGDR--SLRVDIAEGRKQDKSGPSSG 103
>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 = 52.0 bits (125), Expect = 7e-09
Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 19/99 (19%)
Query: 44 NGSPGTPTGPEQLSKTN----------LYIRGL-TQDTTDKDLINMCSQYGPIISTKAIL 92
+GS G + + TN ++I L T D+ + S+YG +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH- 61
Query: 93 DKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
+GY FV + + +A AAV + + Q
Sbjct: 62 -------KGYAFVQYSNERHARAAVLGENGRVLAGQTLD 93
Score = 45.4 bits (108), Expect = 1e-06
Identities = 22/109 (20%), Positives = 40/109 (36%), Gaps = 12/109 (11%)
Query: 123 KGIHAQMARQQEQDPTN--LYIANLPLNF-KECDLESLLAKYVTVVSTRILRDNNNTSKG 179
K + + + + N ++I NL K+ D+E++ +KY V + KG
Sbjct: 11 KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKG 63
Query: 180 VGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
F + ++ + NG L G L + A R + G
Sbjct: 64 YAFVQYSNERHARAAVLGENGRVLAGQT--LDINMAGEPKPDRSGPSSG 110
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 51.1 bits (123), Expect = 1e-08
Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 2/92 (2%)
Query: 139 NLYIANLPLNFKECDLESLLAK-YVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
+L++ +L + + L K Y + +++ D SKG GF + + + + +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
G+ GSK P+ + A + GP
Sbjct: 71 CQGAVGLGSK-PVRLSVAIPKASRVKPVESGP 101
Score = 51.1 bits (123), Expect = 1e-08
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+L++ LT D D L + P K +LD+T +GYGFV F A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQT-GVSKGYGFVKFTDELEQKRALT 69
Query: 119 ALQ 121
Q
Sbjct: 70 ECQ 72
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 13/70 (18%), Positives = 23/70 (32%), Gaps = 6/70 (8%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SKT + + L T ++ S++G + + V+F A A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKA 62
Query: 117 VKALQDKGIH 126
+ L H
Sbjct: 63 FRHLAYSKFH 72
>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 = 50.8 bits (122), Expect = 1e-08
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 11/86 (12%)
Query: 42 QHNGSPGTPTGPEQLSKTNLYIRGL-TQDTTDKDLINMCSQYGPIISTKAILDKTTNKCR 100
H+ S P G K+ L+I L ++ + +DL + S YG I+
Sbjct: 8 HHHSSGLVPRGS--HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------N 57
Query: 101 GYGFVDFESGGYALAAVKALQDKGIH 126
+GF+ F++ A++ +
Sbjct: 58 AFGFIQFDNPQSVRDAIEXESQEMNF 83
Score = 40.0 bits (94), Expect = 7e-05
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 10/86 (11%)
Query: 136 DPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
+ L+I NLPL N + DL + + Y ++ I GF + ++
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDA 73
Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLK 220
I+ + G K L+++ + S +
Sbjct: 74 IEXESQEMNFGKK--LILEVSSSNAR 97
>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 = 50.7 bits (122), Expect = 2e-08
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYG 103
GS G+ P+ T ++ L D T++ + I + + + + +G+G
Sbjct: 4 GSSGSRL-PKSPPYT-AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60
Query: 104 FVDFESGGYALAAVK 118
+ +FE L+A+
Sbjct: 61 YAEFEDLDSLLSALS 75
Score = 48.0 bits (115), Expect = 1e-07
Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 6/97 (6%)
Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKC 191
+ P ++ NLP + E ++ + + R+ R+ +N KG G+A E D
Sbjct: 12 KSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSL 70
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
+ L N +L + V AD K + G
Sbjct: 71 LSALSL-NEESLGNK--RIRVDVADQAQDKDSGPSSG 104
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 50.0 bits (120), Expect = 2e-08
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 5/64 (7%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
+Y+ L +L S YGP+ + + G+ FV+FE A AV+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 120 LQDK 123
L K
Sbjct: 57 LDGK 60
Score = 47.3 bits (113), Expect = 3e-07
Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 12/103 (11%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
+Y+ NL + +LE + Y + + I R+ G F E + ++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 199 NGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN------IYRGP 235
+G + GS+ + V+ + ++ ++ GP
