RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4057
(246 letters)
>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 = 186 bits (473), Expect = 9e-59
Identities = 139/262 (53%), Positives = 165/262 (62%), Gaps = 34/262 (12%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSLYAIFSQFGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQ 138
PMRIQY+KTDSD+I+K+KGTF+ER +K K+ ++ KK+ +
Sbjct: 81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGP 140
Query: 139 QQMQALSVQQPPVSQPAPPAPMATAGVPEQP----------------------------- 169
Q P + P P P
Sbjct: 141 VPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQP 200
Query: 170 -----PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA 224
PN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA
Sbjct: 201 LSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAA 260
Query: 225 KLALHGFKITPTHAMKISFAKK 246
+ AL GFKIT +AMKISFAKK
Sbjct: 261 RDALQGFKITQNNAMKISFAKK 282
Score = 51.8 bits (123), Expect = 4e-08
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 7/88 (7%)
Query: 165 VPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVRLVPNRH--DIAFVEFENE 218
VPE PN +++ NL E+ + L +F+QF ++ + + AFV F+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 219 MQSAAAKLALHGFKITPTHAMKISFAKK 246
+ A ++ GF M+I +AK
Sbjct: 63 SSATNALRSMQGFPFY-DKPMRIQYAKT 89
Score = 51.0 bits (121), Expect = 7e-08
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNA 66
+ +++T++ + L +F+QF ++ + AFV F A A
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHDIAFVEFDNEVQAGAA 260
Query: 67 LRSMQGFPFY-DKPMRIQYSK 86
++QGF + M+I ++K
Sbjct: 261 RDALQGFKITQNNAMKISFAK 281
>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 = 138 bits (348), Expect = 8e-41
Identities = 43/235 (18%), Positives = 83/235 (35%), Gaps = 46/235 (19%)
Query: 14 VYVTHISSTDLK-KSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ V++++ + +SL+ +F +G + + L + A V + A A+ + G
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLAMSHLNG 63
Query: 73 FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
+ KP+RI SK + P E + +K R
Sbjct: 64 HKLHGKPIRITLSKHQNV-------------------QLPREGQEDQGLTKDYGNSPLHR 104
Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
P + PP+ L L+N+P SE L +LF
Sbjct: 105 F-----------------------KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF 141
Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+ G K + +A ++ + ++ A + LH + H +++SF+K
Sbjct: 142 SSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196
Score = 50.3 bits (120), Expect = 6e-08
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
+ +++++I + ++ L +FS G ++ K R A + + A AL +
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-KDRKMALIQMGSVEEAVQALIDL 178
Query: 71 QGFPFYD-KPMRIQYSKT 87
+ +R+ +SK+
Sbjct: 179 HNHDLGENHHLRVSFSKS 196
Score = 47.2 bits (112), Expect = 9e-07
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 171 NQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
N +L ++NL PE + L +LF + + V+++ N+ + A V+ + Q+ A L+
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 230 GFKITPTHAMKISFAKK 246
G K+ ++I+ +K
Sbjct: 63 GHKL-HGKPIRITLSKH 78
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 129 bits (326), Expect = 3e-37
Identities = 42/235 (17%), Positives = 86/235 (36%), Gaps = 46/235 (19%)
Query: 14 VYVTHISSTDLK-KSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ V++++ + +SL+ +F +G + + L + A V + A A+ + G
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--NKKENALVQMADGNQAQLAMSHLNG 94
Query: 73 FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
+ KP+RI SK + + +
Sbjct: 95 HKLHGKPIRITLSKHQNVQLPR-------------------------------------- 116
Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
+ Q+ Q P+ + P + PP+ L L+N+P SE L +LF
Sbjct: 117 --EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI--FPPSATLHLSNIPPSVSEEDLKVLF 172
Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+ G K + +A ++ + ++ A + LH + H +++SF+K
Sbjct: 173 SSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227
Score = 51.2 bits (122), Expect = 4e-08
Identities = 22/105 (20%), Positives = 44/105 (41%), Gaps = 6/105 (5%)
Query: 147 QQPPVSQPAPPAPMATAGV----PEQPPNQILFLTNL-PEETSEMMLSMLFNQFPGFKEV 201
S P + N +L ++NL PE + L +LF + + V
Sbjct: 6 HHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV 65
Query: 202 RLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+++ N+ + A V+ + Q+ A L+G K+ ++I+ +K
Sbjct: 66 KILFNKKENALVQMADGNQAQLAMSHLNGHKL-HGKPIRITLSKH 109
Score = 49.6 bits (118), Expect = 1e-07
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
+ +++++I + ++ L +FS G ++ K R A + + A AL +
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 209
Query: 71 QGFPFYD-KPMRIQYSKT 87
+ +R+ +SK+
Sbjct: 210 HNHDLGENHHLRVSFSKS 227
>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 = 124 bits (313), Expect = 8e-37
Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIK 96
PMRIQY+KTDSD+I+K+K
Sbjct: 80 PMRIQYAKTDSDIIAKMK 97
Score = 51.8 bits (125), Expect = 3e-09
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 165 VPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVRLV--PNRHDIAFVEFENE 218
VPE PN +++ NL E+ + L +F++F ++ + AFV F+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 219 MQSAAAKLALHGFKITPTHAMKISFAKK 246
+ A ++ GF M+I +AK
Sbjct: 62 SSATNALRSMQGFPFY-DKPMRIQYAKT 88
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 111 bits (278), Expect = 3e-31
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 1/88 (1%)
Query: 18 HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD 77
+ L+ LYA+ S G I+DIV + G+A+++F SA + + QG+PF
Sbjct: 40 EVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQG 99
Query: 78 KPMRIQYSKTDSDVISKIKGTFMERPKK 105
P+ I +S+T +++ G+
Sbjct: 100 NPLVITFSETPQSQVAE-DGSLEHHHHH 126
Score = 54.5 bits (131), Expect = 6e-10
Identities = 16/106 (15%), Positives = 41/106 (38%), Gaps = 7/106 (6%)
Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSE----MMLSMLFNQFPGFKEVR 202
+ +P + P P+Q++ +TN+ E + +L L + ++
Sbjct: 5 AAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV 64
Query: 203 L--VPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+ + A++ F + + A A G+ + + I+F++
Sbjct: 65 VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQ-GNPLVITFSET 109
>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 = 97.0 bits (242), Expect = 6e-26
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
+Y+ ++S ++ L ++F++F + + T +MRGQAF+ F A AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
G+ Y K + I++ K
Sbjct: 88 NGYKLYGKILVIEFGKNKKQ 107
Score = 54.2 bits (131), Expect = 7e-10
Identities = 23/99 (23%), Positives = 38/99 (38%), Gaps = 6/99 (6%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI- 210
S + PN++L+L NL +E L LF +F K +
Sbjct: 6 SGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 65
Query: 211 ----AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
AF+ F N+ + A ++G+K+ + I F K
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLY-GKILVIEFGK 103
>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 = 99.0 bits (246), Expect = 1e-25
Identities = 26/241 (10%), Positives = 70/241 (29%), Gaps = 53/241 (21%)
Query: 14 VYVTHISSTDL-KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ V + + + ++ +F +G + + +K G A V + + A+ +
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK--SKPGAAMVEMADGYAVDRAITHLNN 64
Query: 73 FPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQAR 132
+ + M + SK + + + G + +
Sbjct: 65 NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST-------------- 110
Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLF 192
P A Q P+ +L N P E +E +
Sbjct: 111 --------------------------PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEIC 144
Query: 193 NQFPGFKEVRLV-----PNRHDIAFVEFENEMQSAAAKLALHGFKITPT-----HAMKIS 242
++ + + R +E++++ + L+ +++ + +K+
Sbjct: 145 DELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204
Query: 243 F 243
F
Sbjct: 205 F 205
Score = 47.8 bits (113), Expect = 5e-07
Identities = 11/79 (13%), Positives = 31/79 (39%), Gaps = 2/79 (2%)
Query: 169 PPNQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
+ +L + L + + + +F + ++V+ + ++ A VE + A
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61
Query: 228 LHGFKITPTHAMKISFAKK 246
L+ + M + +K+
Sbjct: 62 LNNNFM-FGQKMNVCVSKQ 79
Score = 42.0 bits (98), Expect = 5e-05
Identities = 7/79 (8%), Positives = 23/79 (29%), Gaps = 3/79 (3%)
Query: 9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATN 65
+N ++ + +++ + I + G V + + + + A
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 66 ALRSMQGFPFYDKPMRIQY 84
L + + + Y
Sbjct: 181 TLGFLNHYQMKNPNGPYPY 199
>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 = 95.3 bits (237), Expect = 7e-25
Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 8/94 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQI--------MDIVALKTLKMRGQAFVIFKEIASATN 65
+YV +++ +K L IF ++ DI +K +M+GQAF+ +A
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 66 ALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTF 99
AL+ G+ + KPM +Q++++ +G
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141
Score = 46.4 bits (110), Expect = 9e-07
Identities = 21/137 (15%), Positives = 44/137 (32%), Gaps = 21/137 (15%)
Query: 119 AKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTN 178
+ E + ++ ++ ++ V + P PN +++ N
Sbjct: 3 LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGE----------PNCRIYVKN 52
Query: 179 LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----------AFVEFENEMQSAAAKLAL 228
L + E L +F ++ F AF+ NE +A A
Sbjct: 53 LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEA 112
Query: 229 HGFKITPTHAMKISFAK 245
+G+ + M + FA+
Sbjct: 113 NGYVLF-GKPMVVQFAR 128
>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 = 85.9 bits (213), Expect = 1e-21
Identities = 21/96 (21%), Positives = 47/96 (48%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+Y+ ++ + +Y IF ++G I I T + RG A+V++++I A NA+ + GF
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 74 PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
++ + + Y + E+ K ++++
Sbjct: 71 NVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEK 106
Score = 48.1 bits (115), Expect = 1e-07
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH--DIAFVEFENEMQSAAAKLA 227
N+IL++ NLP + + + +F ++ +++R+ A+V +E+ + A
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 228 LHGFKI 233
L GF +
Sbjct: 67 LSGFNV 72
>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 = 70.4 bits (173), Expect = 5e-15
Identities = 35/233 (15%), Positives = 75/233 (32%), Gaps = 71/233 (30%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
+YV +I ++++ F+ ++ ++A++ + + AF+ F+ + T
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 66 ALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKK 125
A+ + G F + ++I+ RP + P E+P
Sbjct: 67 AM-AFDGIIFQGQSLKIR------------------RPHDYQPLPGMSENP--------- 98
Query: 126 AAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSE 185
+ + VP+ LF+ LP ++
Sbjct: 99 ----------------------------SVYVPGVVSTVVPDSAHK--LFIGGLPNYLND 128
Query: 186 MMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
+ L F K LV + AF E+ + + A L+G ++
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Score = 50.4 bits (121), Expect = 6e-08
Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+++ + + + + + FG + +K T +G AF + +I A+ +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 71 QGFPFYDKPMRIQYS 85
G DK + +Q +
Sbjct: 177 NGMQLGDKKLLVQRA 191
>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 = 68.5 bits (168), Expect = 6e-14
Identities = 34/262 (12%), Positives = 80/262 (30%), Gaps = 52/262 (19%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ + + + ++ + S + + K +G AFV A A+ +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE----LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQS 80
Query: 74 PFYDKPMRIQYSKTDSDVI----------SKIKGTF-----MERPKKVRKQPAPVEDPAE 118
++ + +Q TD+ + + + +ER V +
Sbjct: 81 RLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE--------R 132
Query: 119 AKKSK--------KKAAKEQA-RLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP 169
+SK KK + +A + + + L V + P
Sbjct: 133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH---WTDAGQLT-------PALL 182
Query: 170 PNQILFLTNLPEETSEM-MLSMLFNQFPGFKEVRLVPNRH----DIAFVEFENEMQSAAA 224
++ L + LP +++ L + +L + A +E+E + A
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242
Query: 225 KLALHGFKITPTHAMKISFAKK 246
+ G + +++SF
Sbjct: 243 QQQADGLSLG-GSHLRVSFCAP 263
Score = 50.7 bits (122), Expect = 8e-08
Identities = 10/92 (10%), Positives = 28/92 (30%), Gaps = 3/92 (3%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+ V + + +L S + + +++G A + ++ A A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 71 QGFPFYDKPMRIQYSKTDSDVISKIKGTFMER 102
G +R+ + S + +
Sbjct: 247 DGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQ 278
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 65.4 bits (159), Expect = 8e-14
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ V ++ L+ IFS+FG ++ I+ + QA + + + SA +A S+ G
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDG 88
Query: 73 FPFYDKP--MRIQYSKTDSDVISK 94
Y+ +RI +SK S +
Sbjct: 89 QNIYNACCTLRIDFSKLTSLNVKY 112
Score = 53.5 bits (128), Expect = 2e-09
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 5/105 (4%)
Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQILFLT--NLPEETSEMMLSMLFNQF-PGFKEV 201
SVQ ++ A A + G+ + +L + NL + +L +F++F K +
Sbjct: 1 SVQSGNLALAASAAAVDA-GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII 59
Query: 202 RLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFAK 245
N A +++ + + + AKL+L G I ++I F+K
Sbjct: 60 TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 63.9 bits (155), Expect = 2e-13
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 4/84 (4%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ + + LY + + G++ IV K + QA V F+ + A A ++ G
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK--RNGIQAMVEFESVLCAQKAKAALNG 84
Query: 73 FPFYDK--PMRIQYSKTDSDVISK 94
Y ++I+Y++ + +
Sbjct: 85 ADIYAGCCTLKIEYARPTRLNVIR 108
Score = 48.9 bits (116), Expect = 6e-08
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 168 QPPNQILFLT--NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
N++L L+ N + +L + N + + + A VEFE+ + + AK
Sbjct: 20 SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79
Query: 226 LALHGFKITP-THAMKISFAK 245
AL+G I +KI +A+
Sbjct: 80 AALNGADIYAGCCTLKIEYAR 100
>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 = 63.0 bits (154), Expect = 3e-13
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
T ++V + +L F +FG I I +K A++ ++ + +A A M
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI---DHVKGDSFAYIQYESLDAAQAACAKM 73
Query: 71 QGFPF--YDKPMRIQYSKTD 88
+GFP D+ +R+ ++K+
Sbjct: 74 RGFPLGGPDRRLRVDFAKSG 93
Score = 57.6 bits (140), Expect = 3e-11
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
P L++ L TS L+ F++F + + V A++++E+ + AA +
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD-SFAYIQYESLDAAQAACAKM 73
Query: 229 HGFKIT-PTHAMKISFAK 245
GF + P +++ FAK
Sbjct: 74 RGFPLGGPDRRLRVDFAK 91
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 61.9 bits (151), Expect = 6e-13
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV T L FS FG I+D+ R AFV ++++ SA A+ + G
Sbjct: 18 LYVYGEDMTP--TLLRGAFSPFGNIIDL---SMDPPRNCAFVTYEKMESADQAVAELNGT 72
Query: 74 PFYDKPMRIQYSK 86
+++ ++
Sbjct: 73 QVESVQLKVNIAR 85
Score = 41.5 bits (98), Expect = 2e-05
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
L++ + + +L F+ F ++ + P R+ AFV +E + A
Sbjct: 10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRN-CAFVTYEKMESADQAV 66
Query: 226 LALHGFKITPTHAMKISFAKK 246
L+G ++ + +K++ A+K
Sbjct: 67 AELNGTQVE-SVQLKVNIARK 86
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 61.2 bits (149), Expect = 1e-12
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
Y+ +I + L +F FG I+D K +G F+ + A + ++ F
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDF---KHYPEKGCCFIKYDTHEQAAVCIVALANF 86
Query: 74 PFYDKPMRIQYSK 86
PF + +R + K
Sbjct: 87 PFQGRNLRTGWGK 99
Score = 57.7 bits (140), Expect = 3e-11
Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 7/103 (6%)
Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRL 203
++ PP P + + PP ++ N+P +E L LF F + +
Sbjct: 4 TIGLPPQVNPQAVDHI----IRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH 59
Query: 204 VPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
P + F++++ Q+A +AL F ++ + K+
Sbjct: 60 YPEKG-CCFIKYDTHEQAAVCIVALANFPFQ-GRNLRTGWGKE 100
>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 = 60.9 bits (148), Expect = 3e-12
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
N +YV T L FS FG I+D+ R AFV ++++ SA A+ +
Sbjct: 40 NTLYVYGEDMTP--TLLRGAFSPFGNIIDL---SMDPPRNCAFVTYEKMESADQAVAELN 94
Query: 72 GFPFYDKPMRIQYSK 86
G +++ ++
Sbjct: 95 GTQVESVQLKVNIAR 109
Score = 48.2 bits (115), Expect = 1e-07
Identities = 22/114 (19%), Positives = 44/114 (38%), Gaps = 5/114 (4%)
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ-ILFLTNLPEETSEMMLSMLF 192
M + S P S P + P L++ + + +L F
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAF 58
Query: 193 NQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+ F ++ + P R+ AFV +E + A L+G ++ + +K++ A+K
Sbjct: 59 SPFGNIIDLSMDPPRN-CAFVTYEKMESADQAVAELNGTQVE-SVQLKVNIARK 110
>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 = 62.0 bits (150), Expect = 3e-12
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ V ++ L+ IFS+FG ++ I+ + QA + + + SA +A S+ G
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDG 106
Query: 73 FPFYDKP--MRIQYSKTDSDVISK 94
Y+ +RI +SK S +
Sbjct: 107 QNIYNACCTLRIDFSKLTSLNVKY 130
Score = 56.6 bits (136), Expect = 3e-10
Identities = 26/115 (22%), Positives = 50/115 (43%), Gaps = 4/115 (3%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLT--NLPEETSEMMLSMLF 192
+ Q +QA++ Q A A AG+ + +L + NL + +L +F
Sbjct: 8 GSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIF 67
Query: 193 NQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT-HAMKISFAK 245
++F K + N A +++ + + + AKL+L G I ++I F+K
Sbjct: 68 SKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 59.8 bits (145), Expect = 5e-12
