RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6353
(136 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 = 137 bits (347), Expect = 1e-42
Identities = 70/86 (81%), Positives = 74/86 (86%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
T QSLGYGFVNY P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK
Sbjct: 39 ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPK 98
Query: 91 HMSQQELESLFSPYGRIITSRILCDN 116
M+Q+ELE LFS YGRIITSRIL D
Sbjct: 99 TMTQKELEQLFSQYGRIITSRILVDQ 124
Score = 49.1 bits (118), Expect = 2e-08
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYA 71
T S G GF+ + + +AE+AI LNG + I V +A
Sbjct: 126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 45.6 bits (109), Expect = 4e-07
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP++M+Q+E SLF G I + +++ D
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRD 37
>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 = 133 bits (338), Expect = 3e-41
Identities = 40/92 (43%), Positives = 59/92 (64%), Gaps = 3/92 (3%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T S GY FV++ D+++AI LNG+ ++NK +KVSYARP ESIK NLYV+ LP+
Sbjct: 41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 100
Query: 92 MSQQELESLFSPYGRIITSRILCDNLATENGK 123
++ +L+++F YG I+ IL D G+
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDK---LTGR 129
Score = 49.1 bits (118), Expect = 2e-08
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYA 71
T + G FV Y++ E+A++AI+ LN + + ++ + V A
Sbjct: 127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 45.6 bits (109), Expect = 3e-07
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ M+ +EL +LF G I T RI+ D
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD 38
>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 = 117 bits (296), Expect = 2e-34
Identities = 27/86 (31%), Positives = 54/86 (62%), Gaps = 2/86 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGANLYVSGLP 89
T +SLGY +VN+ +P DAE+A++T+N ++ K +++ +++ PS N+++ L
Sbjct: 53 TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLD 112
Query: 90 KHMSQQELESLFSPYGRIITSRILCD 115
K + + L FS +G I++ +++CD
Sbjct: 113 KSIDNKALYDTFSAFGNILSCKVVCD 138
Score = 71.9 bits (177), Expect = 1e-16
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
S GYGFV++ E AE+AI +NG+ L ++ + V + E + A L K
Sbjct: 139 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE--REAEL--GARAKE 194
Query: 92 MSQQELESLFSPYGRIIT 109
++ GRI+T
Sbjct: 195 FYPYDVPDYAGSSGRIVT 212
Score = 48.4 bits (116), Expect = 6e-08
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ PS+ S A+LYV L +++ L FSP G I++ R+ D
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD 50
>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 = 116 bits (292), Expect = 3e-34
Identities = 19/87 (21%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS----ESIKGANLYVSGLP 89
QS G FV ++ + A +A N L+ +++ +P+ +++ L++ +
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 104
Query: 90 KHMSQQELESLFSPYGRIITSRILCDN 116
K ++ ++ +FS +G+I RIL
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRILRGP 131
Score = 49.5 bits (119), Expect = 1e-08
Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 3/44 (6%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG---LRLQNKTIKVSYA 71
S G FV + A+ AI ++ + + + V +A
Sbjct: 131 PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 47.2 bits (113), Expect = 1e-07
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V +P+ S+++L LF YG + +L D
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38
>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 = 104 bits (262), Expect = 9e-30
Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 5/94 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK--GANLYVSGLP 89
+++ Y FV YH+ DA A+ TLNG +++N +K+++A S +S NL+V L
Sbjct: 37 NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLN 96
Query: 90 KHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
++ + L + F + ++ ++ D + G
Sbjct: 97 VNVDDETLRNAFKDFPSYLSGHVMWD---MQTGS 127
Score = 56.0 bits (136), Expect = 5e-11
Identities = 13/40 (32%), Positives = 27/40 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T S GYGFV++ +DA+ A++++ G L + +++++A
Sbjct: 125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 31.7 bits (73), Expect = 0.034
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LYV L K +++ L+ F G I +I+ D
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID 35
>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 = 106 bits (266), Expect = 2e-29
Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQ 94
G+GF+ AE A L+G L+++ +++ +A GA L V L +S
Sbjct: 57 DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH------GAALTVKNLSPVVSN 110
Query: 95 QELESLFSPYGRIITSRILCDNLATENGK 123
+ LE FS +G + + ++ D + G+
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVD----DRGR 135
Score = 49.7 bits (119), Expect = 3e-08
Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 4/80 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYARPSSESIKGANLYVSG 87
++ G GFV + A KA+ L + + V + +
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK 192
Query: 88 LPKHMSQQELESLFSPYGRI 107
++ ++E F+ G
Sbjct: 193 TQQYHKEREQPPRFAQPGTF 212
Score = 44.3 bits (105), Expect = 2e-06
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 63 NKTIKV-SYARPSSESIKG-ANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
TI + S+ +P ++ L+V LP +++++ + LF YG I
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI 54
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 104 bits (261), Expect = 2e-28
Identities = 27/104 (25%), Positives = 42/104 (40%), Gaps = 11/104 (10%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
SD E+ + G FV E AE AIN + RL+ + + V
Sbjct: 43 LSDYELKY--CFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD----- 95
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
A L V+ LP ++QQ+ E L P+G + ++ G+
Sbjct: 96 -ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE---RTGQ 135
Score = 102 bits (257), Expect = 8e-28
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 8/96 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA---RPSSESIKGANLYVSGL 88
T QS GYGF Y + + A +A + L G L +T+ V + + + + L V L
Sbjct: 133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRL 192
Query: 89 PKHMSQQE-LESLFSPYGRIITSRILCDNLATENGK 123
P + + L S ++ C ++G+
Sbjct: 193 PPGFNDVDALCRALSAVHSPTFCQLACG----QDGQ 224
Score = 59.2 bits (144), Expect = 1e-11
Identities = 13/63 (20%), Positives = 25/63 (39%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
Q G+ + Y E AE+A +GL L ++VS+ P ++
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281
Query: 92 MSQ 94
+++
Sbjct: 282 LNR 284
Score = 46.9 bits (112), Expect = 3e-07
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 61 LQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG----RIITSR 111
L + I+ + + + GLP ++ QE+ L S Y + +
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYK 57
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 90.8 bits (226), Expect = 7e-24
Identities = 24/103 (23%), Positives = 47/103 (45%), Gaps = 14/103 (13%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-----------SIKG 80
T + G+ FV Y PE A+ A+ +N + L + IKV + +
Sbjct: 66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+YV+ + + +S +++S+F +G+I ++ + D GK
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP---TTGK 165
Score = 58.5 bits (142), Expect = 1e-11
Identities = 11/42 (26%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T + GYGF+ Y + + ++ A++++N L + ++V A
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
Score = 41.1 bits (97), Expect = 2e-05
Identities = 8/45 (17%), Positives = 19/45 (42%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
A+ + +YV + + + + F+P+G I + + D
Sbjct: 19 AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWD 63
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 88.1 bits (219), Expect = 2e-22
Identities = 17/102 (16%), Positives = 35/102 (34%), Gaps = 8/102 (7%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-------SIKGANLY 84
S + +++ EDA + LNGL+++ T+ + P + +++G +
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM 214
Query: 85 VSGLPKHMSQ-QELESLFSPYGRIITSRILCDNLATENGKYY 125
+ L + L F +G I I
Sbjct: 215 IRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC 256
Score = 79.3 bits (196), Expect = 6e-19
Identities = 19/113 (16%), Positives = 37/113 (32%), Gaps = 11/113 (9%)
Query: 7 LNKLFTYEKVHLGFSDA-EI--CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
L K + KV+ F I S ++ + + + R + A AI + +
Sbjct: 49 LPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQ 107
Query: 64 KTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
I V + L+++ P +Q+ + L + S L
Sbjct: 108 NEIIV-------SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL 153
Score = 59.6 bits (145), Expect = 1e-11
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYARPSSESIKGANLYVSGLPKHM 92
S+ YG +H D+++ ++ + +K + R + + V LPK
Sbjct: 1 SMEYG---HHARPDSKRPLDEGSPAAAGLTSKKANEALTRNR----ELTTVLVKNLPKSY 53
Query: 93 SQQELESLFSPYGRIITSRILCDN 116
+Q ++ F G II +
Sbjct: 54 NQNKVYKYFKHCGPIIHVDVADSL 77
Score = 50.4 bits (121), Expect = 2e-08
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ + F+ + + AE+A+ +N L N+ I VS A
Sbjct: 249 EHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADK 290
>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 = 84.0 bits (208), Expect = 5e-22
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE------SIKGANLYV 85
T QS GYGFV + A++AI LNG + NK +KV+ A + ++ N Y+
Sbjct: 80 TRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 61.7 bits (150), Expect = 2e-13
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 41 VNYHRPEDAEKAINTLNGL-RLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELES 99
+ D L L + Q + I + P + NL V+ +P + + +L
Sbjct: 4 IPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDV--LRNLMVNYIPTTVDEVQLRQ 61
Query: 100 LFSPYGRIITSRILCD 115
LF YG I + +I+CD
Sbjct: 62 LFERYGPIESVKIVCD 77
>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 = 85.0 bits (211), Expect = 5e-22
Identities = 14/92 (15%), Positives = 41/92 (44%), Gaps = 4/92 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
Q + F+ + ++ +A+ +G+ Q +++K+ L++ GLP +
Sbjct: 47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNY 105
Query: 92 MSQQELESLFSPYGRIITSRILCDNLATENGK 123
++ +++ L + +G + ++ D+ G
Sbjct: 106 LNDDQVKELLTSFGPLKAFNLVKDS---ATGL 134
Score = 57.6 bits (140), Expect = 1e-11
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T S GY F Y ++AI LNG++L +K + V A
Sbjct: 132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 30.3 bits (69), Expect = 0.14
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV +P ++++ + F+ R+
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRL 31
>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 = 81.9 bits (203), Expect = 7e-21
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA--RPSSESIKGANLYVSGLP 89
T + +G+V++ ED EKA+ L GL++ IK+ R S + L L
Sbjct: 50 TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLS 108
Query: 90 KHMSQQELESLFSPYGRIITSR 111
++++ EL+ +F I
Sbjct: 109 FNITEDELKEVFEDALEIRLVS 130
Score = 55.7 bits (135), Expect = 7e-11
Identities = 8/42 (19%), Positives = 18/42 (42%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+S G ++ + DAEK + G + +++ + Y
Sbjct: 132 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 43.7 bits (104), Expect = 2e-06
Identities = 11/48 (22%), Positives = 18/48 (37%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
S+ SES NL++ L + S EL+ S ++
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR 49
>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 = 75.0 bits (185), Expect = 7e-19
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 61 LQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
L+ ++ A+ + NLY+S LP M +QELE++ P+G++I++RIL D+
Sbjct: 8 LKASGVQAQMAKQQEQ--DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61
Score = 56.5 bits (137), Expect = 1e-11
Identities = 11/43 (25%), Positives = 15/43 (34%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
S+ S G GF E E I NG ++ + P
Sbjct: 61 SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 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 = 69.3 bits (170), Expect = 2e-16
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
T S +GFV+Y P A+ AI ++NG ++ K +KV R ++S G
Sbjct: 63 TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111
Score = 58.5 bits (142), Expect = 2e-12
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 54 NTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+ +GL Q+ + A E +GANL++ LP+ Q+L +F P+G ++++++
Sbjct: 3 SGSSGLTQQS----IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVF 58
Query: 114 CD 115
D
Sbjct: 59 ID 60
>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 = 70.3 bits (173), Expect = 2e-16
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T +S G+GF+++ +P ++ + T + L K I A P E K ++V G+
Sbjct: 41 TGRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPD 98
Query: 92 MSQQELESLFSPYGRIITSRILCD 115
+ +E E FS +G II ++++ D
Sbjct: 99 VRPKEFEEFFSQWGTIIDAQLMLD 122
Score = 36.4 bits (85), Expect = 0.001
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T QS G+GFV Y + ++ + +++ I++ A P