Sbjct: 58 DGKVICGSR--VRVELSTGMPRRSRFDRPPARRKLLEVLFNGP 98
>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 = 50.1 bits (120), Expect = 3e-08
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 45 GSPG-TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G + G +K +I + T D++ + +L + G
Sbjct: 1 GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60
Query: 104 FVDFESGGYALAAVKALQ 121
V F++ A K+ +
Sbjct: 61 LVQFKN---EDDARKSER 75
Score = 38.6 bits (90), Expect = 4e-04
Identities = 16/108 (14%), Positives = 35/108 (32%), Gaps = 4/108 (3%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRDNNNTSKGVGFARLESK 188
+I N+P + + D+ L + +L DNN G + +++
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 189 DKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
D + +L + L +E + +++ GP
Sbjct: 68 DDARKSERL-HRKKL-NGREAFVHVVTLEDMREIEKNPPAQG-KSGPS 112
>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 = 49.7 bits (119), Expect = 3e-08
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 4/78 (5%)
Query: 45 GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + + +RGL + ++++ S + + + + G
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 104 FVDFESGGYALAAVKALQ 121
FV F S A KAL+
Sbjct: 61 FVQFAS---QEIAEKALK 75
>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 = 49.2 bits (118), Expect = 4e-08
Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGG 111
P+ T ++ L D T++ + I + + + + +G+G+ +FE
Sbjct: 15 PKSPPYT-AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD 72
Query: 112 YALAAVK 118
L+A+
Sbjct: 73 SLLSALS 79
Score = 45.7 bits (109), Expect = 9e-07
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKC 191
+ P ++ NLP + E ++ + + R+ R+ +N KG G+A E D
Sbjct: 16 KSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSL 74
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
+ L N +L + V AD
Sbjct: 75 LSALSL-NEESLGNR--RIRVDVADQ 97
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 49.0 bits (117), Expect = 6e-08
Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 59 TNLYIRGLTQDTTDK------DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
+ + + + Q D+ + + S++G I + + K +GY F+++ S +
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAH 73
Query: 113 ALAAVKALQDKGI 125
A+ AVK +
Sbjct: 74 AVDAVKNADGYKL 86
Score = 38.6 bits (90), Expect = 3e-04
Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 9/86 (10%)
Query: 138 TNLYIANLPLNFKE------CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
+ + + N+P + + + +K+ + + ++ +KG F S
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGK-TKGYIFLEYASPAHA 74
Query: 192 DQMIQLFNGSTLPGSKEPLLV-KFAD 216
++ +G L + V F D
Sbjct: 75 VDAVKNADGYKLDK-QHTFRVNLFTD 99
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 48.4 bits (116), Expect = 7e-08
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 13/72 (18%)
Query: 58 KTNLYIRGL-TQDTTDKDLINMCSQYGPI--ISTKAILDKTTNKCRGYGFVDFESGGYAL 114
K+ L+I L ++ + +DL + S YG I I+ K +GF+ F++
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----------NAFGFIQFDNPQSVR 59
Query: 115 AAVKALQDKGIH 126
A++ +
Sbjct: 60 DAIECESQEMNF 71
>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 = 49.1 bits (117), Expect = 9e-08
Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 7/84 (8%)
Query: 42 QHNGSPGTPTGPEQLSKTN----LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN 97
SP S +Y++GL + +K +I+ + + + I
Sbjct: 5 SSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG 64
Query: 98 KCRGYGFVDFESGGYALAAVKALQ 121
K G GFV+F + AL
Sbjct: 65 KATGEGFVEFRN---EADYKAALC 85
Score = 36.7 bits (85), Expect = 0.002
Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 1/61 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESK 188
+R + +Y+ LP + + K + S I N + G GF ++
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 189 D 189
Sbjct: 78 A 78
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 11/82 (13%), Positives = 32/82 (39%), Gaps = 6/82 (7%)
Query: 56 LSKTNLYIRGLTQDTTDKDLI---NMCSQYGPIISTKAILDKTTNKCR---GYGFVDFES 109
+ K +++ GL+Q D +++ ++G I + + +V +
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72
Query: 110 GGYALAAVKALQDKGIHAQMAR 131
AL A++ + + + + +
Sbjct: 73 SEDALRAIQCVNNVVVDGRTLK 94
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 47.9 bits (114), Expect = 2e-07