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
V++ + ++ L +FG I + + + QA V F+++ A NA+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYV---VVMPKKRQALVEFEDVLGACNAVNYAADN 80
Query: 74 PFY--DKPMRIQYSKT 87
Y P + YS +
Sbjct: 81 QIYIAGHPAFVNYSTS 96
Score = 52.5 bits (126), Expect = 2e-09
Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
P + ++ + L + E L +F V ++P + A VEFE+ A A+
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR-QALVEFEDV---LGACNAV 74
Query: 229 HGFKITPT----HAMKISFAK 245
+ H ++++
Sbjct: 75 NYAADNQIYIAGHPAFVNYST 95
>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 = 6e-12
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VY I+S + + FS FGQIM+I + +G +FV F SA +A+ S+ G
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEI---RVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 74 PFYDKPMRIQYSKTDSD 90
++ + K D
Sbjct: 85 TIEGHVVKCYWGKESPD 101
Score = 52.3 bits (126), Expect = 3e-09
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 2/94 (2%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA 211
S P N ++ + ++ ++ F+ F E+R+ P + +
Sbjct: 6 SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YS 64
Query: 212 FVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
FV F +A A ++++G I H +K + K
Sbjct: 65 FVRFSTHESAAHAIVSVNGTTIE-GHVVKCYWGK 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 58.6 bits (142), Expect = 2e-11
Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
V ++ + L + ++G++ ++ L T K G A V+F A ++++
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 71 QGFPFYDKPMRIQYS 85
+ Q
Sbjct: 69 HLTSVMGNIIHAQLD 83
Score = 50.5 bits (121), Expect = 1e-08
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 5/71 (7%)
Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSA 222
Q P + + L + E L + ++ +EV ++ + +A V F + +
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 223 AAKLALHGFKI 233
LH +
Sbjct: 63 ETVKNLHLTSV 73
>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 = 61.2 bits (149), Expect = 3e-11
Identities = 37/265 (13%), Positives = 77/265 (29%), Gaps = 50/265 (18%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
V V ++ + + +Y F G I+ + VA K A + F A A+
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103
Query: 73 FPFYDKPMRIQYSK------------TDSDVISKIKGTFMERPKKVRKQPAPV------- 113
+ + + I + +R
Sbjct: 104 V-VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFA 162
Query: 114 ----EDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQ-QPPVSQPAPPAPMATAGVPEQ 168
+A+ +K + + + L + P+ + G
Sbjct: 163 YIDVTSKEDARYCVEK--------LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR--- 211
Query: 169 PPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQS 221
+ + NL E E +L F F +++ + + + AF+ FEN+ +
Sbjct: 212 ----EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 267
Query: 222 AAAKLALHGFKITPTHAMKISFAKK 246
A L ++ + + +S A K
Sbjct: 268 ERA-LQMNRSLLG-NREISVSLADK 290
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 57.1 bits (138), Expect = 4e-11
Identities = 12/78 (15%), Positives = 28/78 (35%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ + +I + L ++ Q+G + + T V + A AL + GF
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGF 77
Query: 74 PFYDKPMRIQYSKTDSDV 91
+ +++ Y +
Sbjct: 78 QLENFTLKVAYIPDEMAA 95
Score = 51.7 bits (124), Expect = 4e-09
Identities = 16/87 (18%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENE 218
++ VP++ + L + N+P +L L Q+ + V + + V + ++
Sbjct: 5 SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64
Query: 219 MQSAAAKLALHGFKITPTHAMKISFAK 245
Q+ A L+GF++ +K+++
Sbjct: 65 DQARQALDKLNGFQL-ENFTLKVAYIP 90
>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 = 57.5 bits (139), Expect = 4e-11
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
V+V + + ++ L +FG I + + + QA V F+ I SA +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYV---MMMPFKRQALVEFENIDSAKECVTFAADV 74
Query: 74 PFY--DKPMRIQYSK 86
P Y + YS
Sbjct: 75 PVYIAGQQAFFNYST 89
Score = 52.9 bits (127), Expect = 2e-09
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 4/82 (4%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFEN--EMQSAA 223
+ + ++ + L E E L +F V ++P + A VEFEN +
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-QALVEFENIDSAKECV 68
Query: 224 AKLALHGFKITPTHAMKISFAK 245
A I +++
Sbjct: 69 TFAADVPVYIAG-QQAFFNYST 89
>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 = 56.9 bits (138), Expect = 4e-11
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV ++ + ++ + F+ + K+R AFV F A A++++ G
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVE---RVKKIRDYAFVHFSNREDAVEAMKALNGK 74
Query: 74 PFYDKPMRIQYSK 86
P+ + +K
Sbjct: 75 VLDGSPIEVTLAK 87
Score = 53.8 bits (130), Expect = 7e-10
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
+IL++ NL TSE M+ FN R+ R D AFV F N + A AL
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR-DYAFVHFSNREDAVEAMKAL 71
Query: 229 HGFKITPTHAMKISFAKK 246
+G + ++++ AK
Sbjct: 72 NGKVLD-GSPIEVTLAKP 88
>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 = 58.3 bits (141), Expect = 5e-11
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++S ++ +Y +FS+ G I I+ G FV + A A NA+R +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
G D+ +R + +
Sbjct: 102 NGTRLDDRIIRTDWDAGFKE 121
Score = 47.5 bits (113), Expect = 4e-07
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
+ L++ NL T+E + LF++ K++ + ++ FVE+ + +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 224 AKLALHGFKI 233
A ++G ++
Sbjct: 97 AMRYINGTRL 106
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 56.4 bits (137), Expect = 6e-11
Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ ++ K L+ IFS +G IM I F+ F S +A+
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-----IKNAFGFIQFDNPQSVRDAIECESQ 67
Query: 73 FPFYDKPMRIQYSKTDS 89
+ K + ++ S +++
Sbjct: 68 EMNFGKKLILEVSSSNA 84
Score = 36.4 bits (85), Expect = 0.001
Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 4/72 (5%)
Query: 163 AGVPEQPPNQILFLTNLP-EETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQS 221
+ PP LF+ NLP + S+ L +F+ + ++ + F++F+N
Sbjct: 2 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA---FGFIQFDNPQSV 58
Query: 222 AAAKLALHGFKI 233
A
Sbjct: 59 RDAIECESQEMN 70
>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 = 55.7 bits (135), Expect = 9e-11
Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 1/80 (1%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
E L++ L + +E L F QF + + +V + AF++F + A
Sbjct: 7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ-CAFIQFATRQAAEVAA 65
Query: 226 LALHGFKITPTHAMKISFAK 245
I + + + +
Sbjct: 66 EKSFNKLIVNGRRLNVKWGR 85
Score = 55.7 bits (135), Expect = 9e-11
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM-QG 72
+YV + T + L F QFG+I I ++ + AF+ F +A A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTI---TVVQRQQCAFIQFATRQAAEVAAEKSFNK 71
Query: 73 FPFYDKPMRIQYSK 86
+ + +++ +
Sbjct: 72 LIVNGRRLNVKWGR 85
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 56.0 bits (135), Expect = 1e-10
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 2/77 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV ++ L + G + + L R +AF+ + + A+A A+ +QG
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVP--LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGL 79
Query: 74 PFYDKPMRIQYSKTDSD 90
+R+ ++ D
Sbjct: 80 RLGTDTLRVALARQQRD 96
Score = 46.7 bits (111), Expect = 2e-07
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 149 PPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH 208
S P P P +++ NLP + L + G +RL
Sbjct: 3 SGSSGPGSPPGEGA------PLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGP 55
Query: 209 D-IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
AF+ + + + A L G ++ ++++ A++
Sbjct: 56 RRRAFLHYPDSAAAQQAVSCLQGLRLGT-DTLRVALARQ 93
>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 = 55.4 bits (134), Expect = 1e-10
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ ++ K L+ IFS +G IM I F+ F S +A+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----KNAFGFIQFDNPQSVRDAIEXESQ 79
Query: 73 FPFYDKPMRIQYSK 86
+ K + ++ S
Sbjct: 80 EMNFGKKLILEVSS 93
Score = 35.0 bits (81), Expect = 0.003
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 174 LFLTNLPEET-SEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
LF+ NLP + S+ L +F+ + ++ + F++F+N A
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIEXESQEM 81
Query: 233 I 233
Sbjct: 82 N 82
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 28 LYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
+ +FSQ G + + FV F E A AL +M G K +++ ++
Sbjct: 32 ILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91
Query: 87 TDSD 90
T S
Sbjct: 92 TPSS 95
Score = 45.3 bits (108), Expect = 9e-07
Identities = 21/91 (23%), Positives = 45/91 (49%), Gaps = 4/91 (4%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI---AFVE 214
+ ++ + + + L++ NL + +E+++ LF+Q K +++ FVE
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVE 61
Query: 215 FENEMQSAAAKLALHGFKITPTHAMKISFAK 245
F +AAA A++G KI +K+++A
Sbjct: 62 FYEHRDAAAALAAMNGRKIL-GKEVKVNWAT 91
>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 = 55.0 bits (133), Expect = 3e-10
Identities = 16/73 (21%), Positives = 34/73 (46%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV ++ K + +F ++G I DI AFV F++ A +A+ G+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 74 PFYDKPMRIQYSK 86
+ +R+++ +
Sbjct: 85 DYDGYRLRVEFPR 97
Score = 43.1 bits (102), Expect = 6e-06
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENEMQSAA 223
P + +++ NLP + + +F ++ +++ L R AFVEFE+ +
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 76
Query: 224 AKLALHGFKI 233
A G+
Sbjct: 77 AVYGRDGYDY 86
>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 = 54.6 bits (132), Expect = 4e-10
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
L+ +F Q G +++ K T + +G FV F A A++ M Y KP+R+
Sbjct: 32 LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK 91
Query: 85 SKTDSD 90
+ +
Sbjct: 92 ASAHNK 97
Score = 44.2 bits (105), Expect = 2e-06
Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP----NRHD-IAF 212
+ ++ + E+ + +++ L E+ SE +L LF Q + +H F
Sbjct: 2 SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61
Query: 213 VEFENEMQSAAAKLALHGFKI 233
VEF +E + A + K+
Sbjct: 62 VEFLSEEDADYAIKIMDMIKL 82
>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 = 54.5 bits (131), Expect = 5e-10
Identities = 14/89 (15%), Positives = 30/89 (33%), Gaps = 9/89 (10%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYA---IFSQFGQIMDIVALK------TLKMRGQAFVIFK 58
+ N V+V +S + F +FG+I +V + A+V +
Sbjct: 12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71
Query: 59 EIASATNALRSMQGFPFYDKPMRIQYSKT 87
A A++ + + ++ T
Sbjct: 72 RSEDALRAIQCVNNVVVDGRTLKASLGTT 100
Score = 32.9 bits (75), Expect = 0.023
Identities = 8/71 (11%), Positives = 24/71 (33%), Gaps = 11/71 (15%)
Query: 174 LFLTNLPEETSEMML---SMLFNQFPGFKEVRLVPNRHDI--------AFVEFENEMQSA 222
+F+ L + ++ + F +F +V + + A+V + +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 223 AAKLALHGFKI 233
A ++ +
Sbjct: 78 RAIQCVNNVVV 88
>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 = 55.2 bits (133), Expect = 8e-10
Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 8/125 (6%)
Query: 114 EDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQI 173
+ + K+KA + R + +A+ + ++ G I
Sbjct: 18 DGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELE---PGPQRSVEGWI 74
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLAL 228
LF+T++ EE E + F + K + L +R A VE+E Q+ AAK AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 229 HGFKI 233
+G +I
Sbjct: 135 NGAEI 139
Score = 49.8 bits (119), Expect = 7e-08
Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNALRSM 70
++VT I + + F +G+I +I + L +T +G A V ++ A A ++
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 71 QGFPFYDKPMRIQYSKT 87
G + +++ +
Sbjct: 135 NGAEIMGQTIQVDWCFV 151
>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 = 53.7 bits (129), Expect = 1e-09
Identities = 22/109 (20%), Positives = 42/109 (38%), Gaps = 12/109 (11%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ ++ + L + FS+FG + ++ + A V F E A A R +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG---GITAIVEFLEPLEARKAFRHLAYS 69
Query: 74 PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKS 122
F+ P+ ++++ G F P+K Q + AE+ S
Sbjct: 70 KFHHVPLYLEWAP---------IGVFGAAPQKKDSQHEQPAEKAESGPS 109
Score = 47.1 bits (112), Expect = 2e-07
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
++ NLP T + F++F V L A VEF +++ A L
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAY 68
Query: 231 FKI 233
K
Sbjct: 69 SKF 71
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 56.8 bits (136), Expect = 1e-09
Identities = 25/142 (17%), Positives = 54/142 (38%), Gaps = 19/142 (13%)
Query: 97 GTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAP 156
++ + R P P ++ ++K ++ R Q + +++ P + P
Sbjct: 42 APYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWD----PHNDPNA 97
Query: 157 PAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IA 211
+ + LF+ + +T+E L F + K + +V ++ A
Sbjct: 98 ----------QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 212 FVEFENEMQSAAAKLALHGFKI 233
F+E+E+E +A G KI
Sbjct: 148 FIEYEHERDMHSAYKHADGKKI 169
Score = 43.7 bits (102), Expect = 3e-05
Identities = 14/102 (13%), Positives = 35/102 (34%), Gaps = 3/102 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
++V ++ + L F +G I I + ++ K RG AF+ ++ +A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 71 QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
G + + + + + + + R
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADV 206
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 53.5 bits (129), Expect = 1e-09
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V + L IF FG + ++ + G AFV F+E SA A+ + G
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVK-----ILNGFAFVEFEEAESAAKAIEEVHGK 88
Query: 74 PFYDKPMRIQYSK 86
F ++P+ + YSK
Sbjct: 89 SFANQPLEVVYSK 101
Score = 43.4 bits (103), Expect = 5e-06
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ P + E L+ +F F KEV+++ + AFVEFE +A A +HG
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSF 90
Query: 234 TPTHAMKISFAKK 246
+++ ++K
Sbjct: 91 A-NQPLEVVYSKL 102
>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 = 54.9 bits (133), Expect = 1e-09
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ ++S + L +F +I + + K +G A++ FK A A L QG
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIR--LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Query: 74 PFYDKPMRIQYSK 86
+ + + Y+
Sbjct: 160 EIDGRSVSLYYTG 172
Score = 48.4 bits (116), Expect = 2e-07
Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
+++ +++ L S+ D +V ++T R +V F+ AL +
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 74
Query: 72 GFPFYDKPMRIQYSKTDSD 90
G + ++++ K
Sbjct: 75 GLKVFGNEIKLEKPKGRDS 93
Score = 40.7 bits (96), Expect = 1e-04
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSA 222
E LF+ NL S L + ++ ++ +V R +V+FE+ +
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA-EDL 67
Query: 223 AAKLALHGFKI 233
L L G K+
Sbjct: 68 EKALELTGLKV 78
Score = 37.2 bits (87), Expect = 0.002
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 9/84 (10%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP---NRHDIAFVEFENEMQSA 222
L NL +E L +F E+RLV IA++EF++E +
Sbjct: 96 VRAART--LLAKNLSFNITEDELKEVFED---ALEIRLVSQDGKSKGIAYIEFKSEADAE 150
Query: 223 AAKLALHGFKITPTHAMKISFAKK 246
G +I ++ + + +
Sbjct: 151 KNLEEKQGAEID-GRSVSLYYTGE 173
>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 = 52.6 bits (127), Expect = 2e-09
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG- 72
+Y+ ++S L +F + + L G AFV + + A A+ ++ G
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAG---QVLLKSGYAFVDYPDQNWAIRAIETLSGK 67
Query: 73 FPFYDKPMRIQYSK 86
+ K M + YS
Sbjct: 68 VELHGKIMEVDYSV 81
Score = 43.0 bits (102), Expect = 5e-06
Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 1/72 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
L++ NL + L LF +++ AFV++ ++ + A L G
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-GYAFVDYPDQNWAIRAIETLSGKVE 69
Query: 234 TPTHAMKISFAK 245
M++ ++
Sbjct: 70 LHGKIMEVDYSV 81
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 53.3 bits (129), Expect = 4e-09
Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ V ++ + LYA+F G I ++ T G AFV F + A++ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
G +K +++ Y++ +
Sbjct: 66 NGITVRNKRLKVSYARPGGE 85
Score = 46.8 bits (112), Expect = 7e-07
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YVT++ T L IF ++G I+ L+ T + RG AFV + + A A+ ++
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 71 QG--FPFYDKPMRIQY 84
+P+ ++
Sbjct: 152 NNVIPEGGSQPLSVRL 167
Score = 42.2 bits (100), Expect = 3e-05
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L + LP++ ++ L LF R++ + AFV+F +EM S A L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 229 HGFKITPTHAMKISFAKK 246
+G + +K+S+A+
Sbjct: 66 NGITV-RNKRLKVSYARP 82
Score = 39.9 bits (94), Expect = 2e-04
Identities = 14/77 (18%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L++TNLP ++ L +F ++ + ++ ++ +AFV + ++ A AL
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 229 HGFKIT-PTHAMKISFA 244
+ + + + A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
>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 = 51.4 bits (124), Expect = 4e-09
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 26 KSLYAIFSQFGQIMD----IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
K LY FS FG I+ + T +G AF+ F ++ A+ +M G ++P+
Sbjct: 20 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT 79
Query: 82 IQYSK 86
+ Y+
Sbjct: 80 VSYAF 84
Score = 30.6 bits (70), Expect = 0.12
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI------AFVEFENEMQSAAAKLA 227
+F+ NL E E +L F+ F + + D AF+ F + S AA A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 228 LHG 230
++G
Sbjct: 68 MNG 70
>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 = 51.2 bits (123), Expect = 7e-09
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 14 VYVTHISSTDLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