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEP 165
Score = 32.1 bits (74), Expect = 0.028
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ +++ GL ++ L F YG + +I+ D
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKD 38
>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 = 67.7 bits (166), Expect = 6e-16
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE--------SIKGANL 83
S GYGFV++ E AE+AI +NG+ L ++ + V + E + + N+
Sbjct: 41 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100
Query: 84 YVSGLPKHMSQQE 96
Y+ ++
Sbjct: 101 YIKNFGPGSTRAA 113
Score = 44.5 bits (106), Expect = 5e-07
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N+++ L K + + L FS +G I++ +++CD
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 40
>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 = 69.7 bits (171), Expect = 7e-16
Identities = 14/112 (12%), Positives = 42/112 (37%), Gaps = 24/112 (21%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP------------------ 73
Q + F+ + ++ +A+ +G+ Q +++K+
Sbjct: 47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGV 105
Query: 74 --SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ L++ GLP +++ +++ L + +G + ++ D+ G
Sbjct: 106 VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGL 154
Score = 60.0 bits (146), Expect = 3e-12
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T S GY F Y ++AI LNG++L +K + V A +++
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 30.8 bits (70), Expect = 0.088
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV +P ++++ + F+ R+
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRL 31
>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 = 66.1 bits (162), Expect = 2e-15
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
T Q GYGFV + EDA+ AI ++ ++L K I+V+ A ++++ G
Sbjct: 53 TGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 38.8 bits (91), Expect = 5e-05
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ P SE + A +YV GL + +S+ L LF G ++ + + D
Sbjct: 6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD 50
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 65.9 bits (161), Expect = 3e-15
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T+ S +GFV++ P+ A+ AI +NG ++ K +KV +
Sbjct: 78 TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 57.8 bits (140), Expect = 5e-12
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI---KGANLYVSGLPKHMSQ 94
G + + + L+ L + + + A + + I +G NL++ LP+ +
Sbjct: 2 AGLPQFG-------SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTD 54
Query: 95 QELESLFSPYGRIITSRILCD 115
+L S F P+G +I++++ D
Sbjct: 55 TDLASTFLPFGNVISAKVFID 75
>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 = 64.9 bits (159), Expect = 5e-15
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T QS G+ F+++HR EDA +AI ++G + + V +A+PS+ S
Sbjct: 53 TGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 45.3 bits (108), Expect = 2e-07
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
P+ + A + V+ L + + +L+ LF P+G I + D
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD 50
>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 = 63.4 bits (155), Expect = 2e-14
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGA 81
Y FV ++ DA A+ +NG ++ K +KV++A S G
Sbjct: 56 PYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100
Score = 36.1 bits (84), Expect = 5e-04
Identities = 8/43 (18%), Positives = 20/43 (46%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ + LYV L + +++ + LFS G + +++ +
Sbjct: 8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE 50
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 61.7 bits (150), Expect = 8e-14
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
++T V Y + A +A++ LNG +L+N T+KV+Y +
Sbjct: 45 CEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAA 95
Score = 43.6 bits (103), Expect = 7e-07
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ L + +P H+ + L+SL YG + + +
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT 50
>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 = 61.4 bits (150), Expect = 9e-14
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S GYGFV++ DAE AI + G L + I+ ++A
Sbjct: 44 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85
Score = 36.4 bits (85), Expect = 4e-04
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+++V L ++ + + F+P+GRI +R++ D
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKD 41
>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 = 61.5 bits (150), Expect = 1e-13
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
S + L+V L K S++++ LF P+G I +L
Sbjct: 9 ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP 51
Score = 50.7 bits (122), Expect = 2e-09
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 7 LNKLFTYEKVHLGFSD----AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG---L 59
LNK + E V F E V S G FV + +A+ AI+ L+G +
Sbjct: 23 LNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTM 82
Query: 60 RLQNKTIKVSYARPSSES 77
+ ++ V +A ES
Sbjct: 83 PGASSSLVVKFADTDKES 100
>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 = 60.8 bits (148), Expect = 2e-13
Identities = 10/47 (21%), Positives = 24/47 (51%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + L++ +P+++ +++L+ LF +G+I +L D
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD 48
Score = 49.2 bits (118), Expect = 6e-09
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG---LRLQNKTIKVSYARPSSE 76
T G F+ Y E A KA + L+ L N+ I+V A S
Sbjct: 51 TGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 60.5 bits (147), Expect = 3e-13
Identities = 11/57 (19%), Positives = 21/57 (36%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGL 88
T + LG V + A++ + L+ + I + +K L V+G
Sbjct: 44 TRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGS 100
Score = 40.1 bits (94), Expect = 2e-05
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ + L ++ + L+ + YG + IL
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLH 41
>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 = 62.3 bits (152), Expect = 4e-13
Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 7/90 (7%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN------LYV 85
T +S G+GFV Y E+ + A+N ++ + ++ A +S + ++V
Sbjct: 51 TKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 109
Query: 86 SGLPKHMSQQELESLFSPYGRIITSRILCD 115
G+ + + L F YG+I I+ D
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 139
Score = 34.6 bits (80), Expect = 0.004
Identities = 10/48 (20%), Positives = 21/48 (43%)
Query: 68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+S + E + L++ GL + + L S F +G + ++ D
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD 48
Score = 33.0 bits (76), Expect = 0.013
Identities = 6/42 (14%), Positives = 15/42 (35%), Gaps = 1/42 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ + G+ FV + + +K + + +V A
Sbjct: 142 SGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALS 182
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 59.6 bits (145), Expect = 7e-13
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
G+ FV + E A KAI ++G N+ ++V Y++ ++
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
Score = 43.4 bits (103), Expect = 1e-06
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+ L+V P + + EL +F P+G + +I
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63
>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 = 59.7 bits (145), Expect = 7e-13
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
GY FV + E A AI ++NG ++ +K + + S + G +
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107
Score = 39.2 bits (92), Expect = 4e-05
Identities = 11/43 (25%), Positives = 22/43 (51%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ S K +Y G+ ++ Q + FSP+G+I+ R+ +
Sbjct: 18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
>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 = 58.7 bits (143), Expect = 8e-13
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
T + GYGFV++ P A+KA+ L +Q + K S PSS
Sbjct: 43 TNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS--GPSS 84
Score = 47.9 bits (115), Expect = 1e-08
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ LY+ GL + Q+L L PYG+I++++ + D
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD 40
>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 = 59.2 bits (144), Expect = 8e-13
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
Y FV++ EDA +A+ LNG L I+V+ A+P + G
Sbjct: 52 DYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95
Score = 38.8 bits (91), Expect = 5e-05
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
LYV L S++ +E F+ R+
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV 47
>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 = 59.2 bits (144), Expect = 8e-13
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
FV Y + E A++A+ LNG ++++ +KV+ AR G
Sbjct: 50 NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93
Score = 35.3 bits (82), Expect = 8e-04
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
KG LYV G M+ L FSP+G II +
Sbjct: 14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM 45
>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 = 59.8 bits (145), Expect = 9e-13
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
FV Y + E A++A+ LNG ++++ +KV+ AR
Sbjct: 74 NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 110
Score = 35.5 bits (82), Expect = 0.001
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
KG LYV G M+ L FSP+G II +
Sbjct: 38 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM 69
>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 = 61.1 bits (148), Expect = 1e-12
Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 35/115 (30%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK----------------- 79
V A+ A++ LNG +L K I+++ ++ + +
Sbjct: 42 ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 101
Query: 80 ------------------GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
A L++S +P +S+++L+ LFS G ++
Sbjct: 102 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 156
Score = 43.7 bits (103), Expect = 3e-06
Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYARPS 74
+ E+A +A+ L+ L +N ++VS+++ +
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197
Score = 41.4 bits (97), Expect = 2e-05
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 81 ANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCD 115
+ L VS L P+ ++ Q L LF YG + +IL +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN 39
>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 = 58.7 bits (143), Expect = 1e-12
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
T S GY F+N+ + ++ AI +NG L N+ I VSYA G +
Sbjct: 44 TGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
Score = 32.6 bits (75), Expect = 0.010
Identities = 8/36 (22%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITS-RILCD 115
+ +++ L + ++ L FS +G I+ + +I+ D
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD 41
>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 = 58.5 bits (142), Expect = 1e-12
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN----KTIKVSYARPSSES 77
T GY FV + AEK ++ +NG L K K++YA S S
Sbjct: 48 TGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97
Score = 36.5 bits (85), Expect = 4e-04
Identities = 12/53 (22%), Positives = 21/53 (39%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
S S A+L++ L +M + + F+ G + S + N T Y
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGY 54
>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 = 58.8 bits (143), Expect = 1e-12
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
+S G+GFV + PE+A KA+ +NG + K + V+ A+ E
Sbjct: 51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Score = 44.1 bits (105), Expect = 6e-07
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+ NLYV L + + L FSP+G I +++++ +
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG 51
>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 = 57.9 bits (141), Expect = 2e-12
Identities = 13/42 (30%), Positives = 27/42 (64%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T S GYGFV++ +DA+ A++++ G L + +++++A
Sbjct: 39 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80
Score = 38.6 bits (91), Expect = 5e-05
Identities = 7/35 (20%), Positives = 17/35 (48%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL+V L ++ + L + F + ++ ++ D
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 36
>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 = 58.5 bits (142), Expect = 2e-12
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S GYGFV++ DAE AI + G L + I+ ++A
Sbjct: 53 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 94
Score = 39.3 bits (92), Expect = 5e-05
Identities = 9/45 (20%), Positives = 27/45 (60%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ ++ +++V L ++ +++++ F+P+GRI +R++ D
Sbjct: 6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKD 50
>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 = 57.3 bits (139), Expect = 4e-12
Identities = 11/40 (27%), Positives = 24/40 (60%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
Y F+++ + A KA+ +NG L+ + I++ +A+P +
