RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10467
(304 letters)
>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 = 98.3 bits (245), Expect = 6e-26
Identities = 21/78 (26%), Positives = 42/78 (53%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
+ C + +P+ K DV +FLEG+ + N + + D G+ G A +QF ++++A K+
Sbjct: 14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
Query: 201 LLRHKEKIGHRLVTLVMS 218
H++K+ R + +
Sbjct: 74 ERLHRKKLNGREAFVHVV 91
Score = 74.4 bits (183), Expect = 5e-17
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY---- 75
QF + + + +L D+ G+ G+A V+F + DDA+++ + H+ + R ++
Sbjct: 34 QFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL 93
Query: 76 --MEEGTSSKEANGRGTGGFG 94
M E + A G+ G
Sbjct: 94 EDMREIEKNPPAQGKSGPSSG 114
>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 = 92.9 bits (231), Expect = 5e-24
Identities = 42/83 (50%), Positives = 59/83 (71%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S + +RL+GLP+ C KE++ +F GLEIVPNG+T+P D+ GR TG A++QF +E
Sbjct: 9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68
Query: 196 NAEKALLRHKEKIGHRLVTLVMS 218
AEKAL +HKE+IGHR + + S
Sbjct: 69 IAEKALKKHKERIGHRYIEIFKS 91
Score = 74.4 bits (183), Expect = 4e-17
Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 5/71 (7%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY---M 76
QFF IVP + L D GRS+GEA V+F+S + A++AL++HK +G RYIE++
Sbjct: 34 QFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR 93
Query: 77 EEGTSSKEANG 87
E +S ++G
Sbjct: 94 AEVRTSGPSSG 104
>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 = 93.4 bits (232), Expect = 5e-24
Identities = 44/102 (43%), Positives = 64/102 (62%)
Query: 117 RRAKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIP 176
R + + M + S + + +RL+GLP+ C KE++ +F GLEIVPNGIT+P
Sbjct: 17 RGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLP 76
Query: 177 HDYAGRCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
D G+ TG A++QF +E AEKAL +HKE+IGHR + + S
Sbjct: 77 VDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKS 118
Score = 74.1 bits (182), Expect = 1e-16
Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
QFF IVP I L D G+ +GEA V+F+S + A++AL +HK +G RYIE++
Sbjct: 61 QFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVF 116
>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 = 91.8 bits (228), Expect = 2e-23
Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
C+ L+GLP+E + + V F + L+IV + I I + G+ TG +++F ++ + + A
Sbjct: 24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83
Query: 201 LLRHKEKIGHRLVTL 215
L RHK+ +G+R + +
Sbjct: 84 LCRHKQYMGNRFIQV 98
Score = 72.2 bits (177), Expect = 4e-16
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FFK IV +I + G+++GE VEF + D + AL RHK MG+R+I+++
Sbjct: 44 DFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH 99
>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 = 86.2 bits (214), Expect = 1e-21
Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S ++L+G P+ +++V +FL L+ V I I + G TG ++ F ++E
Sbjct: 4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGNKTGYIFVDFSNEE 61
Query: 196 NAEKALLRHKEKIGHRLVTLVMS 218
++AL ++E +G R + +
Sbjct: 62 EVKQALKCNREYMGGRYIEVFRE 84
Score = 81.2 bits (201), Expect = 8e-20
Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTS 81
+F P+ PV I ++ + G +G V+FS+ ++ ++AL+ ++ MG RYIE++ E
Sbjct: 29 EFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE---K 85
Query: 82 SKEANG 87
S ++G
Sbjct: 86 SGPSSG 91
>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 = 86.3 bits (214), Expect = 2e-21
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
C+ ++GLPY + D+ F L + + I GR TG A ++F E+A A
Sbjct: 14 TGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGEADVEFATHEDAVAA 71
Query: 201 LLRHKEKIGHRLVTLVMS 218
+ + K + HR V L ++
Sbjct: 72 MAKDKANMQHRYVELFLN 89
Score = 84.0 bits (208), Expect = 1e-20
Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTS 81
FF P+ P+ + + GR +GEADVEF++ +DA A+ + K+NM RY+EL++ S
Sbjct: 34 NFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN---S 90
Query: 82 SKEANGRG 89
+ +G G
Sbjct: 91 TAGTSGSG 98
>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 = 85.8 bits (213), Expect = 2e-21
Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S +++Q +P+ +++ F G +++P + + ++ G TG A + F ++