V++ ++++ +KKS + IFS++G++ ++ +G AFV + A A+ G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAG-CSVH----KGYAFVQYSNERHARAAVLGENG 84
Query: 73 FPFYDKPMRIQYSK 86
+ + I +
Sbjct: 85 RVLAGQTLDINMAG 98
Score = 36.6 bits (85), Expect = 0.001
Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 168 QPPNQILFLTNLP-EETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
+ N +F+ NL + + +F+++ + AFV++ NE + AA L
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG---YAFVQYSNERHARAAVL 80
Query: 227 ALHGFKI 233
+G +
Sbjct: 81 GENGRVL 87
>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 = 51.3 bits (123), Expect = 7e-09
Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD------IAFVEFE 216
G N LF+ +P+ + + G +V + + D AFVE+E
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60
Query: 217 NEMQSAAAKLALHGFKITP-THAMKISFAK 245
+ +A A+ L +I H + + +A+
Sbjct: 61 SHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90
Score = 41.7 bits (98), Expect = 2e-05
Identities = 15/96 (15%), Positives = 39/96 (40%), Gaps = 11/96 (11%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL-----KTLKMRGQAFVIFKEIASATNALR 68
+++ I ++ + ++ + + V + +K RG AFV ++ +A A R
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 69 SMQ--GFPFYDKPMRIQYSKT----DSDVISKIKGT 98
+ + + + +++ D DV+ + G
Sbjct: 71 KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106
>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 = 53.1 bits (128), Expect = 8e-09
Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 2/101 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ + K+LY FS FG I+ V +G FV F+ +A A+ M G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 73 FPFYDKPMRIQYSKTDSDVISKIKGTFME-RPKKVRKQPAP 112
D+ + + K+ + +++ E P V
Sbjct: 166 MLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGS 206
Score = 50.0 bits (120), Expect = 1e-07
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
LY FS G I+ I + T + G A+V F++ A A AL +M KP+RI +
Sbjct: 32 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91
Query: 85 SKTDS 89
S+ D
Sbjct: 92 SQRDP 96
Score = 44.6 bits (106), Expect = 6e-06
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 14/100 (14%)
Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD 209
P+ P AP P L++ +L + +E ML F+ +R+ +
Sbjct: 2 PLGSMNPSAP--------SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMIT 53
Query: 210 -----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
A+V F+ + A ++ I ++I ++
Sbjct: 54 RRSLGYAYVNFQQPADAERALDTMNFDVI-KGKPVRIMWS 92
Score = 40.7 bits (96), Expect = 2e-04
Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV--PNRH-DIAFVEFENEMQSAAAKLALHG 230
+F+ NL + L F+ F ++V N FV FE + + A ++G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 231 FKITPTHAMKISFAKK 246
+ + + K
Sbjct: 166 MLLN-DRKVFVGRFKS 180
>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 = 51.2 bits (123), Expect = 1e-08
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
G ILF+T + EE +E + F ++ K + L +R VE+E
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 219 MQSAAAKLALHGFKI 233
++ AA L+G +
Sbjct: 75 KEAQAAMEGLNGQDL 89
Score = 47.4 bits (113), Expect = 3e-07
Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
++VT + ++ ++ F+++G+I +I T ++G V ++ A A+
Sbjct: 25 LFVTGVHEEAT-EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 70 MQGFPFYDKPMRIQYSK 86
+ G +P+ + +
Sbjct: 84 LNGQDLMGQPISVDWCF 100
>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 = 51.3 bits (123), Expect = 1e-08
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 5/94 (5%)
Query: 145 SVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV 204
+ Q PN L + L T+E L +F+++ +V +V
Sbjct: 20 HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79
Query: 205 PNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
++ AFV FEN + AK +G ++
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Score = 49.7 bits (119), Expect = 4e-08
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ V +S ++ L +FS++G I D+ + + + RG AFV F+ + A A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 71 QGFPFYDKPMRIQYSKT 87
G + +R+ +S T
Sbjct: 109 NGMELDGRRIRVDFSIT 125
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 49.7 bits (119), Expect = 1e-08
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 12 NFVYVTHISSTD------LKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASAT 64
+ + V ++ LK ++ IFS+FG+I + + K +G F+ + A A
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 65 NALRSMQGFPFYDK 78
+A+++ G+ +
Sbjct: 62 DAVKNADGYKLDKQ 75
Score = 32.0 bits (73), Expect = 0.032
Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 9/80 (11%)
Query: 171 NQILFLTNLP---EETSEMMLSML---FNQFPGFKEVRLVPNRHD---IAFVEFENEMQS 221
+ ++ + N+P + E + +++ F++F F+E+ + +
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60
Query: 222 AAAKLALHGFKITPTHAMKI 241
A G+K+ H ++
Sbjct: 61 VDAVKNADGYKLDKQHTFRV 80
>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 = 50.3 bits (121), Expect = 1e-08
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+ V +S T ++ L +FS++G I D+ + + + RG AFV F+ + A A
Sbjct: 18 LGVFGLSLYTT-ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 70 MQGFPFYDKPMRIQYSKT 87
G + +R+ +
Sbjct: 77 ANGMELDGRRIRVSGPSS 94
Score = 47.2 bits (113), Expect = 2e-07
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 160 MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
++ PN L + L T+E L +F+++ +V +V ++ AFV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 215 FENEMQSAAAKLALHGFKI 233
FEN + AK +G ++
Sbjct: 64 FENVDDAKEAKERANGMEL 82
>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 = 51.8 bits (125), Expect = 1e-08
Identities = 14/80 (17%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ V ++ ++ ++F G+I ++ T + G FV + + A A+ ++
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
G K +++ Y++ S
Sbjct: 65 NGLRLQTKTIKVSYARPSSA 84
Score = 46.8 bits (112), Expect = 7e-07
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K L +FSQ+G+I+ +V T RG F+ F + A A++ +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 71 QG--FPFYDKPMRIQY 84
G +P+ +++
Sbjct: 151 NGQKPSGATEPITVKF 166
Score = 42.2 bits (100), Expect = 3e-05
Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L + LP+ ++ LF + +LV ++ FV + + + A L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 229 HGFKITPTHAMKISFAKK 246
+G ++ +K+S+A+
Sbjct: 65 NGLRLQT-KTIKVSYARP 81
Score = 38.7 bits (91), Expect = 5e-04
Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L+++ LP+ ++ L LF+Q+ R++ ++ + F+ F+ +++ A L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 229 HGFKIT-PTHAMKISFA 244
+G K + T + + FA
Sbjct: 151 NGQKPSGATEPITVKFA 167
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 50.0 bits (120), Expect = 1e-08
Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 10/93 (10%)
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHD-----IAFVEFE 216
G + L N+ T + + + +RL+ ++ AFV+
Sbjct: 2 GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 217 NEMQSAAAKLALHGFKITPT---HAMKISFAKK 246
+ M ++ L + + FAK
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 42.3 bits (100), Expect = 8e-06
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQ--IMDIVALK---TLKMRGQAFVIFKEIASATN 65
+ + + +I+ + S+ S + + +I +K T + RG AFV A+
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68
Query: 66 ALRSMQG----FPFYDKPMRIQYSK 86
L+ +Q K + + ++K
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAK 93
>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 = 49.7 bits (119), Expect = 1e-08
Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 4/76 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ V ++ + ++ + + + + + AFV A NA++ +
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD----LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63
Query: 74 PFYDKPMRIQYSKTDS 89
F K + +Q TD+
Sbjct: 64 SFRGKDLIVQLQPTDA 79
Score = 48.6 bits (116), Expect = 4e-08
Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 3/72 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
+ + NLP++++ + L + K + N+ AFV N Q+ A H +
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKR-TAFVTLLNGEQAQNAIQMFHQYSF 65
Query: 234 TPTHAMKISFAK 245
+ +
Sbjct: 66 R-GKDLIVQLQP 76
>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 = 50.0 bits (120), Expect = 1e-08
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ ++S + + L +F +I + + K +G A++ FK A A L QG
Sbjct: 19 LLAKNLSFNIT-EDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 73 FPFYDKPMRIQYSK 86
+ + + Y+
Sbjct: 76 AEIDGRSVSLYYTG 89
Score = 38.4 bits (90), Expect = 2e-04
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 10/73 (13%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
+ + L NL +E L +F E+RLV D IA++EF++E
Sbjct: 11 KKVRAARTLLAKNLSFNITEDELKEVFEDA-L--EIRLV--SQDGKSKGIAYIEFKSEAD 65
Query: 221 SAAAKLALHGFKI 233
+ G +I
Sbjct: 66 AEKNLEEKQGAEI 78
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
++ A F+ FG+I D +K T K +G FV F A NA++ M G + +R
Sbjct: 22 AIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 81
Query: 84 YSK 86
++
Sbjct: 82 WAT 84
Score = 40.6 bits (96), Expect = 3e-05
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ +L E + ++ F F + R+V + FV F N+ + A +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 229 HGFKITPTHAMKISFAKK 246
G + ++ ++A +
Sbjct: 69 GGQWLG-GRQIRTNWATR 85
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 49.9 bits (120), Expect = 2e-08
Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
++VT + ++ ++ F+++G+I +I T ++G V ++ A A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 71 QGFPFYDKPMRIQYSK 86
G +P+ + +
Sbjct: 86 NGQDLMGQPISVDWCF 101
Score = 49.2 bits (118), Expect = 3e-08
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAA 223
ILF+T + EE +E + F ++ K + L +R VE+E ++ A
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80
Query: 224 AKLALHGFKI 233
A L+G +
Sbjct: 81 AMEGLNGQDL 90
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 49.5 bits (119), Expect = 2e-08
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V ++ K L F++ G ++ + ++ K +G V F+ A A R M
Sbjct: 11 IFVRNLPFDFT-WKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 72 GFPFYDKPMRIQ 83
G + + ++
Sbjct: 70 GMKLSGREIDVR 81
Score = 29.8 bits (68), Expect = 0.21
Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 7/75 (9%)
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
G +F+ NLP + + ML FN+ + + V+FE+
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIK--MENGKSKGCGVVKFESP 58
Query: 219 MQSAAAKLALHGFKI 233
+ A ++G K+
Sbjct: 59 EVAERACRMMNGMKL 73
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V ++V ++++T ++ L FSQFG++ + K++ AF+ F E A A+
Sbjct: 11 VKV-LFVRNLANTVTEEILEKAFSQFGKLERVK-----KLKDYAFIHFDERDGAVKAMEE 64
Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
M G + + I ++K
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQ 85
Score = 43.0 bits (102), Expect = 5e-06
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 4/86 (4%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQ 220
++G ++LF+ NL +E +L F+QF + V+ + D AF+ F+
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDG 57
Query: 221 SAAAKLALHGFKITPTHAMKISFAKK 246
+ A ++G + ++I FAK
Sbjct: 58 AVKAMEEMNGKDLE-GENIEIVFAKP 82
>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 = 49.1 bits (118), Expect = 2e-08
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI T K RG AFV F+ A A+ +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 71 QGFPFYDKPMRIQYSK 86
+ + +R+ +K
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 41.4 bits (98), Expect = 2e-05
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
++L++ L EE + +L F F ++++ + AFVEFE +AA
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 224 AKLALHGFKI 233
A ++ ++
Sbjct: 65 AIDNMNESEL 74
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ VT++S + L +F FG I I K T + +G AF+ F A A+ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
GF + + ++++K ++
Sbjct: 78 SGFGYDHLILNVEWAKPSTN 97
Score = 49.1 bits (118), Expect = 4e-08
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
N + +TNL E+T E L LF F + L ++ AF+ F
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 221 SAAAKLALHGF 231
+A A + GF
Sbjct: 70 AARAIAGVSGF 80
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 50.6 bits (122), Expect = 3e-08
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 26 KSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
++L F F + + ++T RG FV F A NA+ SMQG +P+RI
Sbjct: 102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Query: 83 QYS 85
++
Sbjct: 162 NWA 164
Score = 49.8 bits (120), Expect = 6e-08
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 28 LYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
L F G I +I + K K AFV + + A AL+++ G + ++I ++
Sbjct: 17 LKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA 76
Query: 86 KTDS 89
Sbjct: 77 FQSQ 80
Score = 41.7 bits (99), Expect = 4e-05
Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
L++ NL + +E +L F ++++ ++++ AFVE+ + A L+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 230 GFKITPTHAMKISFAKK 246
G +I + +KI++A +
Sbjct: 63 GKQI-ENNIVKINWAFQ 78
Score = 38.3 bits (90), Expect = 7e-04
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ +L + L F FP + ++ + FV F ++ + A ++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 229 HGFKITPTHAMKISFAKK 246
G + ++I++A K
Sbjct: 150 QGQDLN-GRPLRINWAAK 166
>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 = 48.8 bits (117), Expect = 4e-08
Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VY+ I ++ + + S G ++++ + T + +G AF+ F+++ S+ +A+R++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 71 QGFPFYDKPMRIQYSK 86
G+ + ++ YS
Sbjct: 65 NGYQLGSRFLKCGYSS 80
Score = 42.2 bits (100), Expect = 8e-06
Identities = 14/69 (20%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAA 224
P+++++L ++P + +E + L + ++++ + AF+EF + SA+A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 225 KLALHGFKI 233
L+G+++
Sbjct: 61 VRNLNGYQL 69
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 49.0 bits (117), Expect = 4e-08
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASAT 64
I V + LKK+L ++FS+ G+++++ + T K +G FV + A
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68
Query: 65 NALRSMQGFPF 75
++S G
Sbjct: 69 KIIKSFHGKRL 79
Score = 33.9 bits (78), Expect = 0.010
Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 5/78 (6%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLA 227
+ + + L+ LF++ + + FVE + + +
Sbjct: 14 APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Query: 228 LHGFKITPTHAMKISFAK 245
HG ++ H + + K
Sbjct: 74 FHGKRLDLKHRLFLYTMK 91
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 48.8 bits (117), Expect = 4e-08
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 4/83 (4%)
Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDI 210
LF++ LP ++ L + K++RLV NR +
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60
Query: 211 AFVEFENEMQSAAAKLALHGFKI 233
A+VE+ENE Q++ A + + G I
Sbjct: 61 AYVEYENESQASQAVMKMDGMTI 83
Score = 48.8 bits (117), Expect = 5e-08
Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++++ + + K+ L I G + D +V + K +G A+V ++ + A+ A+ M
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 72 GFPFYDKPMRIQYSK 86
G + +++ S
Sbjct: 80 GMTIKENIIKVAISN 94
>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 = 48.7 bits (117), Expect = 4e-08
Identities = 14/73 (19%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V ++S+ + L ++F + G++++ ++ AFV ++ A A A+ + G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECD-----VVKDYAFVHMEKEADAKAAIAQLNGK 66
Query: 74 PFYDKPMRIQYSK 86
K + ++ S
Sbjct: 67 EVKGKRINVELST 79
Score = 44.1 bits (105), Expect = 2e-06
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+F+ N+ + L LF + E +V D AFV E E + AA L+G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVK---DYAFVHMEKEADAKAAIAQLNG 65
>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 = 49.3 bits (118), Expect = 4e-08
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY 76
+S D+++ +F++FG + + ++ + G A V F+ A A A++ +G P
Sbjct: 47 VSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD 102
Query: 77 DKPMRIQYSKTDSD 90
+PM IQ + D
Sbjct: 103 GRPMDIQLVASQID 116
Score = 41.2 bits (97), Expect = 3e-05
Identities = 21/114 (18%), Positives = 34/114 (29%), Gaps = 9/114 (7%)
Query: 141 MQALSVQQPPVSQPAPP----APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP 196
M +++ Q P G L ++NL S+ + LF +F
Sbjct: 1 MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60
Query: 197 GFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
K+ + +R A V FE + A G + M I
Sbjct: 61 TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQLVAS 113
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 49.0 bits (117), Expect = 5e-08
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 12 NFVYVTHISSTD------LKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASAT 64
+ + V ++ LK ++ IFS+FG+I + + K +G F+ + A A
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 75
Query: 65 NALRSMQGFPF 75
+A+++ G+
Sbjct: 76 DAVKNADGYKL 86
Score = 32.4 bits (74), Expect = 0.032
Identities = 10/89 (11%), Positives = 31/89 (34%), Gaps = 9/89 (10%)
Query: 167 EQPPNQILFLTNLPEETSEM------MLSMLFNQFPGFKEVRLVPNRHD---IAFVEFEN 217
+ ++ + N+P+ + ++ +F++F F+E+ +
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYAS 70
Query: 218 EMQSAAAKLALHGFKITPTHAMKISFAKK 246
+ A G+K+ H +++
Sbjct: 71 PAHAVDAVKNADGYKLDKQHTFRVNLFTD 99
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 50.8 bits (122), Expect = 5e-08
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV + + ++F FG+I + T K +G F+ +++ S+ +A+ SM
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 71 QGFPFYDKPMRIQYS 85
F + +R+ +
Sbjct: 188 NLFDLGGQYLRVGKA 202
Score = 48.1 bits (115), Expect = 4e-07
Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 3/94 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VYV I + ++ F+ FG I I T+K +G AFV ++ +A AL M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 71 QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPK 104
+ +++ I E
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
Score = 40.8 bits (96), Expect = 2e-04
Identities = 16/105 (15%), Positives = 33/105 (31%), Gaps = 20/105 (19%)