Sbjct: 46 DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ 85
Score = 41.9 bits (99), Expect = 4e-06
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
SS K L+V L ++++ LE FS +G++ + L D
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>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 = 57.8 bits (140), Expect = 5e-12
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
+ +SLG V++ R DA KA+ G+ L + + + +
Sbjct: 72 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116
Score = 42.7 bits (101), Expect = 3e-06
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
GA L VS L +S +++ LF+ +G + + + D
Sbjct: 26 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 70
>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 = 59.9 bits (144), Expect = 7e-12
Identities = 13/80 (16%), Positives = 34/80 (42%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVS 86
+ + + + G FV + A A+ ++ G +K +++ YA+ S+ I
Sbjct: 43 ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
Query: 87 GLPKHMSQQELESLFSPYGR 106
+ +++ +S +P +
Sbjct: 103 ERDRKREKRKPKSQETPATK 122
Score = 48.3 bits (114), Expect = 9e-08
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYAR 72
FV + A A + L G ++ QN +K+S+A+
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281
Score = 36.8 bits (84), Expect = 0.001
Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELES----LFSPYGRIITSRIL 113
A P + +Y++ L + + + EL+ +FS +G+I+ +
Sbjct: 2 AVPETRP--NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS 46
Score = 33.7 bits (76), Expect = 0.010
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+++ LP+ ++ L LF+ + R++
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242
>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 = 56.9 bits (138), Expect = 8e-12
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
+S G G V + + +A +AI+ NG L ++ + V +
Sbjct: 54 KSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP 96
Score = 43.8 bits (104), Expect = 8e-07
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ G+ ++V+ L + ++L+ +FS G ++ + IL D ++GK
Sbjct: 4 GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED----KDGK 54
>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 = 56.5 bits (137), Expect = 9e-12
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+ +GFV + PE AI LNG+RL + I VS
Sbjct: 55 KPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92
Score = 40.3 bits (95), Expect = 1e-05
Identities = 9/47 (19%), Positives = 17/47 (36%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S ++ ++V L + ++ L LF G + I D
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD 51
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 58.6 bits (141), Expect = 9e-12
Identities = 11/125 (8%), Positives = 29/125 (23%), Gaps = 37/125 (29%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR------------------------ 72
G V ++AI LN + + + V ++
Sbjct: 43 GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSE 102
Query: 73 -------------PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
+ L+ P ++++ + G + + + +
Sbjct: 103 SRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS 162
Query: 120 ENGKY 124
E
Sbjct: 163 ERSSS 167
Score = 41.6 bits (97), Expect = 2e-05
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 79 KGANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCDN 116
L V GL M+ + ++F YG + + +
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41
Score = 40.1 bits (93), Expect = 6e-05
Identities = 7/39 (17%), Positives = 16/39 (41%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
++ G + + DA + + LN +++N Y
Sbjct: 161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
>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 = 57.0 bits (138), Expect = 1e-11
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T++S G+ F+ + P DA+ A +NG L K IKV A+ S
Sbjct: 44 TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88
Score = 41.5 bits (98), Expect = 6e-06
Identities = 9/40 (22%), Positives = 22/40 (55%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
E+ L++ GL + +++ L+++F +G I ++ D
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD 42
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 56.0 bits (136), Expect = 1e-11
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
+S G G V + PE AE+A +NG++L + I V R +S G
Sbjct: 44 NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
Score = 44.5 bits (106), Expect = 3e-07
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
SS S ++V LP + + L+ F+ G ++ + I +N
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN 44
>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 = 57.5 bits (139), Expect = 1e-11
Identities = 18/80 (22%), Positives = 37/80 (46%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
+ G+ FV Y+ DAE A+ +NG RL ++ I+ + E + G +
Sbjct: 77 KKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRD 136
Query: 92 MSQQELESLFSPYGRIITSR 111
+Q+ ++ YG++ ++
Sbjct: 137 EYRQDYDAGRGGYGKLAQNQ 156
Score = 37.1 bits (86), Expect = 5e-04
Identities = 11/49 (22%), Positives = 19/49 (38%)
Query: 67 KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ K LYV L + +++++ LFS G I + D
Sbjct: 26 RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD 74
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 56.2 bits (136), Expect = 1e-11
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G F+ Y E A I L Q + ++ + +
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE 100
Score = 40.0 bits (94), Expect = 2e-05
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
Y+ +P ++ +L LF +G I+ + +
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE 62
>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 = 57.7 bits (139), Expect = 3e-11
Identities = 20/115 (17%), Positives = 42/115 (36%), Gaps = 35/115 (30%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA------------------------- 71
V A+ A++ LNG +L K I+++ +
Sbjct: 73 ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132
Query: 72 -----RPSSESIKGAN-----LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+P S++ + L++S +P +S+++L+ LFS G ++
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
Score = 48.1 bits (114), Expect = 8e-08
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 71 ARPSSESIKGANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCD 115
A P + L VS L P+ ++ Q L LF YG + +IL +
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN 70
Score = 43.4 bits (102), Expect = 4e-06
Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYARPS 74
+ E+A +A+ L+ L +N ++VS+++ +
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
>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 = 55.3 bits (134), Expect = 3e-11
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
G+GF+ AE A L+ + L+ K ++V +A S+ G +
Sbjct: 52 GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPS 97
Score = 40.3 bits (95), Expect = 1e-05
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
L+V LP ++++E+ LF YG+ I
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI 47
>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 = 55.0 bits (133), Expect = 3e-11
Identities = 14/42 (33%), Positives = 26/42 (61%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
S+G+GFV Y +PE A+KA+ L G + ++V + +++
Sbjct: 49 SMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90
Score = 41.1 bits (97), Expect = 6e-06
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + L++ L +++ L+ +FS G I + I
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKK 40
>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 = 54.9 bits (133), Expect = 3e-11
Identities = 11/52 (21%), Positives = 25/52 (48%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
+ + + + G FV + A A+ ++ G +K +++ YA+ S+ I
Sbjct: 42 ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDII 93
Score = 31.4 bits (72), Expect = 0.022
Identities = 8/38 (21%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 82 NLYVSGLPKHMSQQELE----SLFSPYGRIITSRILCD 115
+Y++ L + + + EL+ ++FS +G+I+ +
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS 47
>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 = 55.0 bits (133), Expect = 4e-11
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T S G+GFV+++ EDA+ A + + + + +A+P E
Sbjct: 50 TGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95
Score = 36.5 bits (85), Expect = 4e-04
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSR 111
+ P++ S L+V GL + +++ L+ F RI+T R
Sbjct: 6 SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDR 48
>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 = 54.9 bits (133), Expect = 4e-11
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T + G+ FV + PE A KA ++G Q + + V + E+
Sbjct: 46 TKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91
Score = 39.1 bits (92), Expect = 3e-05
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
SS S + L+V L S+++LE LFS YG + D
Sbjct: 3 SGSSGSGR---LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID 43
>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 = 55.0 bits (133), Expect = 4e-11
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T +S GYGF+ + E A+KA+ LNG L + +KV + ++
Sbjct: 64 TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 41.9 bits (99), Expect = 4e-06
Identities = 12/54 (22%), Positives = 23/54 (42%)
Query: 62 QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ S LYV L ++++ L +F P+GRI + +++ D
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 56.4 bits (136), Expect = 4e-11
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
+ +SLG V++ R DA KA+ G+ L + + + +
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169
Score = 42.5 bits (100), Expect = 6e-06
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
GA L VS L +S +++ LF+ +G + + + D
Sbjct: 79 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123
>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 = 54.9 bits (133), Expect = 4e-11
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T + G+ FV + EDA AI+ +N L +TI+V+ A+P
Sbjct: 50 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94
Score = 44.5 bits (106), Expect = 3e-07
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ S + LYV GL + + + L + F P+G I +I D
Sbjct: 3 SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 47
>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 = 54.5 bits (132), Expect = 5e-11
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
S GY +V + P++AEKA+ ++G ++ + I +
Sbjct: 43 PHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA 84
Score = 42.5 bits (101), Expect = 1e-06
Identities = 8/43 (18%), Positives = 23/43 (53%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
S+K +++ L +++++ + +FS YG+I + + +
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHP 43
>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 = 54.2 bits (131), Expect = 5e-11
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSE 76
GY FV+Y A +AI TL+G + L K ++V Y+
Sbjct: 40 VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 85
Score = 37.6 bits (88), Expect = 1e-04
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
SS S LY+ L ++ +L LF + ++L
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL 41
>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 = 54.1 bits (131), Expect = 6e-11
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + G+ FV + EDA AI+ +N L +TI+V+ A+
Sbjct: 45 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
Score = 39.8 bits (94), Expect = 1e-05
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + LYV GL + + + L + F P+G I +I D
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 42
>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 = 54.6 bits (132), Expect = 6e-11
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T + G F+ + E A +A++ +NG +L K + + + + +
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 107
Score = 37.3 bits (87), Expect = 3e-04
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LY+ L +++++L SLF+ + I
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60
>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 = 53.8 bits (130), Expect = 1e-10
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+ +SLG V++ R DA KA+ NG+ L + + +
Sbjct: 66 SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105
Score = 43.8 bits (104), Expect = 8e-07
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ G L VS L +S +++ LF+ +G + + + D
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD 64
>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 = 56.3 bits (135), Expect = 1e-10
Identities = 12/75 (16%), Positives = 21/75 (28%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
QS G+ V ++K ++ L L + V+ S +
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167
Query: 92 MSQQELESLFSPYGR 106
MS + R
Sbjct: 168 MSGEGKAGPPGGSSR 182
Score = 38.9 bits (90), Expect = 2e-04
Identities = 9/55 (16%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENGK 123
+ + K LY+ L + ++L G I+ + + NG+
Sbjct: 59 NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---RANGQ 110
>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 = 54.4 bits (131), Expect = 1e-10
Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 1/73 (1%)