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
S + P + S+ + + GL + +DL + + G + D G G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54
Query: 105 VDFESGGYALAAVKALQDK 123
V+F AV+ L +
Sbjct: 55 VEFVRKEDMTYAVRKLDNT 73
Score = 40.6 bits (95), Expect = 6e-05
Identities = 13/97 (13%), Positives = 32/97 (32%), Gaps = 8/97 (8%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
+ ++ LP + DL+ + + V + RD G G K+ ++ +
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
+ + + + + + G + GP
Sbjct: 72 NTKFRSHE--GETAYIRVKVDGPRSPSYGRSRSSGPS 106
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 47.3 bits (113), Expect = 2e-07
Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 8/67 (11%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
++++ G + L +GP+ ++DK + V+ G A
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVG---AREAV 61
Query: 120 LQDKGIH 126
L
Sbjct: 62 LSQSQHS 68
Score = 27.3 bits (61), Expect = 2.2
Identities = 10/91 (10%), Positives = 28/91 (30%), Gaps = 7/91 (7%)
Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
+++++ P L + V S + +D + + +
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAV 61
Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLKKRGAG 225
+ + +L G + L V+ + + A
Sbjct: 62 LSQ-SQHSLGGHR--LRVRPREQKEFQSPAS 89
>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 = 46.4 bits (111), Expect = 3e-07
Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 10/91 (10%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
G S +++ T D T+ +L SQYG + + R + FV F
Sbjct: 1 GSSGSSG--VFVGRCTGDMTEDELREFFSQYGDV--MDVFI---PKPFRAFAFVTFADDQ 53
Query: 112 YALAAVKA---LQDKGIHAQMARQQEQDPTN 139
A + ++ +H A + +
Sbjct: 54 IAQSLCGEDLIIKGISVHISNAEPKHNSNSG 84
>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 = 47.2 bits (112), Expect = 4e-07
Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 2/87 (2%)
Query: 32 GTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
G+H + Q G + +RGL T ++++ S + + +
Sbjct: 18 GSHMASMTGGQQMGRGSNSADSANDGF--VRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75
Query: 92 LDKTTNKCRGYGFVDFESGGYALAAVK 118
K G FV F S A A+
Sbjct: 76 PVDPEGKITGEAFVQFASQELAEKALG 102
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 46.4 bits (110), Expect = 7e-07
Identities = 14/97 (14%), Positives = 35/97 (36%), Gaps = 8/97 (8%)
Query: 27 GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
GS + H + + + P + + ++ L + + +DL ++ +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMSKLPA-----KRYRITMKNLPEGCSWQDLKDLARENSLET 56
Query: 87 STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK 123
+ T G G ++F S + A++ L +
Sbjct: 57 T---FSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90
Score = 41.7 bits (98), Expect = 3e-05
Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 4/85 (4%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
+ + NLP DL+ L + + N G G S++ + ++ N
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETT--FSSVNTRDFDGTGALEFPSEEILVEALERLN 88
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGA 224
GS + V+ D+ R +
Sbjct: 89 NIEFRGSV--ITVERDDNPPPIRRS 111
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 45.1 bits (107), Expect = 8e-07
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 61 LYIRGLTQDTTDK------DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
+ + + Q D+ + + S++G I + + K +GY F+++ S +A+
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 115 AAVKAL 120
AVK
Sbjct: 62 DAVKNA 67
Score = 32.4 bits (74), Expect = 0.026
Identities = 10/79 (12%), Positives = 27/79 (34%), Gaps = 8/79 (10%)
Query: 140 LYIANLPLNFKE------CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQ 193
+ + N+P + + + +K+ + + ++ +KG F S
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGK-TKGYIFLEYASPAHAVD 62
Query: 194 MIQLFNGSTLPGSKEPLLV 212
++ +G L + V
Sbjct: 63 AVKNADGYKL-DKQHTFRV 80
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 46.0 bits (109), Expect = 8e-07
Identities = 20/99 (20%), Positives = 32/99 (32%), Gaps = 13/99 (13%)
Query: 45 GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
G+P GP N + + GL + +DL + + G + D G G
Sbjct: 2 GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 54
Query: 104 FVDFESGGYALAAVKALQDK-----GIHAQMARQQEQDP 137