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFN 193
QQM + + A M+ +++ ++ E E + F
Sbjct: 6 SMTGGQQMG----RGSAAQRQGALAIMSR-----------VYVGSIYYELGEDTIRQAFA 50
Query: 194 QFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
F K + + + AFVE+E + A ++ +
Sbjct: 51 PFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML 95
Score = 40.4 bits (95), Expect = 2e-04
Identities = 14/87 (16%), Positives = 32/87 (36%), Gaps = 5/87 (5%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
S P+ E +++ ++ ++ S+ + +F F K L +
Sbjct: 106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165
Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
F+E+E S A +++ F +
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDL 192
>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 = 48.3 bits (116), Expect = 5e-08
Identities = 10/73 (13%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+++ ++ ++ + ++F Q+G++++ ++ FV ++ +A +A+R++ +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECD-----IIKNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 74 PFYDKPMRIQYSK 86
+ + ++ SK
Sbjct: 66 KLHGVNINVEASK 78
Score = 43.0 bits (102), Expect = 4e-06
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP E +E + LF Q+ E ++ N FV E++ + A LH +K+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAEDAIRNLHHYKL 67
>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 = 49.1 bits (117), Expect = 5e-08
Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 8/109 (7%)
Query: 141 MQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE 200
M + S P P++++ + LP + +E + L F
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60
Query: 201 VRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPT----HAMKISFAK 245
+ ++ ++ AF+E E AA ++ + + I F+
Sbjct: 61 LLMLKGKNQ-AFIEMNTE---EAANTMVNYYTSVTPVLRGQPIYIQFSN 105
Score = 47.2 bits (112), Expect = 3e-07
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+++ + + + ++ FG++ ++ LK + QAF+ +A +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNL---LMLKGKNQAFIEMNTEEAANTMVNYYTSV 90
Query: 74 PFY--DKPMRIQYSK 86
+P+ IQ+S
Sbjct: 91 TPVLRGQPIYIQFSN 105
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 50.2 bits (120), Expect = 5e-08
Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
+ V+++ + +F++FG + + ++ + G A V F+ A A A++ +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 72 GFPFYDKPMRIQYSKTDSD 90
G P +PM IQ + D
Sbjct: 151 GVPLDGRPMDIQLVASQID 169
Score = 41.8 bits (98), Expect = 4e-05
Identities = 19/104 (18%), Positives = 30/104 (28%), Gaps = 5/104 (4%)
Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN 206
+ P G L ++NL S+ + LF +F K+ + +
Sbjct: 64 KPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123
Query: 207 RHD----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
R A V FE + A G + M I
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLD-GRPMDIQLVAS 166
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ ++++S S +++L +F + I + + K +G AF+ F A AL S
Sbjct: 18 LVLSNLSYSAT-EETLQEVFEKATFI-KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 73 FPFYDKPMRIQYSK 86
+ +R++
Sbjct: 76 REIEGRAIRLELQG 89
Score = 44.6 bits (106), Expect = 1e-06
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
++ L L+NL +E L +F + ++ VP + AF+EF +
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEK---ATFIK-VPQNQNGKSKGYAFIEFASFED 65
Query: 221 SAAAKLALHGFKI 233
+ A + + +I
Sbjct: 66 AKEALNSCNKREI 78
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 28 LYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
LY +F Q G + I + K + FV FK S + A+ + G Y +P+ +
Sbjct: 33 LYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV 89
Score = 41.8 bits (99), Expect = 1e-05
Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 6/82 (7%)
Query: 158 APMATAGVPEQPPNQI--LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IA 211
++G+ +F+ NL E +L LF Q +V + +R
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
Query: 212 FVEFENEMQSAAAKLALHGFKI 233
FV F++ + A L+G ++
Sbjct: 61 FVCFKHPESVSYAIALLNGIRL 82
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 48.9 bits (117), Expect = 6e-08
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 11/84 (13%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
++V + +S+ F Q G I T K++G+A V F + S
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 63 ATNALRSMQGFPFYDKPMRIQYSK 86
A A+ G F P+++ ++
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFAT 93
Score = 42.8 bits (101), Expect = 1e-05
Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 14/93 (15%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRHD-----IAFV 213
+ N +F+ L E + ++ F Q G + L +R A V
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 214 EFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
F++ + AA G + + + +K+SFA +
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSG-NPIKVSFATR 94
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEF 215
G ILF+T++ EE E + F + K + L +R A VE+
Sbjct: 16 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 216 ENEMQSAAAKLALHGFKI 233
E Q+ AAK AL+G +I
Sbjct: 76 ETHKQALAAKEALNGAEI 93
Score = 48.4 bits (116), Expect = 8e-08
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
++VT I + + F +G+I +I T +G A V ++ A A ++
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 71 QGFPFYDKPMRIQYSK 86
G + +++ +
Sbjct: 89 NGAEIMGQTIQVDWCF 104
>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 = 48.0 bits (115), Expect = 8e-08
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V +IS T + L A F ++G +++ ++ AFV + A A+R +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECD-----IVKDYAFVHMERAEDAVEAIRGLDNT 67
Query: 74 PFYDKPMRIQYSK 86
F K M +Q S
Sbjct: 68 EFQGKRMHVQLST 80
Score = 42.6 bits (101), Expect = 6e-06
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 4/70 (5%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQ 220
++G + ++ + N+ + L F ++ E +V D AFV E
Sbjct: 1 GSSGSSGKASTKL-HVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAED 56
Query: 221 SAAAKLALHG 230
+ A L
Sbjct: 57 AVEAIRGLDN 66
>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 = 48.0 bits (115), Expect = 9e-08
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
+P+ PP FL NLP + +E + F VRL + + EFE+
Sbjct: 14 LPKSPPY-TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDL 71
Query: 219 MQSAAAKLALHGFKI 233
S + L+L+ +
Sbjct: 72 -DSLLSALSLNEESL 85
Score = 34.9 bits (81), Expect = 0.004
Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 27 SLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
S+ F I + + +++G + F+++ S +AL S+ ++ +R+
Sbjct: 35 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV 92
Query: 83 QYSK 86
+
Sbjct: 93 DVAD 96
>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 = 48.0 bits (115), Expect = 9e-08
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
+P+ PP FL NLP + +E + F VRL + + EFE+
Sbjct: 10 LPKSPPY-TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDL 67
Query: 219 MQSAAAKLALHGFKI 233
S + L+L+ +
Sbjct: 68 -DSLLSALSLNEESL 81
Score = 36.9 bits (86), Expect = 7e-04
Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 27 SLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
S+ F I + + +++G + F+++ S +AL S+ +K +R+
Sbjct: 31 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV 88
Query: 83 QYSK 86
+
Sbjct: 89 DVAD 92
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 48.1 bits (115), Expect = 9e-08
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRSM-QGFPFYDKP 79
++ + +FS FG++ + K T RG FV F A A ++ Y +
Sbjct: 29 QREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR 88
Query: 80 MRIQYSKTDSDVIS 93
+ ++++ ++ V S
Sbjct: 89 LVLEWADSEVTVQS 102
Score = 43.8 bits (104), Expect = 3e-06
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI------AFVE 214
++ VP++ + + N+P + ++ + LF+ F K VRL FV+
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 215 FENEMQSAAAKLAL-HGFKI 233
F + + A AL H +
Sbjct: 65 FITKQDAKKAFNALCHSTHL 84
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 49.5 bits (119), Expect = 9e-08
Identities = 14/92 (15%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
+YV +I ++++ F+ ++ ++A++ + + AF+ F+ + T
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 66 ALRSMQGFPFYDKPMRIQYSK--TDSDVISKI 95
A+ + G F + ++I+ K+
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKL 97
Score = 49.2 bits (118), Expect = 1e-07
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 11/83 (13%)
Query: 6 AHICVTNF-VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIA 61
+ + Y+ + + + FG + +K T +G AF + +I
Sbjct: 95 HKLFIGGLPNYLND-------DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 147
Query: 62 SATNALRSMQGFPFYDKPMRIQY 84
A+ + G DK + +Q
Sbjct: 148 VTDQAIAGLNGMQLGDKKLLVQR 170
Score = 44.9 bits (107), Expect = 3e-06
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ LP ++ + L F K LV + AF E+ + + A L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 229 HGFKI 233
+G ++
Sbjct: 157 NGMQL 161
Score = 41.4 bits (98), Expect = 7e-05
Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 11/70 (15%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP---------NRHD-IAFVEFENEMQSAA 223
L++ N+P +E + FN + P N+ AF+EF +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV-DETT 65
Query: 224 AKLALHGFKI 233
+A G
Sbjct: 66 QAMAFDGIIF 75
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 48.0 bits (115), Expect = 1e-07
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNAL 67
V+N + +S D+++ +F++FG + + ++ + G A V F+ A A A+
Sbjct: 34 VSNLDF--GVSDADIQE----LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAM 87
Query: 68 RSMQGFPFYDKPMRIQYSKT 87
+ G P +PM IQ +
Sbjct: 88 KQYNGVPLDGRPMNIQLVTS 107
Score = 38.0 bits (89), Expect = 3e-04
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 4/77 (5%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFE 216
G L ++NL S+ + LF +F K+ + +R A V FE
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFE 78
Query: 217 NEMQSAAAKLALHGFKI 233
+ + A +G +
Sbjct: 79 RKADALKAMKQYNGVPL 95
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+ V +++ T SL +F ++G++ D+ + T RG AFV F + A +A +
Sbjct: 16 LKVDNLTYRTS-PDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 70 MQGFPFYDKPMRIQYSK 86
M G + +R+Q ++
Sbjct: 75 MDGAELDGRELRVQVAR 91
Score = 46.1 bits (110), Expect = 5e-07
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
P+ L + NL TS L +F ++ +V + H AFV F +
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 221 SAAAKLALHGFKI 233
+ A+ A+ G ++
Sbjct: 68 AQDAEAAMDGAEL 80
>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 = 49.5 bits (119), Expect = 1e-07
Identities = 17/89 (19%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----TLKMRGQAFVIFKEIASATNALR 68
++V + T +K L +F Q+G + +I L+ + +G FV F +A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 69 SMQG---FPFYDKPMRIQYSKTDSDVISK 94
++ P P++++ + ++ + +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVE 94
Score = 46.8 bits (112), Expect = 9e-07
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
+++ IS + + +FS FGQI + L+ RG AFV F A A A+++M
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Query: 72 G---FPFYDKPMRIQY 84
PM +++
Sbjct: 158 QAQTMEGCSSPMVVKF 173
Score = 42.2 bits (100), Expect = 3e-05
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-------IAFVEFENEMQSAAAKL 226
+F+ +P SE L LF Q+ E+ ++ +R FV F + A+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 227 ALHGFKITPTHA 238
ALH K+ P
Sbjct: 66 ALHNMKVLPGMH 77
Score = 39.1 bits (92), Expect = 4e-04
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
LF+ + ++ +E + ++F+ F +E R++ R AFV F + A A
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 228 LHGFKITP--THAMKISFA 244
+H + + M + FA
Sbjct: 156 MHQAQTMEGCSSPMVVKFA 174
>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 = 50.1 bits (119), Expect = 1e-07
Identities = 16/151 (10%), Positives = 42/151 (27%), Gaps = 11/151 (7%)
Query: 26 KSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
+ L G + DI+ +K + +G A V AS+ + + + +
Sbjct: 83 EDLTEAVHSLG-VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 141
Query: 80 MRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQ 139
+ +++ + ++ + ++ + + + + R A
Sbjct: 142 PVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPG 201
Query: 140 QMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
+ P PP P
Sbjct: 202 GDRF----PGPAGPGGPPPPFPAGQTHHHHH 228
Score = 47.0 bits (111), Expect = 1e-06
Identities = 16/119 (13%), Positives = 32/119 (26%), Gaps = 8/119 (6%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQ 194
+ + P V L++ NL T++ L+ +
Sbjct: 32 GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91
Query: 195 F--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
E++ NR + A V +E S L ++ ++ K
Sbjct: 92 LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG-QNPVVTPVNK 149
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 47.7 bits (114), Expect = 1e-07
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV ++ + K L FS +G + V + G AFV F++ A +A+R + G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRT-VWIAR-NPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 74 PFYDKPMRIQYSK 86
+R++ S
Sbjct: 61 VICGSRVRVELST 73
Score = 43.8 bits (104), Expect = 3e-06
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
+++ NL + L F+ + + V + N AFVEFE+ + A L G I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
>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 = 47.9 bits (114), Expect = 1e-07
Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
+ P+++L + LP E +E + L F + ++ ++ AF+E E AA
Sbjct: 10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ-AFLELATE---EAAI 65
Query: 226 LALHGFKITPT----HAMKISFAKK 246
++ + + I ++
Sbjct: 66 TMVNYYSAVTPHLRNQPIYIQYSNH 90
Score = 47.5 bits (113), Expect = 1e-07
Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+++ + + + A+ FG++ +I LK + QAF+ +A +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNI---LMLKGKNQAFLELATEEAAITMVNYYSAV 74
Query: 74 PFY--DKPMRIQYSK 86
+ ++P+ IQYS
Sbjct: 75 TPHLRNQPIYIQYSN 89
>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 = 47.3 bits (113), Expect = 1e-07
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 11/82 (13%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
++V + +S+ F Q G I T K++G+A V F + S
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 63 ATNALRSMQGFPFYDKPMRIQY 84
A A+ G F P+++ +
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSF 97
Score = 39.2 bits (92), Expect = 1e-04
Identities = 19/92 (20%), Positives = 34/92 (36%), Gaps = 14/92 (15%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRHD-----IAF 212
N +F+ L E + ++ F Q G + L +R A
Sbjct: 8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 67
Query: 213 VEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
V F++ + AA G + + + +K+SFA
Sbjct: 68 VSFDDPPSAKAAIDWFDGKEFSG-NPIKVSFA 98
>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 = 47.7 bits (114), Expect = 1e-07
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+++ H+ + L +F FG ++ + +T + FV + SA A++SM
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 71 QGFPFYDKPMRIQYSK 86
GF K +++Q +
Sbjct: 88 NGFQIGMKRLKVQLKR 103
Score = 40.8 bits (96), Expect = 5e-05
Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 6/100 (6%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
S + A E P LF+ +LP+E + L +F F ++ ++
Sbjct: 6 SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 65
Query: 210 ---IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
FV ++N + + AA +++GF+I +K+ +
Sbjct: 66 SKCFGFVSYDNPVSAQAAIQSMNGFQIG-MKRLKVQLKRS 104
>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 = 47.6 bits (113), Expect = 2e-07
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 3/78 (3%)
Query: 168 QPPNQILFLTN--LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
Q L + N L S L + + + + PN+ +F + +S A
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-YSFARYRTTEESKRAY 80
Query: 226 LALHGFKITPTHAMKISF 243
+ L+G ++ KI+
Sbjct: 81 VTLNGKEVVDDLGQKITL 98
Score = 45.3 bits (107), Expect = 1e-06
Identities = 7/65 (10%), Positives = 22/65 (33%), Gaps = 3/65 (4%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
V + + + L + + G + ++ + +F ++ + A ++ G
Sbjct: 29 VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN---KPYSFARYRTTEESKRAYVTLNG 85
Query: 73 FPFYD 77
D
Sbjct: 86 KEVVD 90
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 2/78 (2%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
LF+ NLP + +E + LF ++ EV + ++ F+ E + AK+ L
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-FGFIRLETRTLAEIAKVEL 71
Query: 229 HGFKITPTHAMKISFAKK 246
+ +++ FA
Sbjct: 72 DNMPLR-GKQLRVRFACH 88
Score = 46.5 bits (111), Expect = 3e-07
Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 11/84 (13%)
Query: 14 VYV----THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
++V I+ +++K +F ++G+ ++ K +G F+ + A A
Sbjct: 18 LFVGNLPPDITEEEMRK----LFEKYGKAGEV---FIHKDKGFGFIRLETRTLAEIAKVE 70
Query: 70 MQGFPFYDKPMRIQYSKTDSDVIS 93
+ P K +R++++ + + S
Sbjct: 71 LDNMPLRGKQLRVRFACHSASLTS 94
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 47.3 bits (112), Expect = 2e-07
Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 2/85 (2%)
Query: 6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATN 65
A + V+N Y +S +L++ L F++ G++ + + +A V + + A
Sbjct: 10 ADVQVSNIDY--RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIG 67
Query: 66 ALRSMQGFPFYDKPMRIQYSKTDSD 90
A+ S+ + K + + + S
Sbjct: 68 AVNSLHRYKIGSKKILVSLATGASG 92
Score = 27.7 bits (61), Expect = 1.5
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 174 LFLTNLPEETSE----MMLSMLFNQFPGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLA 227
+ ++N+ S +L F + K V L P+ A V+ EN + A +
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS 71
Query: 228 LHGFKITPTHAMKISFAK 245
LH +KI + + +S A
Sbjct: 72 LHRYKIG-SKKILVSLAT 88
>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 = 47.6 bits (114), Expect = 2e-07
Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
+++ ++ S D K+LY FS FG I+ V +G FV F+ +A A+ M
Sbjct: 8 IFIKNLDKSID-NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 72 GFPFYDKPMRIQYSKTDSDVISKIKGTFME 101