Query: 7 LNKLF-TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT 65
L +F Y + L+ + G F+ + A KA+ NG L K
Sbjct: 62 LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121
Query: 66 IKVSYARPSSESI 78
+ V +AR +
Sbjct: 122 MVVQFARSARPKQ 134
Score = 38.7 bits (90), Expect = 9e-05
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 60 RLQNKTI-KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI--ITSRILCDN 116
R+ + + +S R +YV L KH+ +++L+ +F Y T RI+ D
Sbjct: 24 RISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDI 83
Query: 117 LATENGK 123
+ G+
Sbjct: 84 RLMKEGR 90
>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 = 53.8 bits (130), Expect = 1e-10
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
S G+GFV + DA++A L+G ++ + I+V+ A + G
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99
Score = 45.0 bits (107), Expect = 2e-07
Identities = 10/43 (23%), Positives = 19/43 (44%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S L+VS +P +L +F +G+I+ I+ +
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 50
>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 = 53.4 bits (129), Expect = 1e-10
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+S GY F+ + EDA++A+N+ N ++ + I++ P
Sbjct: 49 NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP 90
Score = 33.4 bits (77), Expect = 0.006
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S+ S + L +S L +++ L+ +F I
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI 42
>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 = 53.4 bits (129), Expect = 1e-10
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T +S G+GFV + +DA+ A+ +NG + + I+V A SS++
Sbjct: 50 TQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95
Score = 43.0 bits (102), Expect = 2e-06
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + L+V GL ++Q LE +FS YG+I ++ D
Sbjct: 5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD 47
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 53.6 bits (129), Expect = 2e-10
Identities = 17/60 (28%), Positives = 27/60 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T + G V++ P A+ AI+ +G IKVS+A ++ +G GL H
Sbjct: 53 TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHH 112
Score = 40.1 bits (94), Expect = 2e-05
Identities = 6/32 (18%), Positives = 16/32 (50%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
++ ++V GL ++++ + + F G I
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGII 34
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 54.0 bits (130), Expect = 2e-10
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G+ FV + EDA AI+ +N L +TI+V+ A
Sbjct: 101 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 45.2 bits (107), Expect = 4e-07
Identities = 15/70 (21%), Positives = 23/70 (32%), Gaps = 2/70 (2%)
Query: 46 PEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
PE +N + LYV GL + + + L + F P+G
Sbjct: 31 PESVAY--TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFG 88
Query: 106 RIITSRILCD 115
I +I D
Sbjct: 89 DITDIQIPLD 98
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 53.8 bits (129), Expect = 2e-10
Identities = 5/53 (9%), Positives = 20/53 (37%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
+ + + + G ++ + E A+ + G Q + ++++ +
Sbjct: 63 IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVA 115
Score = 32.6 bits (74), Expect = 0.016
Identities = 5/50 (10%), Positives = 17/50 (34%), Gaps = 4/50 (8%)
Query: 67 KVSYARPSSESIKGANLYVSGLPKHMSQQEL----ESLFSPYGRIITSRI 112
+ + ++ + + +++L +L S G I+ +
Sbjct: 16 SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV 65
>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 = 53.6 bits (129), Expect = 2e-10
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ +S G+ FV + +DA++A NG+ L + I+V ++
Sbjct: 84 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT 125
Score = 43.2 bits (102), Expect = 2e-06
Identities = 12/47 (25%), Positives = 21/47 (44%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ + L V GL + ++++L +FS YG I I+ D
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 53.1 bits (128), Expect = 2e-10
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
S G+GFV + DA++A L+G ++ + I+V+ A
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 106
Score = 44.2 bits (105), Expect = 5e-07
Identities = 9/43 (20%), Positives = 20/43 (46%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ + L+VS +P +L +F +G+I+ I+ +
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 64
>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 = 52.6 bits (127), Expect = 2e-10
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T +S GY F+ + E + A+ LNG +L ++ +K Y+ S S
Sbjct: 40 TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDIS 85
Score = 39.1 bits (92), Expect = 3e-05
Identities = 7/35 (20%), Positives = 19/35 (54%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+Y+ +P +++++ L S G +I +++ D
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFD 37
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 53.0 bits (128), Expect = 2e-10
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSESIK 79
T S GYGFV + + ++A+ G + L +K +++S A P + +K
Sbjct: 46 QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK 95
Score = 29.9 bits (68), Expect = 0.100
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 1/44 (2%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFS-PYGRIITSRILCDN 116
S S +L+V L + L F Y +++ D
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ 46
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 52.7 bits (127), Expect = 3e-10
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYARPS 74
T Q+ G+ FV DA + + L L++ KTI V +A+ +
Sbjct: 49 TQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
Score = 33.1 bits (76), Expect = 0.005
Identities = 5/38 (13%), Positives = 12/38 (31%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+ + + H + + SPY + + I
Sbjct: 4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNI 41
>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 = 52.6 bits (127), Expect = 3e-10
Identities = 8/45 (17%), Positives = 16/45 (35%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
QS G+ V ++K ++ L L + V+ +
Sbjct: 41 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85
Score = 36.4 bits (85), Expect = 3e-04
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 5/44 (11%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENGK 123
LY+ L + ++L G I+ + + NG+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQ 43
>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 = 52.7 bits (127), Expect = 3e-10
Identities = 8/46 (17%), Positives = 19/46 (41%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+S G ++ + DAEK + G + +++ + Y +
Sbjct: 49 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94
Score = 38.0 bits (89), Expect = 8e-05
Identities = 7/40 (17%), Positives = 14/40 (35%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSR 111
S + L L ++++ EL+ +F I
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 47
>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 = 52.6 bits (127), Expect = 3e-10
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T G+ FV +H DA+ A ++G L + ++V AR
Sbjct: 51 TKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARY 92
Score = 44.9 bits (107), Expect = 3e-07
Identities = 11/47 (23%), Positives = 15/47 (31%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + L V L S L +F YGR+ I +
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPRE 48
>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 = 52.2 bits (126), Expect = 3e-10
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T +S GYGF+ + E A +A+ LNG L + ++V + +
Sbjct: 43 TGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD 87
Score = 41.4 bits (98), Expect = 5e-06
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + LYV L ++++ L +F P+G+I ++ D
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD 40
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 52.8 bits (127), Expect = 3e-10
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVS 86
+ + +T ++ G +V Y DA+ A++ L+G + N+ + V Y + K
Sbjct: 38 IRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQK------- 90
Query: 87 GLPKHMSQQELESLFSPYG 105
+ +++L+ L YG
Sbjct: 91 -MDTKKKEEQLKLLKEKYG 108
Score = 38.1 bits (89), Expect = 1e-04
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LY+ LP ++ +E+ +F YG I R+
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT 43
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 51.9 bits (125), Expect = 5e-10
Identities = 10/46 (21%), Positives = 21/46 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+ G +V Y A +A+ ++G+ ++ IKV+ + S
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99
Score = 44.2 bits (105), Expect = 5e-07
Identities = 12/41 (29%), Positives = 25/41 (60%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S S++ L++SGLP +++ELE + +G + R++ +
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN 52
>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 = 52.3 bits (126), Expect = 5e-10
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPSSESIKGA 81
T G+GFV++ +DA+KA N L + L + + + +A G
Sbjct: 53 GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGP 104
Score = 41.1 bits (97), Expect = 7e-06
Identities = 11/50 (22%), Positives = 22/50 (44%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ + + V +P +Q+E+ LFS +G + T R+ T +
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 53.4 bits (128), Expect = 5e-10
Identities = 12/46 (26%), Positives = 16/46 (34%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
QS GY V K + L G L + + V A + S
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
Score = 36.8 bits (85), Expect = 5e-04
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 5/64 (7%)
Query: 62 QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLAT 119
N S + A +YV + Q+L + G ++ + +
Sbjct: 37 PNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN---R 93
Query: 120 ENGK 123
NG+
Sbjct: 94 ANGQ 97
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 52.8 bits (127), Expect = 5e-10
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S G+ FV +H DAE A++ ++G L + ++V AR
Sbjct: 85 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 126
Score = 42.4 bits (100), Expect = 4e-06
Identities = 15/47 (31%), Positives = 19/47 (40%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
SY RP + +L V L S L +F YGR+ I D
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82
>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 = 51.8 bits (125), Expect = 5e-10
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
+ +S G+ FV + +DA++A NG+ L + I+VS
Sbjct: 53 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93
Score = 42.2 bits (100), Expect = 2e-06
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S R + + L V GL + ++++L +FS YG I I+ D
Sbjct: 6 SGNRANPDP--NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 50
>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 = 53.3 bits (128), Expect = 6e-10
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T S GY V Y + A A LNG + +TI+V +
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 151
Score = 45.6 bits (108), Expect = 4e-07
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 45 RPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-----------SIKGANLYVSGLPKHMS 93
E A+ G + SY R +E S++G L+V+ + +
Sbjct: 26 LKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQ 85
Query: 94 QQELESLFSPYGRIITSRILCD 115
+ E++ F YG I + D
Sbjct: 86 EDEIQEKFCDYGEIKNIHLNLD 107
>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 = 53.3 bits (128), Expect = 6e-10
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S G+ FV +H DAE A++ ++G L + ++V AR
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149
Score = 43.7 bits (103), Expect = 2e-06
Identities = 17/86 (19%), Positives = 25/86 (29%), Gaps = 10/86 (11%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK----------GANLYVSGLP 89
V+ E K NG+ + + +E +L V L
Sbjct: 20 AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79
Query: 90 KHMSQQELESLFSPYGRIITSRILCD 115
S L +F YGR+ I D
Sbjct: 80 YRTSPDTLRRVFEKYGRVGDVYIPRD 105
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 51.9 bits (125), Expect = 6e-10
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T GY V Y ++A+ A+ LNG L + I V +
Sbjct: 61 TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102
Score = 41.9 bits (99), Expect = 4e-06
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S++G L+V+G+ + +++++ F+ YG I + D
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD 58
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 52.4 bits (126), Expect = 7e-10
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T GY V Y ++A+ A+ LNG L + I V +
Sbjct: 60 TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101
Score = 39.7 bits (93), Expect = 4e-05
Identities = 10/40 (25%), Positives = 23/40 (57%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S++G L+V+G+ + +++++ F+ YG I + D
Sbjct: 18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD 57
>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 = 51.6 bits (124), Expect = 8e-10