V+F AV+ L + R + P
Sbjct: 55 VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP 93
Score = 43.3 bits (102), Expect = 9e-06
Identities = 11/97 (11%), Positives = 28/97 (28%), Gaps = 6/97 (6%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
+ ++ LP + DL+ + + V + RD G G K+ ++ +
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
+ + + + + R
Sbjct: 73 NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRS 109
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 45.2 bits (106), Expect = 5e-06
Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 3/97 (3%)
Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARL 185
+ + ++YI P + D++ L V++ ++ R + KG F
Sbjct: 98 EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 157
Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
+S + + ++ G LL+ F D K+
Sbjct: 158 DSIESAKKFVETP-GQKYKE--TDLLILFKDDYFAKK 191
Score = 45.2 bits (106), Expect = 5e-06
Identities = 17/101 (16%), Positives = 32/101 (31%), Gaps = 1/101 (0%)
Query: 23 SSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY 82
S + + T + ++YI+G D T D+
Sbjct: 74 SKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK 133
Query: 83 GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK 123
G +++ + + +G FV F+S A V+ K
Sbjct: 134 GQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK 173
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 43.7 bits (103), Expect = 6e-06
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 12/88 (13%)
Query: 43 HNGSPGTPTGPE---QLSKTN---LYIRGLTQDTTDKDLINMCSQYGPIISTKA---ILD 93
+GS G T E LSK N + +RGL T ++++ Q+ PI K +
Sbjct: 2 SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61
Query: 94 KTTNKCRGYGFVDFESGGYALAAVKALQ 121
+ G FV F A AL+
Sbjct: 62 YPDGRPTGDAFVLFAC---EEYAQNALR 86
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 43.4 bits (102), Expect = 7e-06
Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 7/93 (7%)
Query: 35 PITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILD 93
++ + G P +Q +++ L +D ++ + YG I +
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI---- 57
Query: 94 KTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
+ + F++ E+ A+A V K +
Sbjct: 58 --LMRMKSQAFIEMETREDAMAMVDHCLKKALW 88
>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 = 42.8 bits (101), Expect = 8e-06
Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLIN-----MCSQYGPIISTKAILDKTTNKCRGYGFVD 106
GP ++ LY+ + T++ +++ M +L N+ + + F++
Sbjct: 1 GPLGSARR-LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59
Query: 107 FESGGYALAAVK 118
F S A+
Sbjct: 60 FRSVDETTQAMA 71
Score = 34.7 bits (80), Expect = 0.005
Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 7/72 (9%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTR------ILRDNNNTSKGVGFARLESKDKCDQ 193
LY+ N+P E + + + +L N K F S D+ Q
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 194 MIQLFNGSTLPG 205
+ +G G
Sbjct: 69 AMAF-DGIIFQG 79
>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 = 43.3 bits (102), Expect = 1e-05
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS + + + +++RGL T+ D+ N S P+ I + G
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGPDGRVTGEA 89
Query: 104 FVDFESGGYALAAVKALQ 121
V+F + AV A+
Sbjct: 90 DVEFAT---HEEAVAAMS 104
>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 = 42.4 bits (100), Expect = 1e-05
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 45 GSPGTPTGPEQLSKTN--LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ +G S T +++RGL T+ D+ N S P+ I + G
Sbjct: 1 GSSGS-SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGE 57
Query: 103 GFVDFESGGYALAAVK 118
V+F + A+AA+
Sbjct: 58 ADVEFATHEDAVAAMA 73
Score = 36.6 bits (85), Expect = 0.001
Identities = 7/60 (11%), Positives = 18/60 (30%), Gaps = 1/60 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKD 189
+ Q +++ LP E D+ + + + I + G + +
Sbjct: 8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHE 66
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 42.6 bits (100), Expect = 1e-05
Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 65 GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG 124
GL + L+ + + G + + +K Y F + + + A L K
Sbjct: 34 GLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKE 87