G D+ + + K+ + +++ E
Sbjct: 67 GMLLNDRKVFVGRFKSRKEREAELGARAKE 96
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
+F+ NL + L F+ F ++V + + FV FE + + A ++G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 231 FKI 233
+
Sbjct: 68 MLL 70
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 47.7 bits (114), Expect = 2e-07
Identities = 27/114 (23%), Positives = 46/114 (40%), Gaps = 6/114 (5%)
Query: 137 QQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP 196
Q ALS + A A E P LF+ +LP+E ++ L+ F F
Sbjct: 6 QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG 65
Query: 197 GFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
++ ++ FV F+N + A A++GF++ T +K+ K
Sbjct: 66 NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG-TKRLKVQLKK 118
Score = 47.4 bits (113), Expect = 2e-07
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+++ H+ L + F FG ++ + +T + FV F SA A+++M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 71 QGFPFYDKPMRIQYSK 86
GF K +++Q K
Sbjct: 103 NGFQVGTKRLKVQLKK 118
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 48.2 bits (115), Expect = 2e-07
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI T K RG AFV F+ A A+ +M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 71 QGFPFYDKPMRI 82
+ + +R+
Sbjct: 126 NESELFGRTIRV 137
Score = 44.8 bits (106), Expect = 3e-06
Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 5/98 (5%)
Query: 141 MQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKE 200
A + + + ++L++ L EE + +L F F +
Sbjct: 33 SVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITD 92
Query: 201 VRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
+++ + AFVEFE +AAA ++ ++
Sbjct: 93 IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 130
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI T K RG AFV F+ A A+ +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 71 QGFPFYDKPMRIQYSK 86
+ + +R+ +K
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 41.8 bits (99), Expect = 1e-05
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
++ ++L++ L EE + +L F F ++++ + AFVEF
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 216 ENEMQSAAAKLALHGFKI 233
E +AAA ++ ++
Sbjct: 62 ELAEDAAAAIDNMNESEL 79
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
++V ++ ++ + +F FG I + L+ +G AFV F A A+ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 72 G---FPFYDKPMRIQYSKTDSD 90
G P + ++++ TD +
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 43.8 bits (104), Expect = 3e-06
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFE 216
++ ++ LF+ L ++ SE + LF F E ++ AFV+F
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64
Query: 217 NEMQSAAAKLALHGFKITP--THAMKISFAKK 246
+ ++ AA ALHG + P + ++ + FA
Sbjct: 65 SHTEAQAAIHALHGSQTMPGASSSLVVKFADT 96
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 47.8 bits (114), Expect = 2e-07
Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 5/87 (5%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
Q + P+ L + NL TS L +F ++ +V + +R+
Sbjct: 28 QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87
Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
AFV F ++ + A A+ G +
Sbjct: 88 SRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Score = 44.0 bits (104), Expect = 4e-06
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ V +++ +L +F ++G++ D+ + T + RG AFV F + A +A+ +M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 71 QGFPFYDKPMRIQYSKTD 88
G + +R+Q ++
Sbjct: 110 DGAVLDGRELRVQMARYG 127
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----- 209
+ + +++G +P ++ + N+P S + F + +
Sbjct: 2 SSGSSGSSSG---KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
Query: 210 IAFVEFENEMQSAAAKLALHGFKI 233
A V FE+ ++ AA + L+ I
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPI 82
Score = 41.5 bits (98), Expect = 2e-05
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 3/66 (4%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
+ F + I V LK G+A V F+ AT A+ + P + ++
Sbjct: 29 IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK 88
Query: 82 IQYSKT 87
+ +
Sbjct: 89 LSGPSS 94
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 8/93 (8%)
Query: 161 ATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
++ + + I LF+ +P E L LF +F E+ ++ +R AF+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 215 FENEMQSAAAKLALHGFKITP--THAMKISFAK 245
+ + A+ ALH K P +++ A
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
Score = 46.9 bits (112), Expect = 3e-07
Identities = 20/84 (23%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+++ I +K L +F +FG+I ++ LK T +G AF+ + E SA A ++
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 71 QG---FPFYDKPMRIQYSKTDSDV 91
P ++P++++ + ++S
Sbjct: 76 HEQKTLPGMNRPIQVKPADSESRG 99
>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 = 47.8 bits (114), Expect = 2e-07
Identities = 28/121 (23%), Positives = 48/121 (39%), Gaps = 8/121 (6%)
Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
Q L+ Q +QQ Q P P+ N L + +P E+ L
Sbjct: 3 QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN--LMVNYIPTTVDEVQLR 60
Query: 190 MLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
LF ++ + V++V +R FV+F++ + A L+GF I +K++ A
Sbjct: 61 QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI-LNKRLKVALA 119
Query: 245 K 245
Sbjct: 120 A 120
Score = 42.8 bits (101), Expect = 1e-05
Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+ V +I +T + L +F ++G I + +T + RG FV F+ +SA A+ +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 71 QGFPFYDKPMRIQYSK 86
GF +K +++ +
Sbjct: 105 NGFNILNKRLKVALAA 120
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 49.0 bits (116), Expect = 2e-07
Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 3/83 (3%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
+ + H+ ++ + +FS+ G I I + ++ + FV FK A+A A +
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRI---RYVESKNCGFVKFKYQANAEFAKEA 198
Query: 70 MQGFPFYDKPMRIQYSKTDSDVI 92
M + + + +
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTGL 221
Score = 43.6 bits (102), Expect = 2e-05
Identities = 14/86 (16%), Positives = 34/86 (39%), Gaps = 11/86 (12%)
Query: 157 PAPMATAGVPEQPPNQILFLTNLPEETS---------EMMLSMLFNQFPGFKEVRLVPNR 207
M G + N+ L++ + + E + +F++ +R V ++
Sbjct: 121 REDMGGIG-SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK 179
Query: 208 HDIAFVEFENEMQSAAAKLALHGFKI 233
+ FV+F+ + + AK A+ +
Sbjct: 180 N-CGFVKFKYQANAEFAKEAMSNQTL 204
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 46.9 bits (112), Expect = 3e-07
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 9/86 (10%)
Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEM 219
+P +PP ++ NLP T + + +F + VRLV ++ +VEF+
Sbjct: 10 LPTEPPY-TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEV- 66
Query: 220 QSAAAKLALHGFKITPTHAMKISFAK 245
S L G + ++++ A+
Sbjct: 67 DSLKEALTYDGALLG-DRSLRVDIAE 91
Score = 34.6 bits (80), Expect = 0.005
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
+ AIF I + ++ T K +G +V F E+ S AL + G D+ +R+
Sbjct: 31 DIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD 88
Query: 84 YSK 86
++
Sbjct: 89 IAE 91
>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 = 3e-07
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV ++ + K L F +G + + + G AFV F++ A +A+R + G
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR--NPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 74 PFYDKPMRIQYSK 86
+R++ S
Sbjct: 134 TLCGCRVRVELSN 146
Score = 46.8 bits (111), Expect = 6e-07
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
P + +++ NL ++ L F + + V + N AFVEFE+ +A A L
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130
Query: 229 HGFKI 233
G +
Sbjct: 131 DGRTL 135
>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 = 46.9 bits (112), Expect = 3e-07
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 2/91 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
V+V ++ K L +FS G ++ DI+ K K RG V F++ A A+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 72 GFPFYDKPMRIQYSKTDSDVISKIKGTFMER 102
G +D+PM ++ + ++
Sbjct: 78 GQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108
Score = 34.2 bits (79), Expect = 0.008
Identities = 11/90 (12%), Positives = 31/90 (34%), Gaps = 5/90 (5%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFE 216
++ + +F+ NL + L +F+ ++ ++ V FE
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFE 64
Query: 217 NEMQSAAAKLALHGFKITPTHAMKISFAKK 246
+++ A +G + M + ++
Sbjct: 65 QSIEAVQAISMFNGQLLF-DRPMHVKMDER 93
>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 = 47.9 bits (114), Expect = 3e-07
Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 5/86 (5%)
Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD 209
+ + L + NL TS L +F ++ +V + +R+
Sbjct: 49 TKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 108
Query: 210 -----IAFVEFENEMQSAAAKLALHG 230
AFV F ++ + A A+ G
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDG 134
Score = 44.8 bits (106), Expect = 4e-06
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+ V +++ T +L +F ++G++ D+ + T + RG AFV F + A +A+ +
Sbjct: 73 LKVDNLTYRTS-PDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 70 MQGFPFYDKPMRIQYSKT 87
M G + +R+Q ++
Sbjct: 132 MDGAVLDGRELRVQMARY 149
>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 = 46.0 bits (110), Expect = 4e-07
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV----ALKTLKMRGQAFVIFKEIASATNALRS 69
V++ ++ K + IFS +G+I I + +G A+V F+ A AL+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 70 MQGFPFYDKPMRIQYSK 86
M G + +
Sbjct: 67 MDGGQIDGQEITATAVL 83
Score = 43.7 bits (104), Expect = 2e-06
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 6/66 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
+ + L ++ + +F+ + K + + R A+VEFEN ++ A
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 228 LHGFKI 233
+ G +I
Sbjct: 67 MDGGQI 72
>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 = 46.6 bits (111), Expect = 4e-07
Identities = 27/102 (26%), Positives = 51/102 (50%), Gaps = 15/102 (14%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSM 70
+++ ++ T+ +K L A+F + G I +++ +K T K RG AF+ F+ A A NA + M
Sbjct: 10 LFIGGLNRETN-EKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 71 QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
G + K ++++ +K S + R+ PA
Sbjct: 69 NGKSLHGKAIKVEQAKKPS-----------FQSGGRRRPPAS 99
Score = 40.0 bits (94), Expect = 8e-05
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
LF+ L ET+E ML +F + EV L+ +R AF+ FEN + A ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 230 GFKI 233
G +
Sbjct: 70 GKSL 73
>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 = 46.6 bits (111), Expect = 4e-07
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
+ A F+ FG+I D +K T K +G FV F A NA++ M G + +R
Sbjct: 31 DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 90
Query: 84 YSK 86
++
Sbjct: 91 WAT 93
Score = 40.8 bits (96), Expect = 4e-05
Identities = 16/95 (16%), Positives = 36/95 (37%), Gaps = 10/95 (10%)
Query: 161 ATAGVPEQPPNQI----LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IA 211
++G Q + +F+ +L E + + F F + R+V +
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 212 FVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
FV F N+ + A + G + ++ ++A +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLG-GRQIRTNWATR 94
>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 = 45.6 bits (109), Expect = 5e-07
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+YV + + + L IF FG+I +IV +K T + +G F+ F + A AL
Sbjct: 8 LYVGSLHFNIT-EDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 70 MQGFPFYDKPMRIQYSK 86
+ GF +PMR+ +
Sbjct: 67 LNGFELAGRPMRVGHVT 83
Score = 41.4 bits (98), Expect = 2e-05
Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
+ L++ +L +E ML +F F + L+ + F+ F + +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 224 AKLALHGFKI 233
A L+GF++
Sbjct: 63 ALEQLNGFEL 72
>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 = 45.3 bits (108), Expect = 6e-07
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 14 VYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
VYV+++ T+ LY IFS++G+++ + +K T K +G AF++F + SA N R
Sbjct: 19 VYVSNLPFSLTN--NDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 69 SMQGFPFYDKPMRIQYS 85
++ + + ++ +
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 42.2 bits (100), Expect = 1e-05
Identities = 11/73 (15%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQ 220
P ++++NLP + L +F+++ +V ++ ++ +AF+ F ++
Sbjct: 11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 221 SAAAKLALHGFKI 233
+ A++ ++
Sbjct: 71 AQNCTRAINNKQL 83
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 46.8 bits (111), Expect = 7e-07
Identities = 14/107 (13%), Positives = 32/107 (29%), Gaps = 9/107 (8%)
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFN 193
Q+ + P + P +G+ + +++ + T++ L +
Sbjct: 20 FQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAA--VYVGSFSWWTTDQQLIQVIR 77
Query: 194 QF--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKI 233
E++ NR + A V +E L G +
Sbjct: 78 SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL 124
Score = 44.5 bits (105), Expect = 5e-06
Identities = 20/106 (18%), Positives = 35/106 (33%), Gaps = 15/106 (14%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNA 66
VYV S T + L + G D+V LK + +G A V+ S
Sbjct: 58 VYVGSFSWWTT-DQQLIQVIRSIGVY-DVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 67 LRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAP 112
L + G + + ++ + + F + +K P
Sbjct: 116 LELLPGKVLNGEKVDVRPAT------RQNLSQFEAQARKRECVRVP 155
>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 = 44.8 bits (107), Expect = 7e-07
Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+Y+ + + L + +G+I+ A+ T K +G FV F ++A A+ ++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 71 QGFPFYDKPMR 81
+ + +
Sbjct: 68 KASGVQAQMAK 78
Score = 39.4 bits (93), Expect = 7e-05
Identities = 11/65 (16%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L++ L T++ L L + + + ++ FV+F++ + A AL
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 229 HGFKI 233
+
Sbjct: 68 KASGV 72
>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 = 45.4 bits (108), Expect = 8e-07
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 160 MATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFE 216
++ + + L ++N+P + L +F QF +V ++ N FV FE
Sbjct: 4 GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 63
Query: 217 NEMQSAAAKLALHGFKI 233
N + A+ LHG +
Sbjct: 64 NSADADRAREKLHGTVV 80
Score = 40.7 bits (96), Expect = 3e-05
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V++I L +F QFG+I+D+ + +G FV F+ A A A +
Sbjct: 18 LHVSNIPFRFR-DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 72 GFPFYDKPMRIQYSK 86
G + + + +
Sbjct: 77 GTVVEGRKIEVNNAT 91
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 45.6 bits (108), Expect = 8e-07
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+++ + + + ++ FG++ ++ LK + QAF+ +A +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNL---LMLKGKNQAFIEMNTEEAANTMVNYYTSV 75
Query: 74 P--FYDKPMRIQYSK 86
+P+ IQ+S
Sbjct: 76 TPVLRGQPIYIQFSN 90
Score = 45.2 bits (107), Expect = 9e-07
Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
P++++ + LP + +E + L F + ++ ++ AF+E E AA
Sbjct: 13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ-AFIEMNTE---EAANTM 68
Query: 228 LHGFKITPT----HAMKISFAK 245
++ + + I F+
Sbjct: 69 VNYYTSVTPVLRGQPIYIQFSN 90
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 48.7 bits (115), Expect = 9e-07
Identities = 37/235 (15%), Positives = 66/235 (28%), Gaps = 76/235 (32%)
Query: 8 ICVTNFV---YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASAT 64
VT+F+ THIS +L ++ ++ K L R Q T
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTP-----DEVKSLLL-KYLDCRPQDL---PREVLTT 325
Query: 65 NALR-SMQGFPFYDKPMRIQYSKT-DSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKS 122
N R S+ D K + D ++ I + + V +PAE
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN-----------VLEPAE---- 370
Query: 123 KKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFL--TNLP 180
++ LSV P +P +L L ++
Sbjct: 371 --------------YRKMFDRLSVFPPSAH------------IPTI----LLSLIWFDVI 400
Query: 181 EETSEMML------SMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
+ +++ S++ Q + + I + ALH
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQPKEST-ISI----PSIYL----ELKVKLENEYALH 446
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+YV ++ + L FS FG I V ++ + +G FV F AT A+ M G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 73 FPFYDKPMRIQYSK 86
KP+ + ++
Sbjct: 78 RIVATKPLYVALAQ 91
Score = 32.6 bits (75), Expect = 0.028
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 9/66 (13%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI------AFVEFENEMQSAAAKLA 227
L++ NL + + L F+ F +++ + FV F + ++ A
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM---MEGGRSKGFGFVCFSSPEEATKAVTE 74
Query: 228 LHGFKI 233
++G +
Sbjct: 75 MNGRIV 80
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
L +FS +G + ++ T K +G AFV F A A + G F + + +
Sbjct: 24 DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL 83
Query: 84 YSK 86
S
Sbjct: 84 PST 86
Score = 44.5 bits (106), Expect = 1e-06
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 5/72 (6%)
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
G + LF+ NL +SE L LF+ + E+ + AFV F
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 219 MQSAAAKLALHG 230
+ A + G
Sbjct: 61 EHAVKAYAEVDG 72
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 3/68 (4%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
+ F + I V LK G+A V F+ AT A+ + P + ++
Sbjct: 29 IDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK 88
Query: 82 IQYSKTDS 89
+ S
Sbjct: 89 LVLGSGPS 96
Score = 43.8 bits (104), Expect = 3e-06
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 155 APPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----- 209
+ + A++G +P I+ + N+P S + F + +
Sbjct: 2 SSGSSGASSG---KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58
Query: 210 IAFVEFENEMQSAAAKLALHGFKI 233
A V FE+ ++ AA + L+ I
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPI 82