Identities = 15/51 (29%), Positives = 22/51 (43%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
T + G V+Y P A+ A+ +G Q +KVS AR G +
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111
Score = 42.0 bits (99), Expect = 4e-06
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+ E + +YV GL ++ +L F G +
Sbjct: 6 SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV 42
>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 = 51.8 bits (124), Expect = 9e-10
Identities = 14/50 (28%), Positives = 22/50 (44%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
+ +V Y R EDA +AI +N + + +T+K S S G
Sbjct: 58 GSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSG 107
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 51.0 bits (122), Expect = 1e-09
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
F++Y A++A++ L GLRL T++V+ AR
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93
Score = 33.7 bits (77), Expect = 0.003
Identities = 8/37 (21%), Positives = 16/37 (43%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+ P + A++YV LP+ +L+ G +
Sbjct: 10 SPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV 46
>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 = 51.1 bits (123), Expect = 1e-09
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T S GY V Y + A A LNG + +TI+V +
Sbjct: 64 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 105
Score = 39.6 bits (93), Expect = 3e-05
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S++G L+V+ + + + E++ F YG I + D
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61
>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 = 50.3 bits (121), Expect = 2e-09
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
YGFV+ AE AI L+ +L I V ++ S++ G
Sbjct: 43 NYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86
Score = 42.6 bits (101), Expect = 2e-06
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
SS S L++ LP+ ++QE+ SLF YG+++ I
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI 40
>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 = 50.3 bits (121), Expect = 2e-09
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
Y FV+ R EDA +AI L+ Q K + V + + G
Sbjct: 45 DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 40.7 bits (96), Expect = 8e-06
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
S ++ L+V + + QEL + F YG +I I
Sbjct: 4 GSSGKA--STKLHVGNISPTCTNQELRAKFEEYGPVIECDI 42
>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 = 50.6 bits (121), Expect = 2e-09
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
G G V + R ED A+ L+ + ++ + +Y R +
Sbjct: 51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91
Score = 33.2 bits (76), Expect = 0.006
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+ VSGLP S Q+L+ G + + + D
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG 51
>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 = 50.3 bits (121), Expect = 2e-09
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T + +G+V++ ED EKA+ L GL++ IK+ + +
Sbjct: 54 TGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGT 98
Score = 34.2 bits (79), Expect = 0.003
Identities = 10/46 (21%), Positives = 16/46 (34%)
Query: 67 KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+ SES NL++ L + S EL+ S +
Sbjct: 4 MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV 49
>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 = 49.9 bits (120), Expect = 3e-09
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
Y FV+ + DA+ AI LNG ++ K I V + +
Sbjct: 44 DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK 83
Score = 40.3 bits (95), Expect = 1e-05
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
S S ++V + + QEL SLF GR+I +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV 41
>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 = 50.0 bits (120), Expect = 3e-09
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
+ L + + FV + P DAE A+ +G ++V + R
Sbjct: 52 IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 99
Score = 38.1 bits (89), Expect = 1e-04
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
+ + +YV LP + +++E +F YG I
Sbjct: 14 IRGPAGNNDCR---IYVGNLPPDIRTKDIEDVFYKYGAI 49
>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 = 49.5 bits (119), Expect = 4e-09
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G F+ + + A+ +N +L + IK S A
Sbjct: 54 TRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 45.3 bits (108), Expect = 1e-07
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + + +YVS LP ++ +L +FS YG+++ I+ D
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD 51
>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 = 49.7 bits (119), Expect = 4e-09
Identities = 13/46 (28%), Positives = 19/46 (41%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
GY FV Y A A+ NG L +T+ ++ A G +
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108
Score = 36.2 bits (84), Expect = 5e-04
Identities = 9/58 (15%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 57 NGLRLQNKTIKVSYARPSSE-SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRI 112
+G + ++ S ++ + +++ L + + ++E++FS YGR+ +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60
>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 = 49.6 bits (119), Expect = 5e-09
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T + GYGF Y E A A+ LNG + ++V A
Sbjct: 46 TGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS 87
Score = 40.7 bits (96), Expect = 1e-05
Identities = 8/35 (22%), Positives = 23/35 (65%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+++V +P ++++L+ +FS G +++ R++ D
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYD 43
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 48.4 bits (116), Expect = 1e-08
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 37 GYGFVNYHRPEDAEKAI-NTLNGLRLQNKTIKVSYAR 72
F+ + + AE A + N L + + + V + R
Sbjct: 49 QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
Score = 40.7 bits (96), Expect = 7e-06
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
LYV GL +++ +L + F +G I T ++
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV 45
>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 = 48.3 bits (115), Expect = 2e-08
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
G G V + R ED A+ L+ + ++ + +Y R +
Sbjct: 52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD 91
Score = 30.6 bits (69), Expect = 0.068
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
Y PS S + VSGLP S Q+L+ G + + + D
Sbjct: 7 RYGPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG 52
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 48.0 bits (115), Expect = 2e-08
Identities = 6/39 (15%), Positives = 16/39 (41%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+GF+ + P+ AI + K + + + ++
Sbjct: 46 AFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA 84
Score = 36.8 bits (86), Expect = 3e-04
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 80 GANLYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
+ L++ LP K++S+++L +FSPYG I+ I
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>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 = 48.1 bits (115), Expect = 2e-08
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G V++ P A+ AI+ +G IKVS+A
Sbjct: 59 TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 38.8 bits (91), Expect = 5e-05
Identities = 6/35 (17%), Positives = 14/35 (40%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
++V GL ++++ + + F G I
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGII 40
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 48.3 bits (115), Expect = 2e-08
Identities = 11/59 (18%), Positives = 20/59 (33%)
Query: 15 KVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
K + E ++T G G + + E +A+ LN + + I V
Sbjct: 46 KDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN 104
Score = 29.8 bits (67), Expect = 0.12
Identities = 9/38 (23%), Positives = 14/38 (36%)
Query: 72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIIT 109
S K + + LP+ S Q+L+ L T
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETT 57
>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 = 47.7 bits (114), Expect = 2e-08
Identities = 6/39 (15%), Positives = 16/39 (41%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+GF+ + P+ AI + K + + + ++
Sbjct: 58 AFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96
Score = 37.3 bits (87), Expect = 2e-04
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 69 SYARPSSESIKGANLYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
S P + + L++ LP K++S+++L +FSPYG I+ I
Sbjct: 12 SGLVPRGSHM-KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>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 = 47.3 bits (113), Expect = 3e-08
Identities = 9/58 (15%), Positives = 20/58 (34%)
Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+C+ G V + ++A A+ LN + ++ +K+ S
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96
Score = 33.8 bits (78), Expect = 0.004
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
SS + V +P +S E+ F Y I S L N E G
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EKGM 55
>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 = 48.0 bits (114), Expect = 5e-08
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G+ FV + P DA A+ L+G L ++V +
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
Score = 36.4 bits (84), Expect = 7e-04
Identities = 14/93 (15%), Positives = 24/93 (25%), Gaps = 16/93 (17%)
Query: 36 LGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK---------------- 79
G AEK + A + +
Sbjct: 13 KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL 72
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+YV L + ++ ELE F YG + + +
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV 105
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 46.9 bits (112), Expect = 5e-08
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G+ FV + P DAE A+ L+G + ++V +
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG 74
Score = 36.9 bits (86), Expect = 3e-04
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+YV L + ELE FS YG + T I
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI 32
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 46.5 bits (111), Expect = 6e-08
Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYARPSSES 77
+ ++ Y + A+ A + G L ++ ++V +A+ S
Sbjct: 54 SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96
Score = 42.6 bits (101), Expect = 2e-06
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 62 QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+ K+ Y + + + L+V GL + S L F +G I T +
Sbjct: 3 SGSSGKIGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV 50
>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 = 47.0 bits (112), Expect = 6e-08
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN------GLRLQNKTIKVSYARPSSESIKGAN 82
T S G F + E A+K + + GL+L + +KV A E+ G +
Sbjct: 53 TEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
Score = 39.6 bits (93), Expect = 3e-05
Identities = 6/45 (13%), Positives = 19/45 (42%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ S+ +G +++ L ++ L + +G + R++
Sbjct: 6 SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH 50
>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 = 46.0 bits (110), Expect = 7e-08
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T + G+GFV + E +AI L+ +TI+V+ A P
Sbjct: 39 TKKPKGFGFVEM-QEESVSEAIAKLDNTDFMGRTIRVTEANP 79
Score = 39.8 bits (94), Expect = 2e-05
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N+YV L + ++++ LFS +G++ +++ D
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD 36
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 46.0 bits (109), Expect = 1e-07
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+ + V + P +A KA L + + + + +A
Sbjct: 40 VLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81
Score = 33.6 bits (77), Expect = 0.005
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
+ LP E++ FS +G +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLG 38
>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 = 44.9 bits (107), Expect = 2e-07
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
G+G+ + + A++ LN L N+ I+V A + +
Sbjct: 62 GFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQD 100
Score = 28.0 bits (63), Expect = 0.44
Identities = 4/33 (12%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG----RIITSR 111
++ LP ++++ ++ F R+
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLNISAVRLPREP 54
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 44.3 bits (105), Expect = 3e-07
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKV 68
++ GY F+ Y P A A+ +G +L + T +V
Sbjct: 42 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV 80
Score = 25.4 bits (56), Expect = 3.5
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 11/47 (23%)
Query: 83 LYVSGLPKHMS------QQELESLFSPYGRIITSRILCDNLATENGK 123
+ V +P+ + + +FS +G+I D E+GK
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-----DFYPEEDGK 45
>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 = 44.9 bits (107), Expect = 3e-07
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
T S GYGFV+++ D +K + + + K +K+ A