Query: 125 I 125
+
Sbjct: 88 V 88
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 45 GSPGTPTGPEQLSKTN--LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ P ++ + + + G+ + D+ + + +L + G
Sbjct: 1 GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR--VDAVHLLKDHVGRNNGN 58
Query: 103 GFVDFESGGYALAAVK 118
G V F S A+K
Sbjct: 59 GLVKFLSPQDTFEALK 74
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 40.7 bits (95), Expect = 7e-05
Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 51 TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC--RGYGFVDFE 108
+G K +++ GL D + ++ ++GP++ ++ + +GY F+ F+
Sbjct: 3 SGSSGSRK--VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 109 SGGYALAAVKALQDKGIHAQ 128
++V+AL D +
Sbjct: 61 EE----SSVQALIDACLEED 76
>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 = 40.3 bits (94), Expect = 9e-05
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 6/99 (6%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI--LDKTTNKCRG 101
+GS G GPE + +RGL + +D+ N S + + + G
Sbjct: 3 SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62
Query: 102 YGFVDFESGGYALAAV----KALQDKGIHAQMARQQEQD 136
FV+ ES A+ +++ + I + + E D
Sbjct: 63 EAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMD 101
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 39.2 bits (92), Expect = 1e-04
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
+G + + +RG + T+K+++ + P+ I+ GY FVDF +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGNKTGYIFVDFSN 59
Query: 110 GGYALAAVKALQ 121
+AL+
Sbjct: 60 ---EEEVKQALK 68
>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 = 39.5 bits (92), Expect = 2e-04
Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 2/73 (2%)
Query: 48 GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI--LDKTTNKCRGYGFV 105
G+ E + +GL T +D++N S I L K RG +
Sbjct: 1 GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
Query: 106 DFESGGYALAAVK 118
+ ES A++
Sbjct: 61 EMESEQDVQKALE 73
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 38.9 bits (90), Expect = 3e-04
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 7/95 (7%)
Query: 32 GTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
G+ + + G+ P+G ++ L I+ T L +C+ G +
Sbjct: 1 GSSGSSGKRITRPGNTDDPSGGNKV--LLLSIQNPLYPITVDVLYTVCNPVGKVQRIV-- 56
Query: 92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
+ V+FES A A AL I+
Sbjct: 57 ---IFKRNGIQAMVEFESVLCAQKAKAALNGADIY 88
>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 = 39.3 bits (91), Expect = 4e-04
Identities = 17/124 (13%), Positives = 36/124 (29%), Gaps = 14/124 (11%)
Query: 3 MQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLY 62
M +H +A + +S S + + SP +
Sbjct: 1 MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSP----------VLRII 50
Query: 63 IRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD 122
+ L T L + S++G ++ T + + + A A +L
Sbjct: 51 VENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSLDG 106
Query: 123 KGIH 126
+ I+
Sbjct: 107 QNIY 110
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 40.2 bits (93), Expect = 4e-04
Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 15/91 (16%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDK---------DLINMCSQYGPIISTKAILDKTTNKCR 100
G + LY+ G+ K + + S+ G I + + K
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------ 179
Query: 101 GYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
GFV F+ A A +A+ ++ + +
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDK 210
>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 = 38.4 bits (89), Expect = 5e-04
Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 2/105 (1%)
Query: 16 ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
++H ++G G+H + Q G GPE + +RGL + +D+
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDV 61
Query: 76 INMCSQYGPIISTKAI--LDKTTNKCRGYGFVDFESGGYALAAVK 118
N S + + + G FV+ S A+K
Sbjct: 62 QNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.0 bits (93), Expect = 8e-04
Identities = 38/255 (14%), Positives = 74/255 (29%), Gaps = 70/255 (27%)
Query: 54 EQLSKTNLYIR--GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
E + L + G + + Q+ ++ L +FE+
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEP---SKVGQFDQVL--NLCLT------------EFENC- 94