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQI------MDIVALKTLKMRGQAFVIFKEIASATNA 66
+++ +++ ST +++L +FS+ G I L G FV +K+ A A
Sbjct: 8 LFIKNLNFSTT-EETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 67 LRSMQGFPFYDKPMRIQYSK 86
L+ +QG + ++ S+
Sbjct: 67 LKQLQGHTVDGHKLEVRISE 86
Score = 44.2 bits (105), Expect = 2e-06
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--------AFVEFENEMQSAAAK 225
LF+ NL T+E L +F++ K + ++ FVE++ Q+ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 226 LALHGFKITPTHAMKISFAKK 246
L G + H +++ +++
Sbjct: 68 KQLQGHTVD-GHKLEVRISER 87
>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 = 44.5 bits (106), Expect = 2e-06
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
++ LF+ L +T+E L +F+++ EV +V +R FV F
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 216 ENEMQSAAAKLALHGFKI 233
EN + A +A++G +
Sbjct: 62 ENIDDAKDAMMAMNGKSV 79
Score = 44.2 bits (105), Expect = 2e-06
Identities = 26/81 (32%), Positives = 47/81 (58%), Gaps = 5/81 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
++V +S T+ ++SL +FS++GQI ++V +K T + RG FV F+ I A +A+ +
Sbjct: 15 LFVGGLSFDTN-EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
M G + +R+ + SD
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSD 94
>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 = 43.6 bits (104), Expect = 2e-06
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 26 KSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
++L F F + + ++T RG FV F A NA+ SMQG +P+RI
Sbjct: 16 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75
Query: 83 QYSK 86
++
Sbjct: 76 NWAA 79
Score = 40.6 bits (96), Expect = 3e-05
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ +L + L F FP + ++ + FV F ++ + A ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 229 HGFKITPTHAMKISFAKK 246
G + ++I++A K
Sbjct: 64 QGQDLN-GRPLRINWAAK 80
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAF 212
+ ++ P++ LF+ L E+T+E L F+ R+V +R F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGF 58
Query: 213 VEFENEMQSAAAKLALHGFKI 233
V+F +E + AAK A+ +I
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEI 79
Score = 38.8 bits (91), Expect = 2e-04
Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
++V +S T +++L F + + +T +G FV F A A +M+
Sbjct: 18 LFVKGLSEDTT-EETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 73 FPFYDKPMRIQYSK 86
+ + ++K
Sbjct: 77 GEIDGNKVTLDWAK 90
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 11/80 (13%), Positives = 27/80 (33%), Gaps = 6/80 (7%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFV 213
+ + +P P + + + +P E + F+ V L+ + V
Sbjct: 3 SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLV 61
Query: 214 EFENEMQSAAAKLALHGFKI 233
+F + + A L + +
Sbjct: 62 KFLSPQDTFEA-LKRNRMLM 80
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
V+ +++ + L FS G++ D+ + + + +G A+V F EI S A+ +
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 71 QGFPFYDKPMRIQYSKT 87
G P+ +Q S+
Sbjct: 87 TGQRLLGVPIIVQASQA 103
Score = 40.4 bits (95), Expect = 7e-05
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 148 QPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR 207
+ PV +P PE+ + +F L L F+ ++VR++ +R
Sbjct: 8 KSPVREPVDNLS------PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61
Query: 208 HD-----IAFVEFENEMQSAAAKLALHGFKI 233
+ IA+VEF QS + L G ++
Sbjct: 62 NSRRSKGIAYVEFCEI-QSVPLAIGLTGQRL 91
>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 = 45.8 bits (109), Expect = 3e-06
Identities = 12/72 (16%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V ++ + ++ +F ++G+ ++ + RG F+ + A A + G
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEV---FINRDRGFGFIRLESRTLAEIAKAELDGT 81
Query: 74 PFYDKPMRIQYS 85
+P+RI+++
Sbjct: 82 ILKSRPLRIRFA 93
Score = 44.3 bits (105), Expect = 1e-05
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 166 PEQPPNQI--LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAA 223
E+ Q LF+ NLP + +E LF ++ EV + +R F+ E+ +
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-FGFIRLESRTLAEI 73
Query: 224 AKLALHGFKITPTHAMKISFAKK 246
AK L G + ++I FA
Sbjct: 74 AKAELDGTILKS-RPLRIRFATH 95
Score = 40.1 bits (94), Expect = 3e-04
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQ 71
+ V ++S + L FSQFG + V + + G+ FV F A AL
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158
Query: 72 G 72
Sbjct: 159 D 159
Score = 35.1 bits (81), Expect = 0.013
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 4/86 (4%)
Query: 165 VPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQ 220
+ L + NL S +L F+QF ++ +V + FVEF +
Sbjct: 90 IRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPP 149
Query: 221 SAAAKLALHGFKITPTHAMKISFAKK 246
+ A T + +
Sbjct: 150 ARKALERCGDGAFLLTTTPRPVIVEP 175
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 43.6 bits (102), Expect = 4e-06
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
K L + ++G+++++V K G A V F + +A A+++ G D P++I +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSS--KKPGTAVVEFATVKAAELAVQNEVGLV--DNPLKISW 86
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 43.6 bits (103), Expect = 4e-06
Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 11/84 (13%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-----------TLKMRGQAFVIFKEIAS 62
+YV ++ + L F Q G + T K +G A V +++ +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 63 ATNALRSMQGFPFYDKPMRIQYSK 86
A A+ G F +++ ++
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLAR 101
Score = 37.8 bits (88), Expect = 6e-04
Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 15/103 (14%)
Query: 158 APMATAGVPEQPP-NQILFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRH 208
++G P++ N +++ L + + L+ F Q G + + ++
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 209 D-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
A V +E+ + AA G +K+S A+K
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG-SKLKVSLARK 102
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 43.2 bits (102), Expect = 7e-06
Identities = 14/100 (14%), Positives = 36/100 (36%), Gaps = 6/100 (6%)
Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF 195
A MQ + + P +A ++ + +++ N+ ++ L F+
Sbjct: 1 AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 196 PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHG 230
+ ++ ++ A++EF S A +A+
Sbjct: 61 GSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDE 99
Score = 37.8 bits (88), Expect = 5e-04
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VYV ++ + L A FS G I I L + +G A++ F E S A+ +M
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97
Query: 71 QGFPFYDKPMRIQYSKT 87
F + +++ +T
Sbjct: 98 DETVFRGRTIKVLPKRT 114
>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 = 42.6 bits (101), Expect = 8e-06
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 27 SLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
L S+ D+ + +T R +V F+ AL + G + ++++
Sbjct: 33 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 91
Query: 85 SK 86
K
Sbjct: 92 PK 93
Score = 40.7 bits (96), Expect = 4e-05
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ NL S L + ++ ++ V + +V+FE+ A L L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKA-LEL 77
Query: 229 HGFKITPTHAMKISFAKK 246
G K+ + +K+ K
Sbjct: 78 TGLKVF-GNEIKLEKPKG 94
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition
motif, C-terminal helix, N-terminal helix, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 42.2 bits (100), Expect = 1e-05
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 11 TNFVYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATN 65
V+V +I +T+ + L IFS+ G ++ + T K +G F +++ +A +
Sbjct: 8 LRSVFVGNIPYEATE--EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 66 ALRSMQGFPFYDKPMRIQYSK 86
A+R++ G F + +R+ +
Sbjct: 66 AMRNLNGREFSGRALRVDNAA 86
Score = 37.6 bits (88), Expect = 5e-04
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 16/86 (18%)
Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---- 208
PA + + +F+ N+P E +E L +F++ RLV +R
Sbjct: 1 DPAVDRSLRS-----------VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP 49
Query: 209 -DIAFVEFENEMQSAAAKLALHGFKI 233
F E++++ + +A L+G +
Sbjct: 50 KGYGFCEYQDQETALSAMRNLNGREF 75
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 6/73 (8%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
P+ + + L LP S+ + F+ +P AFV+F ++
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69
Query: 221 SAAAKLALHGFKI 233
+ A L H +I
Sbjct: 70 AEKA-LKKHKERI 81
Score = 31.6 bits (72), Expect = 0.055
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALR 68
K+ + FS + + + L + G+AFV F A AL+
Sbjct: 29 KEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 18/80 (22%), Positives = 26/80 (32%), Gaps = 10/80 (12%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEF 215
AP G P + + ++ LP S L + + +V R VEF
Sbjct: 3 APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEF 58
Query: 216 EN--EMQSAAAKLALHGFKI 233
+M A K L K
Sbjct: 59 VRKEDMTYAVRK--LDNTKF 76
Score = 38.3 bits (89), Expect = 3e-04
Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 12/81 (14%)
Query: 14 VYVTHISST----DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V V+ + + DLK + G + + G V F T A+R
Sbjct: 19 VVVSGLPPSGSWQDLKD----HMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRK 70
Query: 70 MQGFPFYDKPMRIQYSKTDSD 90
+ F Y + D
Sbjct: 71 LDNTKFRSHEGETAYIRVKVD 91
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 41.9 bits (99), Expect = 1e-05
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+YV + + + L IF FG+I I + T + +G F+ F + A AL
Sbjct: 29 LYVGSLHFNIT-EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 70 MQGFPFYDKPMRIQYSK 86
+ GF +PM++ +
Sbjct: 88 LNGFELAGRPMKVGHVT 104
Score = 41.1 bits (97), Expect = 2e-05
Identities = 15/101 (14%), Positives = 31/101 (30%), Gaps = 16/101 (15%)
Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF 195
+ + A L++ +L +E ML +F F
Sbjct: 2 GHHHHHHSHMAAAMANNLQKGSAGPMR-----------LYVGSLHFNITEDMLRGIFEPF 50
Query: 196 PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGF 231
+ ++L+ + F+ F + + A L+GF
Sbjct: 51 GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGF 91
>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 = 42.5 bits (100), Expect = 2e-05
Identities = 12/92 (13%), Positives = 27/92 (29%), Gaps = 6/92 (6%)
Query: 146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP 205
+ Q + + + + LP + +E + F+ V +
Sbjct: 21 MASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEI 79
Query: 206 NRHD----IAFVEFENEMQSAAAKLALHGFKI 233
A VEF ++ AA ++ +
Sbjct: 80 GPDGRVTGEADVEFATHEEAVAA-MSKDRANM 110
Score = 26.0 bits (57), Expect = 8.8
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 25 KKSLYAIFSQFGQI-MDIVALKTLKMRGQAFVIFKEIASATNAL 67
+ +Y FS + + I ++ G+A V F A A+
Sbjct: 60 ENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM 103
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 41.9 bits (99), Expect = 2e-05
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
L ++N+P + L +F QF +V ++ N FV FEN + A+ LHG
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 231 FKI 233
+
Sbjct: 92 TVV 94
Score = 38.5 bits (90), Expect = 3e-04
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V++I L +F QFG+I+D+ + +G FV F+ A A A +
Sbjct: 32 LHVSNIPFRFR-DPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90
Query: 72 GFPFYDKPMRIQYSK 86
G + + + +
Sbjct: 91 GTVVEGRKIEVNNAT 105
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKE-VRLVPNRHD----IAFVEFENEMQSAA 223
+TN+P ++M + P + V ++ + + A V+F+NE +
Sbjct: 13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72
Query: 224 AKLALHGFKI 233
+ LH K+
Sbjct: 73 S-ERLHRKKL 81
Score = 33.9 bits (78), Expect = 0.013
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 4/78 (5%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNAL 67
++T+I + K + + V + + GQA V FK A +
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74
Query: 68 RSMQGFPFYDKPMRIQYS 85
R + + +
Sbjct: 75 R-LHRKKLNGREAFVHVV 91
>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 = 41.5 bits (97), Expect = 2e-05
Identities = 15/92 (16%), Positives = 36/92 (39%), Gaps = 8/92 (8%)
Query: 20 SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
S ++ + ++F + + K+ K + + F SA +A + F K
Sbjct: 19 SESETRAKFESLFRTYDKDTTFQYFKSFK---RVRINFSNPLSAADARLRLHKTEFLGKE 75
Query: 80 MRIQYSKTDSDVISKIKGTFMERPKKVRKQPA 111
M++ +++T I + + P + P+
Sbjct: 76 MKLYFAQT-----LHIGSSHLAPPNPDKSGPS 102
Score = 28.4 bits (63), Expect = 0.75
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 9/83 (10%)
Query: 169 PPNQILFLTNLPEE-----TSEMMLSMLFNQFPGFKEVRLVPNRHDI-AFVEFENEMQSA 222
+ L ++ + LF + K+ + + F N + +A
Sbjct: 3 SGSSGLIACVANDDVFSESETRAKFESLFRTYD--KDTTFQYFKSFKRVRINFSNPLSAA 60
Query: 223 AAKLALHGFKITPTHAMKISFAK 245
A+L LH + MK+ FA+
Sbjct: 61 DARLRLHKTEFL-GKEMKLYFAQ 82
>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 = 41.0 bits (97), Expect = 3e-05
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 7/64 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKL 226
L++ NL T++ L+ + E++ NR + A V +E S
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 227 ALHG 230
L
Sbjct: 64 LLPK 67
Score = 36.8 bits (86), Expect = 7e-04
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 11/81 (13%)
Query: 14 VYVTHIS--STDLKKSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATN 65
+Y+ +++ +TD + L G + DI+ +K + +G A V AS+
Sbjct: 4 LYIGNLTWWTTD--EDLTEAVHSLG-VNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
Query: 66 ALRSMQGFPFYDKPMRIQYSK 86
+ + + + + S
Sbjct: 61 LMDLLPKRELHGQNPVVTPSN 81
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 41.1 bits (97), Expect = 3e-05
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 3/78 (3%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALR 68
TN +Y++++ + ++ L + FGQ++ I+ + RG F + +
Sbjct: 26 TN-LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84
Query: 69 SMQGFPFYDKPMRIQYSK 86
G P ++
Sbjct: 85 HFNGKFIKTPPGVSAPTE 102
Score = 34.9 bits (81), Expect = 0.005
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
L+++NLP E L + F R++ + F E+ + A +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 230 GFKI 233
G I
Sbjct: 88 GKFI 91
>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 = 41.0 bits (96), Expect = 5e-05
Identities = 17/87 (19%), Positives = 27/87 (31%), Gaps = 6/87 (6%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD- 209
S +P + ++L LP E + F + + + +
Sbjct: 6 SGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK 65
Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
FVEF NE AA L H +
Sbjct: 66 ATGEGFVEFRNEADYKAA-LCRHKQYM 91
Score = 30.6 bits (69), Expect = 0.16
Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
K + F + + D + + K G+ FV F+ A AL ++ ++
Sbjct: 39 NKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQ 97
Query: 82 I 82
+
Sbjct: 98 V 98
>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 = 40.6 bits (95), Expect = 5e-05
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 11/75 (14%)
Query: 163 AGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF--PGFKEVRLVPNRHDIAFVEFEN--E 218
+ N++ ++ LP S L + + +V R VEF +
Sbjct: 8 GPPSRRSENRV-VVSGLPPSGSWQDLKDHMREAGDVCYADVY----RDGTGVVEFVRKED 62
Query: 219 MQSAAAKLALHGFKI 233
M A K L K
Sbjct: 63 MTYAVRK--LDNTKF 75
Score = 39.4 bits (92), Expect = 1e-04
Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
V V+ + + + L + G + + G V F T A+R +
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNT 73
Query: 74 PFYDKPMRIQYSKTDSD 90
F Y + D
Sbjct: 74 KFRSHEGETAYIRVKVD 90
>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 = 39.5 bits (93), Expect = 7e-05
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
KK L F++FG+++D T + RG F++FK+ AS L
Sbjct: 25 KKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 40.3 bits (94), Expect = 8e-05
Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 8/75 (10%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFP---GFKEVRLVPNRHD----IAFVEFENE 218
PE ++ L LP S + + G V + R AFVE E+E
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE 71
Query: 219 MQSAAAKLALHGFKI 233
A L +
Sbjct: 72 DDVKLA-LKKDRESM 85
>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 = 40.2 bits (94), Expect = 8e-05
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 6/87 (6%)
Query: 152 SQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-- 209
S + + + + L LP ++ + F+ +P +
Sbjct: 23 SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82
Query: 210 ---IAFVEFENEMQSAAAKLALHGFKI 233
AFV+F ++ + A L H +I
Sbjct: 83 ITGEAFVQFASQELAEKA-LGKHKERI 108
Score = 28.3 bits (63), Expect = 1.1
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNAL 67
FV + + K+ + FS + + + L K+ G+AFV F A AL
Sbjct: 42 DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101
Query: 68 R 68
Sbjct: 102 G 102
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 39.4 bits (93), Expect = 9e-05
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+++ N+ + L F+ V ++ ++ A++EF ++ +S LAL
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLAL 67
Query: 229 HG 230
Sbjct: 68 DE 69
Score = 38.3 bits (90), Expect = 2e-04
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ + L A F G + + L + +G A++ F + S +L ++
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 71 QGFPFYDKPMRIQYSKT 87
F + +++ +T
Sbjct: 68 DESLFRGRQIKVIPKRT 84
>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 = 39.6 bits (93), Expect = 9e-05
Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 11/84 (13%)
Query: 14 VYVTHIS-STDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
V++ ++S ++ +++L + QFG + + + T +G AF F +A L +
Sbjct: 18 VFIRNLSFDSE-EEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 70 MQ------GFPFYDKPMRIQYSKT 87
G + +++ + T
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVT 100
Score = 38.9 bits (91), Expect = 2e-04
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 161 ATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVE 214
++G+P +F+ NL ++ E L + QF K VR+V + AF +
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63
Query: 215 FENEMQSAAAKLAL 228
F + AA+ L
Sbjct: 64 FMTQ---EAAQKCL 74
>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 = 39.5 bits (92), Expect = 1e-04