Sbjct: 9 SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 68
Query: 196 NAEKALL-RHKEKIGHRLVTLVMS 218
A A++ + IG R V LV+
Sbjct: 69 EATAAVIDLNDRPIGSRKVKLVLG 92
Score = 71.9 bits (177), Expect = 2e-16
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ-RHKSNMGDRYIELYMEE 78
FF ++P ++ L ++ G +GEA V F S D+A A+ + +G R ++L +
Sbjct: 34 DFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL-- 91
Query: 79 GTSSKEANG 87
S ++G
Sbjct: 92 --GSGPSSG 98
>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 = 86.3 bits (214), Expect = 2e-21
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
D + + G+P+ + DV F GL + + + D+ GR G ++F+ ++ +A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGLRVD--AVHLLKDHVGRNNGNGLVKFLSPQDTFEA 72
Query: 201 LLRHKEKIGHRLVTLVMS 218
L R++ + R V + +
Sbjct: 73 LKRNRMLMIQRYVEVSPA 90
Score = 79.8 bits (197), Expect = 5e-19
Identities = 23/71 (32%), Positives = 33/71 (46%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTS 81
FF + + LL D GR++G V+F S D AL+R++ M RY+E+
Sbjct: 35 DFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQ 94
Query: 82 SKEANGRGTGG 92
A G T G
Sbjct: 95 WVAAGGHITSG 105
>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 = 85.7 bits (212), Expect = 3e-21
Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 132 GAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYI 189
G +L + ++L+GLP+ C EDV+ FL I G+ + GR +G A++
Sbjct: 7 GMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFV 66
Query: 190 QFVDKENAEKALLRHKEKIGHRLVTLVMS 218
+ +++ + AL + +E +GHR + + S
Sbjct: 67 ELESEDDVKLALKKDRESMGHRYIEVFKS 95
Score = 64.6 bits (157), Expect = 3e-13
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 22 QFFKPI----VPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
F + + GR SGEA VE S DD + AL++ + +MG RYIE++
Sbjct: 36 NFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFK 94
>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 = 85.0 bits (211), Expect = 4e-21
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S +++Q +P+ +++ F G +++P + + ++ G TG A + F ++
Sbjct: 9 SSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 68
Query: 196 NAEKALL-RHKEKIGHRLVTLVMS 218
A A++ + IG R V L
Sbjct: 69 EATAAVIDLNDRPIGSRKVKLSGP 92
Score = 68.1 bits (167), Expect = 7e-15
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ-RHKSNMGDRYIELYMEE 78
FF ++P ++ L ++ G +GEA V F S D+A A+ + +G R ++L
Sbjct: 34 DFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG-- 91
Query: 79 GTSSK 83
S
Sbjct: 92 --PSS 94
>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 = 85.3 bits (211), Expect = 1e-20
Identities = 23/160 (14%), Positives = 45/160 (28%), Gaps = 41/160 (25%)
Query: 59 ALQRHKSNMGDRYIELYMEEGTSSKEANGRGTGGFGGVKSTPYGVGIFCISQFLAKWMRR 118
H + +
Sbjct: 2 GSSHHHHHHSSGLVPRGSH---------------------------------------MA 22
Query: 119 AKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD 178
+ + + + C+ ++GLPY+ + D+ F L V + I
Sbjct: 23 SMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV--RVHIEIG 80
Query: 179 YAGRCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
GR TG A ++F E A A+ + + + HR + L ++
Sbjct: 81 PDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN 120
Score = 84.5 bits (209), Expect = 2e-20
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM--EEG 79
FF P+ PV + + GR +GEADVEF++ ++A A+ + ++NM RYIEL++ G
Sbjct: 65 NFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTG 124
Query: 80 TSSKEANGRGTGGFG 94
S+ + + G G
Sbjct: 125 ASNGAYSSQVMQGMG 139
>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 = 83.7 bits (207), Expect = 1e-20
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 5/107 (4%)
Query: 132 GAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYI 189
G+ L D +R QGLP+ C EDV F I NGI + G+ G A I
Sbjct: 1 GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
Query: 190 QFVDKENAEKALLRHKEKIGHRLVTLVMSG---AQWFLSPPLTNETP 233
+ +++ +KAL +H+ +G R V + + +P
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSP 107
Score = 65.6 bits (160), Expect = 7e-14
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 22 QFFKPI----VPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FF I L + G+ G+A +E S D Q+AL++H+ MG RY+E+Y
Sbjct: 30 NFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY 87