Query: 112 YALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
Y L+ IHA A+ +++ T L E + + +
Sbjct: 95 Y-------LEGNDIHALAAKLLQENDTTL----------VKTKELIKNYITARIMAKRPF 137
Query: 172 DNNNTSKGVGFARLES-KDKCDQMIQLFNG---------------STLPGSKEPLLVKFA 215
D + S A + + Q++ +F G T L+KF+
Sbjct: 138 DKKSNS-----ALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGD-LIKFS 191
Query: 216 DSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSAD----SQLAYEHPMT-PIPATIQYQRFT 270
L + G + W + ++ L P++ P+ IQ +
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSI-PISCPLIGVIQLAHYV 250
Query: 271 AGPGGTGHIPAGYTP 285
T + G+TP
Sbjct: 251 V----TAKL-LGFTP 260
Score = 34.6 bits (79), Expect = 0.049
Identities = 52/271 (19%), Positives = 84/271 (30%), Gaps = 108/271 (39%)
Query: 48 GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI---LDKTTNKCR---- 100
G P+ P LS I LTQ+ +N + + P + K + L N +
Sbjct: 333 GVPS-P-MLS-----ISNLTQEQVQD-YVNKTNSHLP--AGKQVEISL---VNGAKNLVV 379
Query: 101 -G-----YGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLN--FKEC 152
G YG L KA +++ +N + LP+ F
Sbjct: 380 SGPPQSLYGLN------LTLRKAKAPSGLDQSRIPFSERKLKFSNRF---LPVASPFH-- 428
Query: 153 DLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF---NGSTLPGSKEP 209
LL +++ ++++N V F + D I ++ +GS L
Sbjct: 429 --SHLLVPASDLINKDLVKNN------VSF------NAKDIQIPVYDTFDGSDLRVLSGS 474
Query: 210 LLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPAT--IQYQ 267
+ + D I R P V+ W ++ T AT + +
Sbjct: 475 ISERIVDC-------------IIRLP---VK-W--ETT----------TQFKATHILDF- 504
Query: 268 RFTAGPG--------------GTGH--IPAG 282
GPG GTG I AG
Sbjct: 505 ----GPGGASGLGVLTHRNKDGTGVRVIVAG 531
Score = 30.0 bits (67), Expect = 1.2
Identities = 28/157 (17%), Positives = 42/157 (26%), Gaps = 67/157 (42%)
Query: 1 MTMQLYHRVSNATSP--------ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPT- 51
M M LY TS A+ H G + + V +N P T
Sbjct: 1631 MGMDLY-----KTSKAAQDVWNRADNH------FKDTYGFS---ILDIVINN--PVNLTI 1674
Query: 52 ---GPEQLSKTNLYIRGLTQDTTD---------KDLINMCSQY---GPIISTKAILDKTT 96
G + Y + + D K++ + Y K +L T
Sbjct: 1675 HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSE----KGLLSATQ 1730
Query: 97 N---KCRGYGFVDFESGGYAL-----AAVKALQDKGI 125
AL AA + L+ KG+
Sbjct: 1731 FTQP---------------ALTLMEKAAFEDLKSKGL 1752
>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 = 37.2 bits (86), Expect = 0.001
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 77 NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ 121
M +YG + + D + G +V F A AV L
Sbjct: 46 EMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89
Score = 30.6 bits (69), Expect = 0.18
Identities = 7/53 (13%), Positives = 18/53 (33%)
Query: 148 NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG 200
F E + KY V + + + G + + ++ ++ + N
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90
>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 = 37.9 bits (87), Expect = 0.004
Identities = 35/286 (12%), Positives = 77/286 (26%), Gaps = 110/286 (38%)
Query: 1 MTMQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN 60
M +L +++ + S SSN + +++Q +L K+
Sbjct: 201 MLQKLLYQI---DPNWTSRSDHSSNI--------KLRIHSIQAE--------LRRLLKSK 241
Query: 61 LYIRGLTQDTTDKDLI--NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
Y L L+ N+ + + C K
Sbjct: 242 PYENCL--------LVLLNVQN--------AKAWNAFNLSC------------------K 267
Query: 119 AL---QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVT------------ 163
L + K + ++ T++ + + + +++SLL KY+
Sbjct: 268 ILLTTRFKQVTDFLSAATT---THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324
Query: 164 ----VVST--RILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA-- 215
+S +RD T + + DK +I+ P + + +
Sbjct: 325 TNPRRLSIIAESIRDGLATWD---NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381
Query: 216 --DSGLKKRGAGAGGPNIYRGPGAEV--RLWGRDSADSQLAYEHPM 257
+ +I P + +W + M
Sbjct: 382 PPSA------------HI---P-TILLSLIWF------DVIKSDVM 405
>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 = 34.8 bits (80), Expect = 0.005
Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 10/82 (12%)
Query: 45 GSPGTPT--GPEQLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
GS G+ G + + ++I + L+ + +G I + +