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 16 VTHIS----STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
V HI +L+ L + FG I + + L +AF+ A A+
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL---ILNKINEAFIEMATTEDAQAAVDYYT 73
Query: 72 GFP--FYDKPMRIQYSK 86
P + KP+R+ S+
Sbjct: 74 TTPALVFGKPVRVHLSQ 90
Score = 31.4 bits (71), Expect = 0.080
Identities = 8/60 (13%), Positives = 19/60 (31%), Gaps = 2/60 (3%)
Query: 166 PEQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA 224
+++ + + L L F ++ ++ AF+E + AA
Sbjct: 10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE-AFIEMATTEDAQAA 68
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 39.3 bits (92), Expect = 1e-04
Identities = 12/69 (17%), Positives = 21/69 (30%), Gaps = 6/69 (8%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAA 224
+ + LP +E + F+ V + A VEF + AA
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71
Query: 225 KLALHGFKI 233
+A +
Sbjct: 72 -MAKDKANM 79
Score = 26.6 bits (59), Expect = 3.8
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 25 KKSLYAIFSQFGQI-MDIVALKTLKMRGQAFVIFKEIASATNAL 67
+ +Y FS + + I ++ G+A V F A A+
Sbjct: 29 ENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM 72
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 38.2 bits (90), Expect = 1e-04
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
++ L F QFG++ + + ++ T + RG FV F + A L
Sbjct: 14 QEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 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 = 40.2 bits (95), Expect = 1e-04
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 4/75 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
++V I K FSQ+G I+D + T + RG FV + +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QN 148
Query: 71 QGFPFYDKPMRIQYS 85
+ F D+ + I+ +
Sbjct: 149 KFIDFKDRKIEIKRA 163
Score = 38.3 bits (90), Expect = 7e-04
Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQ 71
+ +L F ++G + D+ +K T + RG F+ F++ +S +++
Sbjct: 17 EDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
Score = 36.0 bits (84), Expect = 0.004
Identities = 8/73 (10%), Positives = 23/73 (31%), Gaps = 6/73 (8%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
EQ +F+ + + F+Q+ + +L+ ++ FV +++
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-D 140
Query: 221 SAAAKLALHGFKI 233
+
Sbjct: 141 AVDRVCQNKFIDF 153
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 13/77 (16%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--------IVALKTLKMRGQAFVIFKEIASATN 65
+YV +I ++++ F+ ++ ++A++ + + AF+ F+ + T
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 66 ALRSMQGFPFYDKPMRI 82
A+ + G F + ++I
Sbjct: 69 AM-AFDGIIFQGQSLKI 84
Score = 35.5 bits (82), Expect = 0.002
Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 11/70 (15%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN--------RHD--IAFVEFENEMQSAA 223
L++ N+P +E + FN + P D AF+EF +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV-DETT 67
Query: 224 AKLALHGFKI 233
+A G
Sbjct: 68 QAMAFDGIIF 77
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 38.9 bits (91), Expect = 2e-04
Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 14/98 (14%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
VY+ + + GQ+++I +TL +G FV+F I SA +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETP 72
Query: 72 GFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
G + + + I K + + + RKQ
Sbjct: 73 GQKYKETDLLI-----------LFKDDYFAKKNEERKQ 99
Score = 37.8 bits (88), Expect = 4e-04
Identities = 9/64 (14%), Positives = 22/64 (34%), Gaps = 5/64 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
+++ P + + + +++ H FV F++ +SA +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI-ESAKKFVETP 72
Query: 230 GFKI 233
G K
Sbjct: 73 GQKY 76
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 37.8 bits (89), Expect = 2e-04
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
+ + F QFG++ D + + T + RG FV F+
Sbjct: 13 VEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 39.2 bits (91), Expect = 2e-04
Identities = 9/61 (14%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFP--FYDKPMRIQYS 85
+ + +G+I + + ++M+ QAF+ + A + F + +++ S
Sbjct: 43 VLKLAEPYGKIKNYI---LMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99
Query: 86 K 86
+
Sbjct: 100 E 100
Score = 37.2 bits (86), Expect = 7e-04
Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 9/102 (8%)
Query: 150 PVSQPAPPAPMATAGVPEQPPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRH 208
S P +Q +++ L+NLP S+ + L + K L+ +
Sbjct: 4 GSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS 63
Query: 209 DIAFVEFENEMQSAAAKLALHGFKITPT----HAMKISFAKK 246
AF+E E A + +K+ ++K
Sbjct: 64 -QAFIEMETR---EDAMAMVDHCLKKALWFQGRCVKVDLSEK 101
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 38.4 bits (90), Expect = 2e-04
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 26 KSLYAIFSQ-FGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD-KPMR 81
LY F + + +V +T +G FV F + AL QG KP+R
Sbjct: 24 GMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR 83
Query: 82 IQYS 85
+ +
Sbjct: 84 LSVA 87
Score = 31.9 bits (73), Expect = 0.046
Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQ-FPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLAL 228
LF+ +L + + ML F + +P + ++V ++ + FV+F +E++ A
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 229 HGFKITPTHAMKISFAKK 246
G + +++S A
Sbjct: 72 QGAVGLGSKPVRLSVAIP 89
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 12/71 (16%)
Query: 26 KSLYAIFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNALRSMQGFPF---- 75
+ F+ G+ ++++K T G FV F ++A+A L + G P
Sbjct: 24 NFISRAFATMGE--TVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT 81
Query: 76 YDKPMRIQYSK 86
K ++ Y+
Sbjct: 82 PAKRFKLNYAT 92
Score = 36.9 bits (86), Expect = 7e-04
Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 9/90 (10%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD-----IAFVEFENEM 219
L++ +L E +S F V+++ NR FVEF +
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 220 QSAAAKLALHGFKI---TPTHAMKISFAKK 246
+ ++G + TP K+++A
Sbjct: 64 TAEKCLHKINGKPLPGATPAKRFKLNYATY 93
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
V+V + + L FSQ+G +MD+ K R AFV F + A +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCGEDL 63
Score = 31.4 bits (72), Expect = 0.052
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-DIAFVEFENEMQSAAAKLALHGFK 232
+F+ + +E L F+Q+ +V +P AFV F ++ A L
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDV-FIPKPFRAFAFVTFADD--QIAQSLCGEDLI 64
Query: 233 I 233
I
Sbjct: 65 I 65
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM,
RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 37.6 bits (88), Expect = 4e-04
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 32 FSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQ 71
FS FG+++ + K T +G FV F E + +
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH 78
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+++L + FSQ+G+++D V +K T + RG FV FK+ L S
Sbjct: 30 QETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 37.3 bits (87), Expect = 5e-04
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 1/60 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
+F++ P LS F F V + ++ A VE + + A L+ +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDV-GAREAVLSQSQHSL 69
Score = 35.4 bits (82), Expect = 0.003
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 4/56 (7%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-AFVIFKEIASATNALR 68
V+V+ L F FG + +V K +G A V ++ + L
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVV---MDKDKGVFAIVEMGDVGAREAVLS 63
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 38.0 bits (89), Expect = 5e-04
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
SL F FG I + V + T K RG FV + A+A A +
Sbjct: 31 DASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
>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 = 36.7 bits (86), Expect = 5e-04
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
++V +S ++ + F FG++ I T K RG F+ FKE +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
Score = 26.3 bits (59), Expect = 2.6
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
+F+ L +T E + F F + + L + F+ F+ E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 7/77 (9%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFE 216
++G + + L P +E + +R+V N H FV+F
Sbjct: 1 GSSGSSGTTCH-TVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFS 58
Query: 217 NEMQSAAAKLALHGFKI 233
NE + A L + +
Sbjct: 59 NEEEVKQA-LKCNREYM 74
Score = 25.3 bits (56), Expect = 7.0
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 2/64 (3%)
Query: 25 KKSLYAIFSQFGQI-MDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
+K++ + + + IV G FV F AL + + +
Sbjct: 24 EKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEVF 82
Query: 84 YSKT 87
K+
Sbjct: 83 REKS 86
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 37.2 bits (86), Expect = 9e-04
Identities = 16/89 (17%), Positives = 25/89 (28%), Gaps = 9/89 (10%)
Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQF----PGFKEVRLVPNRH 208
A + I+ + LP + + F Q G + + V
Sbjct: 5 SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64
Query: 209 D----IAFVEFENEMQSAAAKLALHGFKI 233
AFV F E + A L H +
Sbjct: 65 GRPTGDAFVLFACEEYAQNA-LRKHKDLL 92
Score = 27.5 bits (61), Expect = 2.3
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTL------KMRGQAFVIFKEIASATNALR 68
+ + A F Q I + G AFV+F A NALR
Sbjct: 37 AEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALR 86
>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 = 36.8 bits (85), Expect = 0.001
Identities = 10/53 (18%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 35 FGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
+G++ ++ L + G +V F+ A A+ + F +P+ + S
Sbjct: 51 YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
>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 = 36.0 bits (84), Expect = 0.001
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
V+V + + L F Q+G+++D+ K R AFV F + A +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--PFRAFAFVTFADDKVAQSLCGEDL 69
Score = 26.8 bits (60), Expect = 2.3
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 2/60 (3%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
+F+ E+ + L F Q+ +V + AFV F ++ A L I
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADD--KVAQSLCGEDLII 71
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNAL 67
++ L F QFG++ + + ++ T + RG FV F + A L
Sbjct: 39 QEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 37.7 bits (88), Expect = 0.001
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 4/75 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
++V I + L F Q+G+I I + + K RG AFV F + S +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 165
Query: 71 QGFPFYDKPMRIQYS 85
+ ++ +
Sbjct: 166 KYHTVNGHNCEVRKA 180
Score = 36.9 bits (86), Expect = 0.002
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
+SL + F Q+G + D V ++ T + RG FV + + A+ +
Sbjct: 27 DESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Score = 33.8 bits (78), Expect = 0.027
Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%)
Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--- 209
+ A + +I F+ + E+T E L F Q+ + + ++ +R
Sbjct: 87 KRAVSREDSQRPGAHLTVKKI-FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK 145
Query: 210 --IAFVEFENEMQSAAAKLALHGFKI 233
AFV F++ S + +
Sbjct: 146 RGFAFVTFDDH-DSVDKIVIQKYHTV 170
Score = 28.8 bits (65), Expect = 1.1
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 160 MATAGVPEQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFV 213
M+ + P++P LF+ L ET++ L F Q+ + ++ + + FV
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 214 EFENEMQSAAAKLALHGFKI 233
+ ++ A + K+
Sbjct: 61 TYAT-VEEVDAAMNARPHKV 79
>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 = 36.5 bits (85), Expect = 0.001
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
++SL + Q+G++ D V ++ + + RG FV F +A A+ +
Sbjct: 41 EESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
>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 = 38.5 bits (89), Expect = 0.002
Identities = 46/313 (14%), Positives = 85/313 (27%), Gaps = 127/313 (40%)
Query: 20 SSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKE---------------IASAT 64
+ + L AIF GQ G F+E I +
Sbjct: 148 AVGEGNAQLVAIFG--GQ-------------GNTDDYFEELRDLYQTYHVLVGDLIKFSA 192
Query: 65 NALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQP----APV------- 113
L + + + +++ +++ ++E P + P+
Sbjct: 193 ETLSELIRTTLDAEKV---FTQG-LNILE-----WLENPSNTPDKDYLLSIPISCPLIGV 243
Query: 114 --------------EDPAEAKKSKKKAAKEQARLMQA------------QQQQMQALSV- 146
P E + K A L+ A +A++V
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL 303
Query: 147 -------QQ--PPVSQPA------------PPAPM-ATAGVPEQPPNQILFLTN--LPEE 182
+ P S P P+PM + + + ++ + TN LP
Sbjct: 304 FFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAG 363
Query: 183 TSEMMLSMLFN---QF-----P----GFK-EVRLV--PNRHDIAFVEFENEMQSAAAKLA 227
++ +S L N P G +R P+ D + + F KL
Sbjct: 364 -KQVEIS-LVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSER------KLK 415
Query: 228 L-HGF-KIT-PTH 237
+ F + P H
Sbjct: 416 FSNRFLPVASPFH 428
Score = 34.3 bits (78), Expect = 0.035
Identities = 36/211 (17%), Positives = 62/211 (29%), Gaps = 79/211 (37%)
Query: 1 MNII----LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVI 56
+I LAH VT + + +L+ L G +V A I
Sbjct: 238 CPLIGVIQLAHYVVT--AKLLGFTPGELRSYLKGAT---GHSQGLVT---------AVAI 283
Query: 57 --------FKEIASATNAL--------RSMQGFPFYDKPMRI-QYSK------------- 86
F A+ R + +P P I + S
Sbjct: 284 AETDSWESFFVSVR--KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 87 ---TDSDVISKIKGTFMERP--KKV-------RKQPAPVEDPAEA--------KKSKKKA 126
T V + T P K+V K V P ++ +K+K +
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN-LVVSGPPQSLYGLNLTLRKAKAPS 400
Query: 127 AKEQARLMQAQQQ---QMQALSVQQPPVSQP 154
+Q+R+ ++++ + L PV+ P
Sbjct: 401 GLDQSRIPFSERKLKFSNRFL-----PVASP 426
Score = 34.3 bits (78), Expect = 0.041
Identities = 25/115 (21%), Positives = 40/115 (34%), Gaps = 36/115 (31%)
Query: 141 MQALSVQQPPVS------QPAPPAPMATAGVPEQPPNQIL---FLTNLPEETSEMMLSM- 190
M A S + P++ + P A+ + Q L F LPE T
Sbjct: 1 MDAYSTR--PLTLSHGSLEHVLLVPTASFFIASQ-----LQEQFNKILPEPTEGFAADDE 53
Query: 191 ------LFNQFPGFKEVRLVPNRHD-------IAFVEFE------NEMQSAAAKL 226
L +F G+ + P++ + EFE N++ + AAKL
Sbjct: 54 PTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL 108
Score = 30.0 bits (67), Expect = 0.76
Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 21/88 (23%)
Query: 27 SL--YAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYD----KP 79
SL YA + +M I ++ + RG + A R G Y P
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVVFYRGMT------MQVA--VPRDELGRSNYGMIAINP 1814
Query: 80 MRIQYSKTDSDV------ISKIKGTFME 101
R+ S + + + K G +E
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVE 1842
Score = 27.7 bits (61), Expect = 4.6
Identities = 13/96 (13%), Positives = 28/96 (29%), Gaps = 37/96 (38%)
Query: 142 QALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPG---- 197
A + + P + + A + E ++ L F G
Sbjct: 128 TARIMAKRPFDKKSNSA----------------LFRAVGEGNAQ-----LVAIFGGQGNT 166
Query: 198 ---FKEVRLVPNRHDI--AFVE-FENEMQSAAAKLA 227
F+E+R + + V ++ +A L+
Sbjct: 167 DDYFEELR---DLYQTYHVLVGDL---IKFSAETLS 196
>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 = 37.1 bits (85), Expect = 0.002
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASAT 64
+ VY+ + + GQ+++I +TL +G FV+F I SA
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 164
Query: 65 NALRSMQGFPFYDKPMRIQYSK 86
+ + G + + + I +
Sbjct: 165 KFVETP-GQKYKETDLLILFKD 185
Score = 33.7 bits (76), Expect = 0.035
Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 7/86 (8%)
Query: 153 QPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---- 208
P+ P P T N+ +++ P + + + +++ H
Sbjct: 91 SPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 150
Query: 209 DIAFVEFENEMQSAAAKLALHGFKIT 234
FV F++ +AK +
Sbjct: 151 GSIFVVFDSI---ESAKKFVETPGQK 173
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 36.0 bits (83), Expect = 0.002
Identities = 7/69 (10%), Positives = 20/69 (28%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ + ++ + L + + ++ T G + F AL +
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90
Query: 74 PFYDKPMRI 82
F + +
Sbjct: 91 EFRGSVITV 99
>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 = 35.6 bits (83), Expect = 0.002
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ + + + +FSQFG++ ++ + T K +G FV +E S + A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 71 QGFPFYDKPMRIQYSK 86
F + +R+ +
Sbjct: 63 DNTDFMGRTIRVTEAN 78
Score = 34.5 bits (80), Expect = 0.005
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+++ NL + + LF+QF V+L+ +R FVE + E S A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA-KL 62
Query: 229 HG 230
Sbjct: 63 DN 64
>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 = 35.3 bits (82), Expect = 0.003
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASA 63
I V+V I + + + F+++G + ++ + +T +G FV F
Sbjct: 5 GKIMPNT-VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 64 TNALRSMQGF 73
+ S F
Sbjct: 64 QKIVESQINF 73
Score = 32.2 bits (74), Expect = 0.039
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAA---KL 226
+F+ + E + F ++ KEV+++ +R + FV F N++ ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 227 ALHGFKITPTHAMK 240
HG K+ A++
Sbjct: 72 NFHGKKLKLGPAIR 85
>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 = 0.003
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNAL 67
+ L F +FG + ++V + + RG F+ F++ S A+
Sbjct: 24 ETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
Score = 27.9 bits (63), Expect = 0.96
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ +P E L F +F EV ++ + F+ FE+E QS + +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE-QSVDQAVNM 71
Query: 229 HGFKI 233
H I
Sbjct: 72 HFHDI 76
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 33.9 bits (77), Expect = 0.008
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
L L NL + L L Q N IA ++ ++ A++AL+ +