Sbjct: 46 TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQN 88
Score = 41.1 bits (97), Expect = 8e-06
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V G+ M + E+ S F+ YG + +I+ D
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD 44
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 45.2 bits (107), Expect = 3e-07
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN--GLRLQNKTIKVSYARPSSE 76
++ G+ FV Y A A L ++L I V +A P +
Sbjct: 48 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94
Score = 43.6 bits (103), Expect = 9e-07
Identities = 8/40 (20%), Positives = 17/40 (42%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILC 114
S S L++ G+PK ++E+ + + I+
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVY 42
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 44.3 bits (105), Expect = 3e-07
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 2/69 (2%)
Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
++VH D ++ ++ FV E A+ AI + + K + V
Sbjct: 18 NCQEVHDLLKDYDLKY--CYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75
Query: 72 RPSSESIKG 80
+ G
Sbjct: 76 PTDALLCSG 84
Score = 35.1 bits (81), Expect = 0.001
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG 105
+ V LP+ + QE+ L Y
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD 30
>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 = 44.6 bits (106), Expect = 3e-07
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 20 FSDAEIC-VFLIS----TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
F I V L + G+G+ + + A++ LN L NK I+V A +
Sbjct: 36 FRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQA 94
Query: 75 SE 76
+
Sbjct: 95 QD 96
Score = 28.4 bits (64), Expect = 0.33
Identities = 5/33 (15%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++ LP ++++ ++ F I R+ +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE 49
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 44.2 bits (105), Expect = 4e-07
Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 20 FSDAEIC-VFLIS---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
F D I V L+ T + G+ +V + + ++A+ +G L +++++V A
Sbjct: 36 FKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRK 94
Query: 76 E 76
+
Sbjct: 95 Q 95
Score = 29.9 bits (68), Expect = 0.082
Identities = 7/33 (21%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG----RIITSR 111
YV LP + Q +++++F R++ +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDK 50
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.0 bits (104), Expect = 6e-07
Identities = 5/41 (12%), Positives = 18/41 (43%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+K ++Y+ G P + +++ G+++ ++
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL 47
Score = 32.0 bits (73), Expect = 0.017
Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G FV + E A+K + G + + + +
Sbjct: 50 AFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLI 83
>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 = 43.4 bits (103), Expect = 8e-07
Identities = 9/54 (16%), Positives = 20/54 (37%)
Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+C+ G V + ++A A+ LN + ++ +K+S
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
Score = 32.7 bits (75), Expect = 0.007
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
SS + V +P +S E+ F Y I S L N E G
Sbjct: 8 SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EKGM 55
>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 = 42.9 bits (102), Expect = 1e-06
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ G+ ++ + E ++ L+ + + IKV R
Sbjct: 44 SGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT 84
Score = 38.6 bits (91), Expect = 4e-05
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++YV + + +ELE+ F G + ILCD
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD 41
>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 = 43.9 bits (104), Expect = 1e-06
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
+ GY ++ + + A+ ++ + +TIKV R + I +
Sbjct: 74 SGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNMPGISSTD 123
Score = 38.5 bits (90), Expect = 8e-05
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ + I ++YV + + Q+LE+ FS G I ILCD
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD 71
>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 = 43.1 bits (102), Expect = 2e-06
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
+ +S G +V + + AI L G RL I V ++ + G +
Sbjct: 63 SRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSGPS 112
Score = 37.7 bits (88), Expect = 2e-04
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S E ++ L + ++LE FS G++ RI+ D
Sbjct: 18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 42.8 bits (101), Expect = 2e-06
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYAR 72
T ++ G+ FV DA+K I + +G RL + + +
Sbjct: 50 TGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91
Score = 26.2 bits (58), Expect = 2.0
Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ + ++ L SLFS G+++ D GK
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPID---EATGK 52
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 42.8 bits (101), Expect = 2e-06
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYA 71
++ GY F+ Y P A A+ +G +L + T +V+
Sbjct: 57 DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97
Score = 28.9 bits (65), Expect = 0.22
Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 6/43 (13%)
Query: 72 RPSSESIKGANLYVSGLPK------HMSQQELESLFSPYGRII 108
RP + + V +P+ + + +FS +G+I
Sbjct: 7 RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT 49
>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 = 41.6 bits (98), Expect = 3e-06
Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
V + Q + F+ + ++ +A+ +G+ Q +++K+ RP
Sbjct: 44 VLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR--RP 87
Score = 29.7 bits (67), Expect = 0.091
Identities = 6/26 (23%), Positives = 14/26 (53%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
LYV +P ++++ + F+ R+
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLG 34
>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 = 41.8 bits (98), Expect = 4e-06
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL-----QNKTIKVSYARP 73
Y F Y E++++A TLNG + Q T+ +++
Sbjct: 64 PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
Score = 30.7 bits (69), Expect = 0.058
Identities = 5/33 (15%), Positives = 13/33 (39%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ GL +S+ +L + G + + +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 62
>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 = 41.1 bits (97), Expect = 1e-05
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 4/61 (6%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE---SIKGANLYVSGL 88
T +S GYGFV AE+A N + + V+ A ++ G + VSG
Sbjct: 55 TGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
Query: 89 P 89
Sbjct: 114 S 114
Score = 34.2 bits (79), Expect = 0.003
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GLP H + L F +G I + ++ D
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITD 52
>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 = 40.1 bits (93), Expect = 4e-05
Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 5/80 (6%)
Query: 42 NYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSESIKGAN----LYVSGLPKHMSQQE 96
++H A+ A+ +N ++ N + S A + ++ G + + V L ++
Sbjct: 3 HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62
Query: 97 LESLFSPYGRIITSRILCDN 116
L +FS +G ++ N
Sbjct: 63 LHQIFSKFGTVLKIITFTKN 82
Score = 37.8 bits (87), Expect = 3e-04
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSSESIKGAN 82
+ Y P A+ A +L+G + N T+++ +++ +S ++K N
Sbjct: 85 FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 132
>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 = 39.1 bits (91), Expect = 5e-05
Identities = 8/33 (24%), Positives = 19/33 (57%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+++ LP +++ E+ SL P+G++ +L
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66
Score = 34.5 bits (79), Expect = 0.002
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 37 GYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYARPS 74
F+ + E A +N T L+ + I + ++
Sbjct: 68 NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 38.7 bits (90), Expect = 7e-05
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+++ LP +++ E+ SL P+G++ +L
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML 49
Score = 32.1 bits (73), Expect = 0.014
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 37 GYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYARP 73
F+ + E A +N T L+ + I + ++
Sbjct: 53 NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
>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 = 38.2 bits (89), Expect = 1e-04
Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 20 FSDAEI-CVFLISTAQ--SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
F + V L+ + G G V + P+D +A+ N + + + ++VS A
Sbjct: 37 FHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQW 95
Query: 77 SIKGAN 82
G +
Sbjct: 96 VAAGGH 101
Score = 26.3 bits (58), Expect = 2.2
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S +P + + V G+P + ++ F R+ +L D
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD 50
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 39.4 bits (91), Expect = 1e-04
Identities = 9/43 (20%), Positives = 15/43 (34%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
GFV + +AE A ++ L + K R +
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLL 222
Score = 30.9 bits (69), Expect = 0.10
Identities = 21/109 (19%), Positives = 28/109 (25%), Gaps = 16/109 (14%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHR---PEDAEKAINTLNGLRLQNKTIKVSYARP---- 73
C+F LG H ED K L + Y
Sbjct: 68 GQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGI 127
Query: 74 SSESIKGANLYVSGLP---------KHMSQQELESLFSPYGRIITSRIL 113
S K LYV G+ + + +FS G I R +
Sbjct: 128 GSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV 176
>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 = 38.1 bits (88), Expect = 1e-04
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 8/77 (10%)
Query: 4 QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
Q L + KV V L V +DA A+N+L+ ++ +
Sbjct: 28 QLLQEAFARHGKV--------KSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGS 79
Query: 64 KTIKVSYARPSSESIKG 80
K I VS A +S G
Sbjct: 80 KKILVSLATGASGPSSG 96
Score = 30.0 bits (67), Expect = 0.082
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 74 SSESIKGANLYVSGLPKHMS----QQELESLFSPYGRIITSRILCDN 116
S S GA++ VS + +S QQ L+ F+ +G++ + +
Sbjct: 3 SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT 49
>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 = 37.5 bits (87), Expect = 2e-04
Identities = 6/34 (17%), Positives = 15/34 (44%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GL + + + +L +G I ++
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50
Score = 34.0 bits (78), Expect = 0.003
Identities = 6/53 (11%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 37 GYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYARPSSESIKGANLYVSG 87
V + + A++ + + + + +Y+ + G + SG
Sbjct: 52 RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104
>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 = 37.5 bits (87), Expect = 2e-04
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L++ LP +++ E+ +L P+G++ +L
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML 48
Score = 32.1 bits (73), Expect = 0.015
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 2/38 (5%)
Query: 37 GYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYAR 72
F+ E A +N + L+N+ I + Y+
Sbjct: 52 NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN 89
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 37.0 bits (86), Expect = 2e-04
Identities = 5/33 (15%), Positives = 14/33 (42%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+++ GL + + +L +G I ++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56
Score = 31.3 bits (71), Expect = 0.028
Identities = 7/38 (18%), Positives = 13/38 (34%), Gaps = 2/38 (5%)
Query: 37 GYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYAR 72
V + A A+N N + + V+Y+
Sbjct: 58 RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95
>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 = 37.1 bits (86), Expect = 2e-04
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
G FV + D +KA+ L G + N+ + Y
Sbjct: 60 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
>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 = 38.3 bits (88), Expect = 3e-04
Identities = 15/105 (14%), Positives = 29/105 (27%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
+ + GY F+ Y D A +G ++ + + V R + GL
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199
Query: 92 MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR 136
++ + + + RER R
Sbjct: 200 RRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRER 244
Score = 33.3 bits (75), Expect = 0.015
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V+ + ++ +L F YG I ++
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYS 137
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 35.8 bits (83), Expect = 6e-04