Sbjct: 1 GSSGSSGQKGRVETRRV-VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKIN 53
Query: 102 YGFVDFESGGYALAAVKALQDK 123
F++ + A AAV
Sbjct: 54 EAFIEMATTEDAQAAVDYYTTT 75
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.4 bits (81), Expect = 0.006
Identities = 14/101 (13%), Positives = 29/101 (28%), Gaps = 8/101 (7%)
Query: 29 QNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIIST 88
Q+G + G P + + L T L + S++G ++
Sbjct: 3 QSGNLALAASAAAVDAGMAMAGQSP----VLRIIVENLFYPVTLDVLHQIFSKFGTVLKI 58
Query: 89 KAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM 129
T + + + A A +L + I+
Sbjct: 59 I----TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC 95
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 32.3 bits (73), Expect = 0.034
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L ++ LT L +C Q+GP++S +G + + A A AL
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFH------PYLNQGIALCKYTTREEANKAQMAL 63
Query: 121 QDK-----GIHAQMARQQE 134
+ I A+ + E
Sbjct: 64 NNCVLANTTIFAESPSENE 82
>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 = 32.5 bits (74), Expect = 0.039
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 74 DLINMCSQYGPIISTK--AILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
D+ + CS+YG + S + +D G FV+F S A++ L
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 79
>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 = 33.0 bits (74), Expect = 0.056
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 237 AEVRLWGRDSADSQLAYEHPMTPIPATIQ 265
A ++L+ DSA P I AT++
Sbjct: 27 ASLKLYADDSA--------PALAIKATME 47
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 30.4 bits (69), Expect = 0.21
Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 16/89 (17%)
Query: 45 GSPGTPTGPEQLSKT------NLYIRG--LTQDTTDKDLINM----CSQYGPIISTKAIL 92
GS G+ GP ++ N++ ++ CS++G I +
Sbjct: 1 GSSGSSGGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLL-LF 59
Query: 93 DKTTNKCRGYGFVDFESGGYALAAVKALQ 121
D+ + G V F A ++ L
Sbjct: 60 DRHPD---GVASVSFRDPEEADYCIQTLD 85
>2f8l_A Hypothetical protein LMO1582; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE SAM; 2.20A {Listeria monocytogenes}
SCOP: c.66.1.45
Length = 344
Score = 31.6 bits (72), Expect = 0.25
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 10/85 (11%)
Query: 91 ILDKTTNKCRGYGFVDFE--SGGYALAAVKALQDKGIHAQMARQQEQDPT-------NLY 141
+L+K K + +D + + L+ KG A + D
Sbjct: 121 LLEKVIQKKKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALVGAD 180
Query: 142 IANLPLNFKECD-LESLLAKYVTVV 165
+ + D L +LL V VV
Sbjct: 181 LQRQKMTLLHQDGLANLLVDPVDVV 205
>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 = 29.2 bits (65), Expect = 0.52
Identities = 15/90 (16%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 136 DPTNLYIANLPLNFKECDLESLL----AKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
+ ++ ++N+ +L+ LL A++ V S + + K ++E+
Sbjct: 8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLK--AVVQMENLQDA 65
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKK 221
+ + + GSK +LV A
Sbjct: 66 IGAVNSLHRYKI-GSK-KILVSLATGASGP 93
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 28.8 bits (65), Expect = 0.78
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 79 CSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
C+++G +I +DK N +G +V S A+AAV AL
Sbjct: 38 CNKHGGVIHIY--VDK--NSAQGNVYVKCPSIAAAIAAVNAL 75
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 27.8 bits (62), Expect = 1.9
Identities = 8/51 (15%), Positives = 16/51 (31%), Gaps = 4/51 (7%)
Query: 74 DLINMCSQYGPIISTK--AILDKTTNKCRGYG--FVDFESGGYALAAVKAL 120
++ C ++G + FV+F A++AL
Sbjct: 41 EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
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
0.313 0.131 0.389
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,485,599
Number of extensions: 260745
Number of successful extensions: 1026
Number of sequences better than 10.0: 1
Number of HSP's gapped: 772
Number of HSP's successfully gapped: 337
Length of query: 305
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 212
Effective length of database: 4,105,140
Effective search space: 870289680
Effective search space used: 870289680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)