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-QGIALCKYTTREEANKAQMALNNCVL 68
Query: 234 TPT 236
T
Sbjct: 69 ANT 71
Score = 29.3 bits (65), Expect = 0.36
Identities = 9/81 (11%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
++++ + ++++ +L + Q G + V+ +G A + A A ++
Sbjct: 7 SSWLLLKNLTAQIDGPTLRTLCMQHGPL---VSFHPYLNQGIALCKYTTREEANKAQMAL 63
Query: 71 QGFPFYDKPMRIQYSKTDSDV 91
+ + + ++++V
Sbjct: 64 NNCVLANTTIFAESP-SENEV 83
>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 = 34.0 bits (78), Expect = 0.009
Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 23 DLKKSLYAIFSQFGQIMDIVALKTLK-----MRGQAFVIFKEIASATNALRSMQGFPFYD 77
++ + + S++G + I + + G+ FV F + A++ + G F +
Sbjct: 27 EIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN 86
Query: 78 KPMRIQY 84
+ + +Y
Sbjct: 87 RVVVTKY 93
Score = 25.9 bits (57), Expect = 6.5
Identities = 7/20 (35%), Positives = 8/20 (40%)
Query: 211 AFVEFENEMQSAAAKLALHG 230
FVEF + A L G
Sbjct: 62 IFVEFTSVFDCQKAMQGLTG 81
>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 = 34.2 bits (78), Expect = 0.011
Identities = 16/100 (16%), Positives = 27/100 (27%), Gaps = 8/100 (8%)
Query: 141 MQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP---G 197
+ ++ + PE ++ L LP S + + G
Sbjct: 14 LVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDG 73
Query: 198 FKEVRLVPNRHD----IAFVEFENEMQSAAAKLALHGFKI 233
V + R AFVE +E A L +
Sbjct: 74 AAGVHFIYTREGRQSGEAFVELGSEDDVKMA-LKKDRESM 112
>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 = 33.3 bits (76), Expect = 0.017
Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 8/75 (10%)
Query: 166 PEQPPNQILFLTNLPEETSEMMLSMLFNQF---PGFKEVRLVPNRHD----IAFVEFENE 218
E ++ LP + + F+ G + + NR A +E E+E
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 219 MQSAAAKLALHGFKI 233
A L H +
Sbjct: 66 QDVQKA-LEKHRMYM 79
>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 = 33.2 bits (75), Expect = 0.055
Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 3/76 (3%)
Query: 170 PNQILFLTN--LPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
Q L + N L S L + + + + PN+ +F + +S A +
Sbjct: 17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVT 75
Query: 228 LHGFKITPTHAMKISF 243
L+G ++ KI+
Sbjct: 76 LNGKEVVDDLGQKITL 91
>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 = 31.9 bits (73), Expect = 0.055
Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 10/91 (10%)
Query: 23 DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
++K + ++ G ++ I + +G +V IA+A A+ ++ G F K +
Sbjct: 29 EIKDDVIEECNKHGGVIHIY-VDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 87
Query: 83 QYSKTDSDVISKIKGTFMERPKKVRKQPAPV 113
Y T+ +
Sbjct: 88 AYVPLP---------TYHNLFPDSMTATQLL 109
Score = 26.2 bits (58), Expect = 4.9
Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 204 VPNRHD--IAFVEFENEMQSAAAKLALHG 230
V +V+ + + AA ALHG
Sbjct: 49 VDKNSAQGNVYVKCPSIAAAIAAVNALHG 77
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.8 bits (74), Expect = 0.057
Identities = 11/51 (21%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 101 ERPKKVRK----QPAPVEDPAEAKKSKKKAAKEQAR-----LMQAQQQQMQ 142
+ P+ +RK Q +++ A K ++ +E+A+ Q Q +Q++
Sbjct: 82 QEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVE 132
Score = 28.6 bits (63), Expect = 1.6
Identities = 5/45 (11%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 102 RPKKVRKQPAPVEDPAE--AKKSKKKAAKEQARLMQAQQQQMQAL 144
+ ++ ++P + E K+ ++ A + + +++ + L
Sbjct: 76 QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL 120
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 33.2 bits (75), Expect = 0.077
Identities = 11/65 (16%), Positives = 15/65 (23%), Gaps = 7/65 (10%)
Query: 108 KQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE 167
+A L+ PPV+ P P P A
Sbjct: 7 HHHHSSGLVPRGSHMVIPSA-------SVTSAASDFLAALHPPVTVPDPAPPPPPAPAAG 59
Query: 168 QPPNQ 172
PP+
Sbjct: 60 NPPDT 64
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 30.8 bits (70), Expect = 0.12
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 33 SQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
S+FGQI ++ L G A V F++ A ++++ G
Sbjct: 48 SKFGQIRKLL-LFDRHPDGVASVSFRDPEEADYCIQTLDG 86
Score = 29.3 bits (66), Expect = 0.47
Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 13/85 (15%)
Query: 159 PMATAGVPEQP-PNQILFLTNL--PEETSEMMLSML---------FNQFPGFKEVRLVPN 206
++G P + +++ + N+ P + + L + ++F +++ L
Sbjct: 2 SSGSSGGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR 61
Query: 207 RHD-IAFVEFENEMQSAAAKLALHG 230
D +A V F + ++ L G
Sbjct: 62 HPDGVASVSFRDPEEADYCIQTLDG 86
>3iz5_T 60S ribosomal protein L19 (L19E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_T
Length = 209
Score = 30.8 bits (69), Expect = 0.25
Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 99 FMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPA 158
+ + K + + + D EAK++K KA++E+ A++++ A ++ S +
Sbjct: 141 SIHKSKAEKAREKTLSDQFEAKRAKSKASRERK---IARREERLAPGPERSCTSTSGCSS 197
Query: 159 PMATAGVPE 167
T E
Sbjct: 198 SCGTKEGQE 206
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 29.7 bits (66), Expect = 0.35
Identities = 10/71 (14%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 168 QPPNQILFLTNLPEETSEMMLSMLFNQFPGF-----KEVRLVPNRHDIAFVEFENEMQSA 222
+ ++ L L ++ S ++ + +++ LV + + A + F + +A
Sbjct: 18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAA 76
Query: 223 AAKLALHGFKI 233
+ L+G +
Sbjct: 77 KMLMILNGSQF 87
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 30.7 bits (69), Expect = 0.40
Identities = 13/91 (14%), Positives = 22/91 (24%), Gaps = 12/91 (13%)
Query: 76 YDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQ 135
+ P IQ K + K+ + R ++ E + Q +LM
Sbjct: 543 FAMPYFIQVMKEYLTKVDKLDASESLRKEE------------EQATETQPIVYGQPQLML 590
Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVP 166
+ AP G
Sbjct: 591 TAGPSVAVPPQAPFGYGYTAPAYGQPQPGFG 621
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 29.2 bits (65), Expect = 0.45
Identities = 11/67 (16%), Positives = 19/67 (28%), Gaps = 10/67 (14%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIF-----SQFGQIMDIVALKTLKMRGQAFVIFKEIASAT 64
V V + + L F S G ++ ++ + F+E A A
Sbjct: 7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-----RLGCGGVLTFREPADAE 61
Query: 65 NALRSMQ 71
L
Sbjct: 62 RVLAQAD 68
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 29.2 bits (65), Expect = 0.45
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 27 SLYAIFSQFGQIMDIVALK-----TLKMRGQAFVIFKEIASATNALRS 69
+ A F +FG ++ K +G AF++F+E +S + +
Sbjct: 24 EITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA 71
>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix,
anti-parrallel beta sheet, double straded anti-parallel
beta helix, metal binding protein; 2.00A {Mus musculus}
Length = 404
Score = 30.4 bits (68), Expect = 0.51
Identities = 27/129 (20%), Positives = 51/129 (39%), Gaps = 20/129 (15%)
Query: 86 KTDSDVISKIKGTFMERPKKVRKQPAP----VEDPA-----EAKKSKKKAAKEQARLMQA 136
+ + +I F+ + K +++ +P ++DP+ E + +K
Sbjct: 130 AVEGAIAERIDE-FIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDR 188
Query: 137 QQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQIL-FLTNLPEETSEMMLSMLFNQF 195
QQ + L +Q + A + N++L F TN PE + +M Q
Sbjct: 189 TPQQAEMLGLQAEAPEEKAEEEDL---------RNEVLQFNTNCPECNAPAQTNMKLVQI 239
Query: 196 PGFKEVRLV 204
P FKEV ++
Sbjct: 240 PHFKEVIIM 248
>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 = 29.0 bits (65), Expect = 0.70
Identities = 8/59 (13%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 33 SQFGQIMDIV-------ALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
+FG + ++ + ++ + FV F + A++++ G F + + +
Sbjct: 47 GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>2qdz_A TPSB transporter FHAC; beta barrel, potra domain, membrane, protein
transport; 3.15A {Bordetella pertussis} PDB: 3njt_A
Length = 554
Score = 30.1 bits (67), Expect = 0.73
Identities = 9/51 (17%), Positives = 18/51 (35%)
Query: 129 EQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNL 179
R + Q Q+ ++ +PPV A A P+ + + +
Sbjct: 14 IDDRQRKEQLQRDIERALTRPPVELNPQSEAAAPARKPDATSGHTVTVHAV 64
Score = 29.0 bits (64), Expect = 1.9
Identities = 6/47 (12%), Positives = 16/47 (34%), Gaps = 3/47 (6%)
Query: 126 AAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
A++ R+ Q+++ + + PP + P +
Sbjct: 7 GARDLNRIDDRQRKEQLQ---RDIERALTRPPVELNPQSEAAAPARK 50
>2e3h_A Restin; CAP-Gly, cytoplasmic linker, tubulin binding, structural
protein; 1.45A {Homo sapiens} SCOP: b.34.10.1 PDB:
2e4h_A
Length = 90
Score = 28.1 bits (63), Expect = 0.77
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 97 GTFMERPKKVRKQPAPVEDPAEAKKSKKK 125
G F KV K P PA+AK + +
Sbjct: 60 GLFA-PVHKVTKIGFPSTTPAKAKANAVR 87
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.8 bits (67), Expect = 0.93
Identities = 23/135 (17%), Positives = 39/135 (28%), Gaps = 29/135 (21%)
Query: 111 APVEDPAEAKKSKKKAAKEQARLMQAQ-------QQQMQALSVQQPPVSQPAPPAPMATA 163
V + E +K E + + +A + + S P
Sbjct: 732 QFVPELKEFTAKLRKELVETSEVRKAVSIETALEHKVVNGNSADAAYAQVEIQPRANIQL 791
Query: 164 GVPEQPPNQILFLTNLPEETSEMMLSMLFNQFP---GFKEV------RLVPNRHD-IAFV 213
PE P + + + E +L + + GF EV R R + AF
Sbjct: 792 DFPELKPYKQ--VKQIAPAELEGLLDL--ERVIVVTGFAEVGPWGSART---RWEMEAFG 844
Query: 214 EFENEMQSAAAKLAL 228
EF S + +
Sbjct: 845 EF-----SLEGCVEM 854
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 27.9 bits (61), Expect = 1.8
Identities = 12/60 (20%), Positives = 19/60 (31%)
Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLS 189
R + + + QQ +QP V Q P L + P + + ML
Sbjct: 12 AVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLG 71
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 29.0 bits (64), Expect = 1.9
Identities = 10/43 (23%), Positives = 11/43 (25%)
Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
QA V QP P M T +Q P
Sbjct: 75 QATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117
Score = 28.6 bits (63), Expect = 2.1
Identities = 8/39 (20%), Positives = 10/39 (25%)
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
Q QQ QA + P P+ P
Sbjct: 67 EQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQM 105
Score = 28.6 bits (63), Expect = 2.5
Identities = 11/38 (28%), Positives = 12/38 (31%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
QAQ Q Q + Q P P P A Q
Sbjct: 11 QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMP 48
Score = 28.6 bits (63), Expect = 2.5
Identities = 14/38 (36%), Positives = 17/38 (44%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
Q Q L QQ P++ PA P A G +P NQ
Sbjct: 100 QVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQ 137
Score = 28.3 bits (62), Expect = 3.3
Identities = 8/38 (21%), Positives = 9/38 (23%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
Q Q + Q M VP PN
Sbjct: 58 QQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNA 95
Score = 28.3 bits (62), Expect = 3.3
Identities = 7/39 (17%), Positives = 12/39 (30%)
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
+ QQ+ + + P A + Q P Q
Sbjct: 66 QEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQ 104
Score = 27.5 bits (60), Expect = 4.7
Identities = 6/38 (15%), Positives = 9/38 (23%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
QQQ + +Q M + P
Sbjct: 55 SMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVD 92
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 253
Score = 28.1 bits (62), Expect = 2.2
Identities = 10/75 (13%), Positives = 19/75 (25%)
Query: 98 TFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPP 157
P+ P + A A + +Q++ Q + PP
Sbjct: 19 VQRYIPQPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQKKPKKTPPPKPKKTQ 78
Query: 158 APMATAGVPEQPPNQ 172
P + P +
Sbjct: 79 KPKKPTQKKKSKPGK 93
Score = 27.7 bits (61), Expect = 3.6
Identities = 10/71 (14%), Positives = 21/71 (29%)
Query: 102 RPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMA 161
RP V++ + PA ++ + + +Q ++ P P
Sbjct: 15 RPAPVQRYIPQPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQKKPKKTPPPKP 74
Query: 162 TAGVPEQPPNQ 172
+ P Q
Sbjct: 75 KKTQKPKKPTQ 85
>2cp6_A Restin; microtubule binding, cytoskeleton associated protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.34.10.1
Length = 172
Score = 27.7 bits (61), Expect = 2.8
Identities = 14/74 (18%), Positives = 20/74 (27%), Gaps = 1/74 (1%)
Query: 97 GTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAP 156
G F KV K P PA+AK + + + +LS S +
Sbjct: 97 GLFA-PVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSS 155
Query: 157 PAPMATAGVPEQPP 170
P
Sbjct: 156 RPSRTGLLTETSGP 169
>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase,
wild type, viral protein; 2.38A {Sindbis virus} SCOP:
b.47.1.3 PDB: 1ld4_A 3j0f_A
Length = 264
Score = 27.9 bits (61), Expect = 3.1
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 108 KQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE 167
++P P + +++AA AR A Q Q +V + Q P P
Sbjct: 11 RRPFPAPTAMWRPRRRRQAAPMPARNGLASQIQQLTTAVSALVIGQATRPQN-PRPRPPP 69
Query: 168 QPPNQ 172
+ Q
Sbjct: 70 RQKKQ 74
Score = 27.5 bits (60), Expect = 4.6
Identities = 9/65 (13%), Positives = 22/65 (33%), Gaps = 1/65 (1%)
Query: 106 VRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV 165
V Q ++P ++K + + + + +QP ++P MA
Sbjct: 53 VIGQATRPQNPRPRPPPRQKKQAPKQPPKPKKPKPQEK-KKKQPAKTKPGKRQRMALKLE 111
Query: 166 PEQPP 170
++
Sbjct: 112 ADRLF 116
>2izw_A Coat protein, ryegrass mottle virus coat protein; RNA, assembly,
capsid protein; 2.90A {Ryegrass mottle virus}
Length = 234
Score = 27.6 bits (60), Expect = 4.0
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 121 KSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV 165
+ K K+A + L + +++ Q QQP AP A
Sbjct: 2 RKKGKSASQVIVLKEKSRKKRQKSRGQQPTRQVTPVSAPAAMGTQ 46
>2zkr_p 60S ribosomal protein L19; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 196
Score = 27.3 bits (60), Expect = 4.1
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 98 TFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE--QARLMQAQQQQMQALS 145
+ + K + + + D AEA++SK K A++ + RL +++ ++ LS
Sbjct: 140 EHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLS 189
>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 361
Score = 27.5 bits (60), Expect = 4.1
Identities = 10/43 (23%), Positives = 19/43 (44%)
Query: 101 ERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQA 143
R +++++ VE+ K + + R MQ +MQA
Sbjct: 299 FRSERLKRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQA 341
>3rgf_A Cyclin-dependent kinase 8; protein kinase complex,
transferase,transcription; HET: BAX; 2.20A {Homo
sapiens}
Length = 405
Score = 27.5 bits (61), Expect = 4.7
Identities = 10/74 (13%), Positives = 22/74 (29%), Gaps = 6/74 (8%)
Query: 99 FMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPA 158
F+E P + V + K++ E+ + ++ Q P
Sbjct: 337 FLEDPLPT----SDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGN 392
Query: 159 PMATAGVPEQPPNQ 172
++ PP +
Sbjct: 393 QDSSHTQG--PPLK 404
>3jyw_P 60S ribosomal protein L19; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus}
Length = 176
Score = 26.9 bits (59), Expect = 4.8
Identities = 5/33 (15%), Positives = 7/33 (21%)
Query: 98 TFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQ 130
+ A A A + AA
Sbjct: 139 EHIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 171
>2kgw_A Outer membrane protein A; OMPA-L membrane, transmembrane; NMR
{Mycobacterium tuberculosis} PDB: 2lca_A 2lbt_A
Length = 129
Score = 26.5 bits (59), Expect = 5.0
Identities = 7/31 (22%), Positives = 10/31 (32%), Gaps = 7/31 (22%)
Query: 155 APPAPMATAGVPEQP-------PNQILFLTN 178
APP P A+ + I F +
Sbjct: 1 APPGPPASGPCADLQSAINAVTGGPIAFGND 31
>2ioq_A Chaperone protein HTPG; heat shock protein, HSP90; 3.50A
{Escherichia coli} PDB: 2iop_A
Length = 624
Score = 27.2 bits (61), Expect = 5.4
Identities = 17/86 (19%), Positives = 31/86 (36%)
Query: 58 KEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPA 117
K S + S++ + K + I ++K ER K VR + PA
Sbjct: 478 KPFQSVSKVDESLEKLADEVDESAKEAEKALTPFIDRVKALLGERVKDVRLTHRLTDTPA 537
Query: 118 EAKKSKKKAAKEQARLMQAQQQQMQA 143
+ + + A+L A Q++
Sbjct: 538 IVSTDADEMSTQMAKLFAAAGQKVPE 563
>1hv2_A Elongin C, ELC1; protein-peptide complex, signaling protein; NMR
{Saccharomyces cerevisiae} SCOP: d.42.1.1
Length = 99
Score = 25.8 bits (57), Expect = 5.8
Identities = 11/45 (24%), Positives = 22/45 (48%)
Query: 51 GQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSKTDSDVISKI 95
+ + I + A + L++M PF + RI+ + DS ++ K
Sbjct: 13 DKEYEISRSAAMISPTLKAMIEGPFRESKGRIELKQFDSHILEKA 57
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 27.1 bits (59), Expect = 6.7
Identities = 12/54 (22%), Positives = 19/54 (35%)
Query: 176 LTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
L + PE+ SE +QF + A VEF + + + H
Sbjct: 57 LIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTH 110
>1eys_C Photosynthetic reaction center; membrane protein complex, electron
transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A
{Thermochromatium tepidum} SCOP: a.138.1.2
Length = 382
Score = 26.8 bits (58), Expect = 6.7
Identities = 19/89 (21%), Positives = 28/89 (31%), Gaps = 3/89 (3%)
Query: 74 PFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARL 133
P Y M Y +++ PA + A +++ A E
Sbjct: 295 PLYGAQMAKDYPGLYKTAVTQEALP--GSAPASEAAPAAATEAAPEAPAQEVPAAEAVPA 352
Query: 134 MQAQQQQMQALSVQQPPVSQPAPPAPMAT 162
A SV+ PV + A PAP A
Sbjct: 353 AAEPGAAEAAGSVEPAPVEEVA-PAPAAQ 380
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.1 bits (56), Expect = 8.1
Identities = 6/22 (27%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 137 QQQQMQAL--SVQQ-PPVSQPA 155
++Q ++ L S++ S PA
Sbjct: 18 EKQALKKLQASLKLYADDSAPA 39
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
0.319 0.130 0.365
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: 3,543,219
Number of extensions: 204694
Number of successful extensions: 1441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1123
Number of HSP's successfully gapped: 455
Length of query: 246
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,160,982
Effective search space: 644952210
Effective search space used: 644952210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)