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
S ++ +++VSG P+ + +L F +G +
Sbjct: 1 GSSGSSGLR--SVFVSGFPRGVDSAQLSEYFLAFGPV 35
Score = 26.5 bits (59), Expect = 1.5
Identities = 4/37 (10%), Positives = 10/37 (27%), Gaps = 1/37 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ V E ++ + L ++V
Sbjct: 46 VFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ 81
>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 = 36.3 bits (84), Expect = 6e-04
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
A+ + FV + + KAI LNG + +
Sbjct: 68 AEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>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 = 35.8 bits (83), Expect = 7e-04
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G V++ PE+A+ I TL+G + I
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 101
>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 = 35.9 bits (83), Expect = 7e-04
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 19 GFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
G E V ++ + Q LG V + +DA K+ L+ +L + V
Sbjct: 38 GIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE 94
Score = 30.5 bits (69), Expect = 0.064
Identities = 3/53 (5%), Positives = 18/53 (33%), Gaps = 3/53 (5%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ + +++ +P +++ ++ + + + NG+
Sbjct: 6 SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD---NNGQ 55
>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 = 35.5 bits (82), Expect = 0.001
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
L + + + +S G FV + E AEKA+ + R+ ++ I++ + +
Sbjct: 39 LEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRA 94
Score = 28.2 bits (63), Expect = 0.46
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 70 YARPSSESIKGAN---LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+ S S AN + + GLP S++E+ FS + L +
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD 51
>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 = 35.3 bits (82), Expect = 0.001
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 2/46 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
T S G+GFV + E K ++ + + +
Sbjct: 53 TGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 96
Score = 32.2 bits (74), Expect = 0.017
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+ K ++L V GLP ++Q+L+ FS +G ++ ++ D
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD 50
>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 = 36.3 bits (83), Expect = 0.001
Identities = 5/41 (12%), Positives = 17/41 (41%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
++Y+ G P + +++ G+++ ++ G
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 151
Score = 27.1 bits (59), Expect = 1.7
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 37 GYGFVNYHRPEDAEKAINTLN 57
G FV + E A+K + T
Sbjct: 151 GSIFVVFDSIESAKKFVETPG 171
>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 = 35.2 bits (81), Expect = 0.001
Identities = 14/47 (29%), Positives = 20/47 (42%)
Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
E+ V +G +V + R EDAEKA+ LN + I
Sbjct: 56 EMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 99
Score = 35.2 bits (82), Expect = 0.001
Identities = 9/42 (21%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ G+GF+ + + ++A+N ++ + K ++V A P
Sbjct: 48 KQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEP 88
Score = 34.5 bits (80), Expect = 0.002
Identities = 10/43 (23%), Positives = 19/43 (44%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S K ++V G+P + + EL F +G + ++ D
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYD 45
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 34.9 bits (81), Expect = 0.001
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
+ FV + + A+ L ++ ++ +S A P S G
Sbjct: 43 AFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNSNSG 84
Score = 31.4 bits (72), Expect = 0.019
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
++V M++ EL FS YG ++ I
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI 37
>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 = 36.6 bits (84), Expect = 0.001
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 17/84 (20%)
Query: 15 KVHLGFSDAEICVFLISTAQSLGYGF---VNYHRP----------EDAEKAINTLNGLRL 61
+V FS + + + G VNY+ + N LN ++L
Sbjct: 1816 RVAASFSQEALQYVVERVGKRTG-WLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKL 1874
Query: 62 QN-KTIKVSYARPSSESIKGANLY 84
Q I++ + S E ++G +L+
Sbjct: 1875 QKIDIIELQKS-LSLEEVEG-HLF 1896
Score = 30.0 bits (67), Expect = 0.22
Identities = 28/162 (17%), Positives = 44/162 (27%), Gaps = 64/162 (39%)
Query: 3 YQTLLNKLFTY-EKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
+ +LN T E +L +D I + A L ++ + +
Sbjct: 80 FDQVLNLCLTEFENCYLEGND-------IHALAAKL---------LQENDTTLVK----- 118
Query: 61 LQNKTIKVSYA------RP---SSESI-------KGANLYV--SGLPKHMSQ-------Q 95
+ IK RP S S A L G Q +
Sbjct: 119 -TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG------QGNTDDYFE 171
Query: 96 ELESLFSPYGRIITSRI-----LCDNLATEN---GKYYS-GL 128
EL L+ Y ++ I L K ++ GL
Sbjct: 172 ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL 213
Score = 28.9 bits (64), Expect = 0.60
Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 24/74 (32%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMS--QQELE 98
N H P + I+ +NG + NL VSG P+ + L
Sbjct: 356 TNSHLPAGKQVEISLVNGAK---------------------NLVVSGPPQSLYGLNLTLR 394
Query: 99 SLFSPYGRIITSRI 112
+P G + SRI
Sbjct: 395 KAKAPSG-LDQSRI 407
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 35.4 bits (81), Expect = 0.002
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNK--TIKVSYARPSSESIKGAN 82
V + A+KA LNG + T+K+ YARP+ ++ +
Sbjct: 63 IQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRND 110
>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 = 34.9 bits (81), Expect = 0.002
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAIN----TLNGLRLQNKTIKVSYARPSSESIK 79
T +S G+GFV + +K + L+ KTI A P K
Sbjct: 63 TKRSRGFGFVTFMDQAGVDKVLAQSRHELDS-----KTIDPKVAFPRRAQPK 109
Score = 31.8 bits (73), Expect = 0.022
Identities = 10/49 (20%), Positives = 19/49 (38%)
Query: 67 KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
R S G +++ GL +Q+ L F +G + ++ D
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60
>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 = 34.6 bits (80), Expect = 0.002
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+ +S G+GFV + + + A+ + + ++ A ES
Sbjct: 65 SKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES 109
Score = 30.3 bits (69), Expect = 0.090
Identities = 9/48 (18%), Positives = 22/48 (45%)
Query: 68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
V R E + L++ GL +++ L + + +G++ ++ D
Sbjct: 15 VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD 62
>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 = 34.1 bits (79), Expect = 0.003
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 9/46 (19%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAIN----TLNGLRLQNKTIKVSYARP 73
T QS G+GFV + P + TL+G + I P
Sbjct: 54 TNQSRGFGFVKFKDPNCVGTVLASRPHTLDG-----RNIDPKPCTP 94
Score = 30.3 bits (69), Expect = 0.085
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 69 SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S +S + + L+V GL +Q+ L S FS YG ++ I+ D
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKD 51
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.6 bits (79), Expect = 0.003
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSSESIKGAN 82
+ Y P A+ A +L+G + N T+++ +++ +S ++K N
Sbjct: 67 FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 114
Score = 26.5 bits (58), Expect = 2.1
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
+ V L ++ L +FS +G ++ N
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64
>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 = 34.2 bits (79), Expect = 0.003
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+V A A+N L+G K I +Y
Sbjct: 59 YVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89
>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 = 33.4 bits (77), Expect = 0.005
Identities = 9/43 (20%), Positives = 18/43 (41%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
G+ ++V + M+ +EL+ F YG ++ I
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
Score = 33.0 bits (76), Expect = 0.005
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ FV + + A+ L ++ ++ +S A P
Sbjct: 49 AFAFVTFADDKVAQSLCG--EDLIIKGISVHISNAEP 83
>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 = 33.7 bits (77), Expect = 0.005
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 1/57 (1%)
Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
L + I + ++ G GFV + D + A+ + + N+ I+V
Sbjct: 49 LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKK 104
Score = 31.0 bits (70), Expect = 0.046
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 3/53 (5%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+R S G +Y+ GLP + + F + S + NGK
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG---PNGK 65
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 32.9 bits (75), Expect = 0.007
Identities = 11/47 (23%), Positives = 18/47 (38%)
Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
I + F+ + R E A KA+ LNG + +K +
Sbjct: 44 VIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>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 = 32.3 bits (74), Expect = 0.010
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
GY FV++ E+ ++A+ N + + I+V +
Sbjct: 48 NKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEVFREKSG 87
Score = 25.7 bits (57), Expect = 2.6
Identities = 6/45 (13%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S + + G P +++++ + +P + RI+ +
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRN 44
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 32.1 bits (74), Expect = 0.011
Identities = 6/33 (18%), Positives = 20/33 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GL + + ++++ F +G++ + ++ D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFD 34
Score = 30.5 bits (70), Expect = 0.033
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G+GFV + + EK + + NK ++ A
Sbjct: 37 TNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECKKA 75
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 31.7 bits (73), Expect = 0.012
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GL ++++ F +G + + + D
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMD 34
Score = 28.2 bits (64), Expect = 0.27
Identities = 6/44 (13%), Positives = 15/44 (34%), Gaps = 9/44 (20%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAIN----TLNGLRLQNKTIKVSYA 71
T + G+ F+ + E +K + + ++ A
Sbjct: 37 TNKRRGFCFITFKEEEPVKKIMEKKYHNVGL-----SKCEIKVA 75
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 31.7 bits (73), Expect = 0.013
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAIN----TLNGLRLQNKTIKVSYA 71
T +S G+GFV + +K + L+ KTI A
Sbjct: 38 TKRSRGFGFVTFMDQAGVDKVLAQSRHELDS-----KTIDPKVA 76
Score = 29.8 bits (68), Expect = 0.079
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+++ GL +Q+ L F +G + ++ D
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 35
>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 = 32.2 bits (74), Expect = 0.013
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G+GF+ + EK ++ RL + I A
Sbjct: 49 TGRSRGFGFILFKDAASVEKVLDQKEH-RLDGRVIDPKKA 87
Score = 30.6 bits (70), Expect = 0.043
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
S ++V GL S+++L+ F+ +G ++ I D
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMD 46
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 32.3 bits (73), Expect = 0.015
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
SS S ++V GLP + + E+ + F +G ++
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKA 43
>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 = 32.5 bits (74), Expect = 0.017
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
L I + + + G FV + E AEKA+ + R+ ++ I+V +
Sbjct: 66 LEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQE 121
Score = 29.5 bits (66), Expect = 0.18
Identities = 9/46 (19%), Positives = 19/46 (41%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
S++S + + GLP +++E+ FS + L +
Sbjct: 33 GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 102
Score = 30.8 bits (70), Expect = 0.044
Identities = 7/38 (18%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
G V + EDA A+ + +Q++ +++ +
Sbjct: 56 GEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTA 92
Score = 25.1 bits (55), Expect = 4.8
Identities = 9/35 (25%), Positives = 19/35 (54%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
+ S +S G +++ GLP ++ ++ + FSP
Sbjct: 6 SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN 40
>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 = 31.4 bits (71), Expect = 0.044
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 20 FSDAEICVFLISTAQ---SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV--SYARPS 74
FS I G V + E+A A+ + + +Q++ I++ + +
Sbjct: 67 FSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA 125
Query: 75 SESIKGA 81
S +
Sbjct: 126 SNGAYSS 132
Score = 27.5 bits (61), Expect = 0.97
Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+ + +S G +++ GLP ++ ++ + FSP + I +G+
Sbjct: 37 SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG----PDGR 84
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 30.7 bits (69), Expect = 0.056
Identities = 9/43 (20%), Positives = 16/43 (37%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
S +N+ P A A L+ K +K+ +A+
Sbjct: 45 SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG 87
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 30.3 bits (68), Expect = 0.071
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 83 LYVSGLPKH-MSQQELESLFSPYGRIITSRIL 113
+++S LP S + L PYG+I ++
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM 59
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 29.3 bits (65), Expect = 0.13
Identities = 12/35 (34%), Positives = 13/35 (37%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G Y E+A KA LN L N TI
Sbjct: 44 GIALCKYTTREEANKAQMALNNCVLANTTIFAESP 78
>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 = 30.0 bits (67), Expect = 0.14
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 18 LGFSDAEICVFLISTA--QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
D V I T + G FV +D + A+ + + ++ I+V + +
Sbjct: 68 CTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRT 125
>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 = 28.7 bits (64), Expect = 0.26
Identities = 6/59 (10%), Positives = 19/59 (32%), Gaps = 3/59 (5%)
Query: 18 LGFSDAEICVFLISTAQ--SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
+ E + + G + +D +KA+ + + + + ++V
Sbjct: 35 CRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEINNE 92
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
Length = 118
Score = 29.1 bits (65), Expect = 0.26
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 18 LGFSDAEICVFLISTA--QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
D V I T + G FV +D + A+ + + ++ I+V + +
Sbjct: 41 CTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKSHRT 98
Score = 25.3 bits (55), Expect = 6.0
Identities = 7/35 (20%), Positives = 15/35 (42%)
Query: 71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
E +G + + GLP S +++++ S
Sbjct: 8 MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCT 42
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 28.7 bits (64), Expect = 0.29
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
+ G FV + E A+ A+ + L + I++ + +
Sbjct: 66 RPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAA 105
Score = 24.8 bits (54), Expect = 7.0
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+ + GLP + +E+ + F + I
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPI 50
>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur,
iron-sulfur cluster, pyruvate catabolism, TPP-dependent
enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP:
c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB:
1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A*
2pda_A* 2uza_A*
Length = 1231
Score = 29.4 bits (66), Expect = 0.34
Identities = 18/69 (26%), Positives = 24/69 (34%), Gaps = 21/69 (30%)
Query: 38 YGFVNYHRPEDAEKAI-----------NTLNGLRLQNK---TIKVSYARP-SSESIKGAN 82
Y +Y DAE+ I +N L + + IKV RP SE+ A
Sbjct: 257 YKLFDYVGAPDAERVIVSMGSSCETIEEVINHLAAKGEKIGLIKVRLYRPFVSEAFFAA- 315
Query: 83 LYVSGLPKH 91
LP
Sbjct: 316 -----LPAS 319
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif,
hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 27.9 bits (63), Expect = 0.35
Identities = 4/26 (15%), Positives = 10/26 (38%)
Query: 47 EDAEKAINTLNGLRLQNKTIKVSYAR 72
+ + ++ K +KV+ A
Sbjct: 50 GKGPHVLKVMKNTTVKGKQLKVNKAN 75
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 29.0 bits (64), Expect = 0.52
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL-----QNKTI 66
+ ++ + L+ Y F Y E++++A TLNG + Q T+
Sbjct: 33 SRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL 91
Query: 67 KVSYARPSSESIKGANLYVSGL---PKHMSQQELESLFS 102
+++ GL + +S +E + L
Sbjct: 92 YLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLE 130
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 27.0 bits (59), Expect = 0.99
Identities = 7/43 (16%), Positives = 16/43 (37%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
+ + + AE+A + + I VS+ + E +
Sbjct: 47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCE 89
>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 = 27.1 bits (60), Expect = 1.1
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 83 LYVSGLPK-HMSQQELESLFSPYGRIITSRIL 113
+++ + + +L L P+G I IL
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL 49
>1mi3_A Xylose reductase, XR; aldo-keto reductase, beta-alpha barrel,
dimer, oxidoreductase; HET: NAD; 1.80A {Candida tenuis}
SCOP: c.1.7.1 PDB: 1jez_A* 1k8c_A* 1ye6_A* 1ye4_A*
1sm9_A* 1r38_A* 1z9a_A*
Length = 322
Score = 27.1 bits (61), Expect = 1.8
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
NYH P++ E A+N TL L++
Sbjct: 85 NYHDPKNVETALNKTLADLKV 105
>3krb_A Aldose reductase; ssgcid, SBRI, emerald biostructures, university
of washingto niaid, oxidoreductase, S genomics; HET:
NAP; 1.75A {Giardia lamblia}
Length = 334
Score = 27.2 bits (61), Expect = 2.0
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
HRPE + T++ L++
Sbjct: 96 YNHRPELVREQCKKTMSDLQV 116
>3buv_A 3-OXO-5-beta-steroid 4-dehydrogenase; 5-beta-reductase, catalytic
tetrad, hepes, NADP, bIle catabolism, disease mutation,
lipid metabolism; HET: NAP EPE; 1.35A {Homo sapiens}
PDB: 3bur_A* 3bv7_A* 3caq_A* 3cas_A* 3cav_A* 3g1r_A*
3cot_A* 3dop_A* 3cmf_A* 3uzx_A* 3uzw_A* 3uzy_A* 3uzz_A*
Length = 326
Score = 26.8 bits (60), Expect = 2.3
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAI-NTLNGLRL 61
H PE + TL L+L
Sbjct: 91 TNHVPEMVRPTLERTLRVLQL 111
>1afs_A 3-alpha-HSD, 3-alpha-hydroxysteroid dehydrogenase; oxidoreductase,
NAD; HET: NAP TES; 2.50A {Rattus norvegicus} SCOP:
c.1.7.1 PDB: 1lwi_A*
Length = 323
Score = 26.7 bits (60), Expect = 2.5
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAI-NTLNGLRL 61
+HRPE + TL +L
Sbjct: 88 TFHRPELVRTCLEKTLKSTQL 108
>2hl7_A Cytochrome C-type biogenesis protein CCMH; three-helices bundle,
oxidoreductase; HET: PG4; 1.70A {Pseudomonas
aeruginosa}
Length = 84
Score = 25.3 bits (56), Expect = 3.1
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 9 KLFTYEKVHLGFSDAEICVFLISTAQSLGYG-FVNYHRPE 47
+ Y ++ G SD EI ++++ YG FV Y +P
Sbjct: 49 RKQIYGQLQQGKSDGEIVDYMVAR-----YGDFVRY-KPP 82
>2ao0_A Aldehyde dehydrogenase; TIM barrel, aldo-keto reductase, ternary
complex; HET: NAP FID; 1.85A {Sus scrofa} PDB: 3h4g_A*
3cv7_A* 3fx4_A* 1hqt_A* 1ae4_A* 1cwn_A* 2alr_A
Length = 324
Score = 26.4 bits (59), Expect = 3.2
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
H PED E A+ TL L+L
Sbjct: 83 TKHHPEDVEPALRKTLADLQL 103
>3o3r_A Aldo-keto reductase family 1, member B7; aldose reductase like
protein, AKR1B14, oxidoreductase; HET: NAP; 1.86A
{Rattus norvegicus} PDB: 3qkz_A*
Length = 316
Score = 26.3 bits (59), Expect = 3.3
Identities = 5/21 (23%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
+ ++A TL+ L+L
Sbjct: 82 TFFEKSLMKEAFQKTLSDLKL 102
>1pjz_A Thiopurine S-methyltransferase; polymorphism, S-adenosylmethionine,
drug metabolism; NMR {Pseudomonas syringae PV} SCOP:
c.66.1.36
Length = 203
Score = 26.3 bits (57), Expect = 3.4
Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 87 GLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL 134
G P + Q L + S + ++ + + + G ER+
Sbjct: 150 GPPFSVPQTWLHRVMSGNWEVT--KVGGQDTLHSSARG--LKAGLERM 193
>1s1p_A Aldo-keto reductase family 1 member C3; TIM-barrel, oxidoreductase;
HET: NAP; 1.20A {Homo sapiens} SCOP: c.1.7.1 PDB:
1s1r_A* 1s2a_A* 1s2c_A* 3uwe_A* 3r58_A* 3r43_A* 3r7m_A*
3r6i_A* 3r8h_A* 3r94_A* 3r8g_A* 1zq5_A* 1ry8_A* 1xf0_A*
1ry0_A* 2f38_A* 2fgb_A* 4dbs_A* 4dbu_A* 3gug_A* ...
Length = 331
Score = 26.4 bits (59), Expect = 3.4
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAI-NTLNGLRL 61
+HRPE A+ N+L +L
Sbjct: 88 TFHRPELVRPALENSLKKAQL 108
>1us0_A Aldose reductase; oxidoreductase, NADP, IDD594; HET: NDP LDT CIT;
0.66A {Homo sapiens} SCOP: c.1.7.1 PDB: 1pwl_A* 1t41_A*
1pwm_A* 1x96_A* 1x97_A* 1x98_A* 1z89_A* 1z8a_A* 2dux_A*
2duz_A* 2dv0_A* 2fz8_A* 2fz9_A* 2fzb_A* 2fzd_A* 2hv5_A*
2hvn_A* 2hvo_A* 2i16_A* 2i17_A* ...
Length = 316
Score = 26.3 bits (59), Expect = 3.7
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
YH + A TL+ L+L
Sbjct: 82 TYHEKGLVKGACQKTLSDLKL 102
>1vj0_A Alcohol dehydrogenase, zinc-containing; TM0436, structural G JCSG,
PSI, protein structure initiative, joint center for S
genomics; 2.00A {Thermotoga maritima} SCOP: b.35.1.2
c.2.1.1
Length = 380
Score = 26.0 bits (58), Expect = 4.1
Identities = 7/42 (16%), Positives = 13/42 (30%)
Query: 46 PEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSG 87
L L+N T K + +S +K ++
Sbjct: 301 VPQDPVPFKVYEWLVLKNATFKGIWVSDTSHFVKTVSITSRN 342
>1y9z_A Alkaline serine protease; subtilisin-like alpha/beta domain, insert
beta barrel domain hydrolase; HET: PMS; 1.40A
{Pseudoalteromonas SP} PDB: 1v6c_A* 1wvm_A*
Length = 441
Score = 26.3 bits (58), Expect = 4.4
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 15/52 (28%)
Query: 16 VHLGFSDAEICVFLISTAQSL---------GYGFVNYHRPEDAEKAINTLNG 58
H S +++ L +TA L GYG +N A A L+
Sbjct: 385 YHPECSASQVRAALNATADDLSVAGRDNQTGYGMIN------AVAAKAYLDE 430
>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium
pasteurianum} SCOP: c.37.1.10
Length = 269
Score = 26.1 bits (58), Expect = 4.5
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 88 LPKHMSQQELESLFSPYG 105
+PK M+Q+ LE + YG
Sbjct: 252 IPKPMTQERLEEILMQYG 269
>2kw0_A CCMH protein; oxidoreductase, cytochrome C maturation; NMR
{Escherichia coli}
Length = 90
Score = 24.9 bits (55), Expect = 4.8
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 9 KLFTYEKVHLGFSDAEICVFLISTAQSLGYG-FVNYHRPE 47
+ YE + G S EI ++++ YG FV Y P
Sbjct: 46 RQKVYELMQEGKSKKEIVDYMVAR-----YGNFVTY-DPP 79
>3h7u_A Aldo-keto reductase; stress response, NADP, drought tolerance,
oxidoreductase; HET: NAP; 1.25A {Arabidopsis thaliana}
Length = 335
Score = 26.0 bits (58), Expect = 5.0
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
H P+D +A+N TL L+L
Sbjct: 105 TDHDPQDVPEALNRTLKDLQL 125
>2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding,
phosphorylation, DNA-binding protein; NMR {Mycobacterium
tuberculosis}
Length = 148
Score = 25.4 bits (55), Expect = 5.3
Identities = 8/42 (19%), Positives = 16/42 (38%)
Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
G+ D EI +L + SL + ++ L+ +
Sbjct: 94 GYRDTEIMRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQ 135
>3h7h_B Transcription elongation factor SPT5; helices surrounding beta
sheet, activator, ME binding, nucleus, repressor,
transcription regulation; 1.55A {Homo sapiens}
Length = 106
Score = 25.2 bits (55), Expect = 5.3
Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 6 LLNKLFTYEKVHLGFSDAEICVFLISTAQSL-GYGFVNYHRPEDAEKAINTLNGLRLQNK 64
L+ K Y+ +D + + + + + GY +V ++ ++AI + LRL
Sbjct: 25 LMRKFIAYQF-----TDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYW 79
Query: 65 TIK 67
+
Sbjct: 80 NQQ 82
>3h7r_A Aldo-keto reductase; stress response, NADP, drought tolerance,
oxidoreductase; HET: NAP; 1.40A {Arabidopsis thaliana}
Length = 331
Score = 25.6 bits (57), Expect = 6.0
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
N H PED KA+ TL L++
Sbjct: 101 NDHLPEDVPKALEKTLQDLQI 121
>1qwk_A Aldose reductase, aldo-keto reductase family 1 member C1, XH961;
structural genomics, PSI, protein structure initiative;
1.60A {Caenorhabditis elegans} SCOP: c.1.7.1
Length = 317
Score = 25.6 bits (57), Expect = 7.0
Identities = 5/21 (23%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 42 NYHRPEDAEKAIN-TLNGLRL 61
+ P E + +L L+L
Sbjct: 85 HELAPGKLEGGLRESLKKLQL 105
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease,
hydrolase, magnesium, metal nonsense-mediated mRNA
decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}
Length = 507
Score = 25.4 bits (54), Expect = 8.6
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
++ PK +L LFS +G I S I
Sbjct: 440 DHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI 471
>3icy_A Sensor protein; sensory box histidine kinase/response regulator
domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A
{Chlorobaculum tepidum}
Length = 118
Score = 24.5 bits (54), Expect = 9.8
Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 4/70 (5%)
Query: 1 MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
+Y ++ T A + + A + ++ +D N + LR
Sbjct: 16 AIYHLDVSGQATIRFR----PPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLR 71
Query: 61 LQNKTIKVSY 70
++ + Y
Sbjct: 72 EAKHSLTLVY 81
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
0.318 0.136 0.387
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: 1,999,097
Number of extensions: 104672
Number of successful extensions: 732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 681
Number of HSP's successfully gapped: 401
Length of query: 136
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 52
Effective length of database: 4,356,429
Effective search space: 226534308
Effective search space used: 226534308
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (23.7 bits)