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 83.0 bits (205), Expect = 5e-20
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIV---PNGITIPHDYAGRCTGVAYIQFVDKENA 197
+Q +R++GLP+ E+V F + GI GR TG A++ F +E A
Sbjct: 22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYA 81
Query: 198 EKALLRHKEKIGHRLVTLVMS 218
+ AL +HK+ +G R + L S
Sbjct: 82 QNALRKHKDLLGKRYIELFRS 102
Score = 69.1 bits (169), Expect = 5e-15
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 11/82 (13%)
Query: 22 QFFKPIVPV-----NILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY- 75
FF P+ IL +T GR +G+A V F+ + AQ AL++HK +G RYIEL+
Sbjct: 42 AFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFR 101
Query: 76 -----MEEGTSSKEANGRGTGG 92
+++ + + + G
Sbjct: 102 STAAEVQQVLNRFSSASGPSSG 123
>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 = 82.0 bits (202), Expect = 2e-19
Identities = 25/91 (27%), Positives = 47/91 (51%), Gaps = 2/91 (2%)
Query: 130 RQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVA 187
R +L + ++L+GLP+ C EDV+ FL I G+ + GR +G A
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 188 YIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
+++ +++ + AL + +E +GHR + + S
Sbjct: 92 FVELGSEDDVKMALKKDRESMGHRYIEVFKS 122
Score = 64.6 bits (157), Expect = 3e-13
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 22 QFFKPI----VPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
F + + GR SGEA VE S DD + AL++ + +MG RYIE++
Sbjct: 63 NFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF 120
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 47.0 bits (112), Expect = 3e-07
Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKI 208
G P + +D++++LE V I + G ++ F E+A+K + +K
Sbjct: 18 GFPTDATLDDIKEWLEDKGQV-LNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 76
Query: 209 GHRLVTLVM 217
+ ++
Sbjct: 77 KETDLLILF 85
Score = 43.2 bits (102), Expect = 7e-06
Identities = 8/56 (14%), Positives = 21/56 (37%), Gaps = 1/56 (1%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
++ + V NI + G V F S++ A++ ++ + + +
Sbjct: 30 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF 85
>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 = 49.2 bits (118), Expect = 6e-07
Identities = 33/203 (16%), Positives = 72/203 (35%), Gaps = 56/203 (27%)
Query: 22 QFFKPI--VPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEG 79
+ I V ++I L + S A ++ +S +DA+ +++ + IE
Sbjct: 136 DLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK----LNGLKIE------ 185
Query: 80 TSSKEANGRGTGGFGGVKSTPYGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSA 139
G + K ++S+ + +G +
Sbjct: 186 ----------------------GYTLVT------KVSNPLEKSKRTDSATLEGREI---- 213
Query: 140 VDQCCMRLQGLPYECKKEDV--EKFLEGLEIVPNGITIPHDY--AGRCTGVAYIQFVDKE 195
++ L E E++ E F I I IP A++ F +K+
Sbjct: 214 ------MIRNLSTELLDENLLRESFEGFGSIE--KINIPAGQKEHSFNNCCAFMVFENKD 265
Query: 196 NAEKALLRHKEKIGHRLVTLVMS 218
+AE+AL ++ +G+R +++ ++
Sbjct: 266 SAERALQMNRSLLGNREISVSLA 288
Score = 39.6 bits (93), Expect = 6e-04
Identities = 11/53 (20%), Positives = 20/53 (37%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
P + ++ L+ + +V I +P AYI KE+A +
Sbjct: 124 NFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 176
Score = 39.6 bits (93), Expect = 7e-04
Identities = 12/51 (23%), Positives = 24/51 (47%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
++FK P+ + + D ++ A +EF+ D A A+ + +G I
Sbjct: 60 KYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEI 110
Score = 30.7 bits (70), Expect = 0.56
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
LP + V K+ + G I+ + + + A I+F + A A+ + +
Sbjct: 48 NLPKSYNQNKVYKYFKHCG-PII--HVDVADS-LKKNFRFARIEFARYDGALAAITKTHK 103
Query: 207 KIGHRLV 213
+G +
Sbjct: 104 VVGQNEI 110
>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 = 47.9 bits (113), Expect = 7e-07
Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
+ ++G P + +D++++LE V N I + G ++ F E+A+K
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKF 166
Query: 201 LLRHKEKIGHRLVTLVMSGAQWF 223
+ +K + ++ +F
Sbjct: 167 VETPGQKYKETDLL-ILFKDDYF 188
Score = 42.5 bits (99), Expect = 4e-05
Identities = 7/58 (12%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 22 QFFKPIVPVN-ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEE 78
++ + V I + G V F S++ A++ ++ + + + ++
Sbjct: 128 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD 185
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 44.9 bits (107), Expect = 1e-06
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDY--AGRCTGVAYIQFVDKENAEKALLRHKEK 207
LPY+ +E +++F GL I + +P + R G Y +F D ++ AL ++E
Sbjct: 27 LPYDVTEESIKEFFRGLNIS--AVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES 84
Query: 208 IGHR 211
+G+R
Sbjct: 85 LGNR 88
Score = 39.9 bits (94), Expect = 8e-05
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 22 QFFKPIVPVNILLLTD--DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
+FF+ + + L + + R G EF +D AL ++ ++G+R I
Sbjct: 38 EFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRI 90
>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 = 43.8 bits (104), Expect = 4e-06
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYA--GRCTGVAYIQFVDKENAEKALLRHKEK 207
LPY+ +E +++F GL I + +P + + R G Y +F D ++ AL ++E
Sbjct: 23 LPYDVTEESIKEFFRGLNIS--AVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES 80
Query: 208 IGHR 211
+G++
Sbjct: 81 LGNK 84
Score = 41.1 bits (97), Expect = 3e-05
Identities = 12/73 (16%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 22 QFFKPIVPVNILLLTD--DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEG 79
+FF+ + + L + + R G EF +D AL ++ ++G++ + ++
Sbjct: 34 EFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNK--RIRVDVA 91
Query: 80 TSSKEANGRGTGG 92
+++ + + G
Sbjct: 92 DQAQDKDSGPSSG 104
>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 = 41.9 bits (99), Expect = 3e-05
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKALLRHKEK 207
L + D+E F + V + I D + R G+AY++F + ++ A+ ++
Sbjct: 32 QLAARIRPRDLEDFFSAVGKV-RDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQR 90
Query: 208 IGHR 211
+
Sbjct: 91 LLGV 94
Score = 33.4 bits (77), Expect = 0.021
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 22 QFFKPIVPVN-ILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIE 73
FF + V + +++D ++ RS G A VEF + A+ + I
Sbjct: 44 DFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPII 97
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 41.0 bits (96), Expect = 1e-04
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+ F + + D +GRS G ADV F DA +A+++
Sbjct: 107 ELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Score = 34.8 bits (80), Expect = 0.015
Identities = 20/121 (16%), Positives = 38/121 (31%), Gaps = 3/121 (2%)
Query: 82 SKEANGRGTGGFGGVKSTPYGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSAVD 141
N R GG + + ++ + + L G
Sbjct: 28 KLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVET 87
Query: 142 QCCMRLQGLPYECKKEDV-EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
+ + L + D+ E F E + + +D +GR G A + F + +A KA
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLK--KAAVDYDRSGRSLGTADVHFERRADALKA 145
Query: 201 L 201
+
Sbjct: 146 M 146
>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 = 40.0 bits (94), Expect = 1e-04
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+ F + + D +GRS G ADV F DA +A+++
Sbjct: 54 ELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Score = 30.4 bits (69), Expect = 0.28
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 175 IPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ +D +GR G A + F + +A KA+
Sbjct: 67 VDYDRSGRSLGTADVHFERRADALKAM 93
>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 = 41.2 bits (96), Expect = 1e-04
Identities = 17/172 (9%), Positives = 49/172 (28%), Gaps = 21/172 (12%)
Query: 42 SSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTGGFGGVKSTP 100
G A VE + RA+ + + M + + + + + + G
Sbjct: 41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGL---------- 90
Query: 101 YGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVE 160
+ + + S + + A + + P E +E+
Sbjct: 91 ---------EDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFF 141
Query: 161 KFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR-HKEKIGHR 211
+ + L + + +++ K +A + L + ++ +
Sbjct: 142 EICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNP 193
Score = 32.8 bits (74), Expect = 0.082
Identities = 9/57 (15%), Positives = 18/57 (31%), Gaps = 3/57 (5%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
+C + P ++ + S +E+ S DA L + M +
Sbjct: 143 ICDELGV-KRPTSVKVF-SGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY 197
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ Y +D+E + N ITI D ++G G AYI+F ++ + + A+
Sbjct: 43 NVDYGSTAQDLEAHFSSCGSI-NRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Score = 32.4 bits (74), Expect = 0.050
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 21 SQFFKPIVPVN-ILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
F +N I +L D +G G A +EF+ + A+ ++ R I
Sbjct: 54 EAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTI 107
>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 = 40.8 bits (96), Expect = 2e-04
Identities = 29/196 (14%), Positives = 54/196 (27%), Gaps = 61/196 (31%)
Query: 22 QFFKPIVPVNILLLTDDA-------GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF + + L + A +EF SVD+ +A+ + +++
Sbjct: 23 DFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI 82
Query: 75 YMEEGTSSKEANGRGTGGFGGVKSTPYGVGIFCISQFLAKWMRRAK----RSEMDWALKR 130
RR M
Sbjct: 83 ------------------------------------------RRPHDYQPLPGMSENPSV 100
Query: 131 QGAVLSGSAVDQCCMRL--QGLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTG 185
+ + V +L GLP + V++ L G + + D A G G
Sbjct: 101 YVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFG-PLK--AFNLVKDSATGLSKG 157
Query: 186 VAYIQFVDKENAEKAL 201
A+ ++VD ++A+
Sbjct: 158 YAFCEYVDINVTDQAI 173
Score = 30.8 bits (70), Expect = 0.40
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 34 LLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
L+ D G S G A E+ ++ +A+ + +GD+ +
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186
Score = 30.4 bits (69), Expect = 0.53
Identities = 9/59 (15%), Positives = 21/59 (35%), Gaps = 7/59 (11%)
Query: 149 GLPYECKKEDVEKFLE------GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+P+ +E + F GL P + + A+++F + +A+
Sbjct: 11 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNP-VLAVQINQDKNFAFLEFRSVDETTQAM 68
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 34 LLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+ D +GRS G ADV F DA +A+++
Sbjct: 61 VHYDRSGRSLGTADVHFERKADALKAMKQ 89
Score = 29.2 bits (66), Expect = 0.55
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 118 RAKRSEMDWALKRQGAVLSGSAVDQCCMRL--QGLPYECKKEDV-EKFLEGLEIVPNGIT 174
R K+ W + G A + +L L + D+ E F E +
Sbjct: 3 RPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLK--KAA 60
Query: 175 IPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ +D +GR G A + F K +A KA+
Sbjct: 61 VHYDRSGRSLGTADVHFERKADALKAM 87
>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 = 40.3 bits (95), Expect = 3e-04
Identities = 25/184 (13%), Positives = 48/184 (26%), Gaps = 58/184 (31%)
Query: 22 QFFKPIVPV-NILLLTDDA-GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEG 79
+ +P + L+ + G+S G E+ D A RA + + +
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD----LLGKPL------- 162
Query: 80 TSSKEANGRGTGGFGGVKSTPYGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSA 139
R ++ W Q L+ +
Sbjct: 163 ------GPR---------------TLYV-----------------HWTDAGQ---LTPAL 181
Query: 140 VDQCCMRLQGLPYECKKEDV--EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENA 197
+ C+ + LP D + G+ G A +++ E A
Sbjct: 182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPT--FCQLACGQDGQLKGFAVLEYETAEMA 239
Query: 198 EKAL 201
E+A
Sbjct: 240 EEAQ 243
Score = 36.5 bits (85), Expect = 0.007
Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 18 LLCSQF--FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
LC + G+ G A +E+ + + A+ A Q+ ++G ++ +
Sbjct: 201 ALCRALSAVHSPTFCQLA--CGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 31.9 bits (73), Expect = 0.24
Identities = 8/52 (15%), Positives = 23/52 (44%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LP ++ E+ + + + + G+ G + +++ K++A +A
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Score = 28.8 bits (65), Expect = 2.4
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
+ G A V + + A+ A+ H+S + +R +
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLREREL 87
Score = 28.4 bits (64), Expect = 2.5
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
GLP + ++V L E+ + + + G A++ ++ E AE A+
Sbjct: 29 GLPGDVTNQEVHDLLSDYELK-------YCFVDKYKGTAFVTLLNGEQAEAAI 74
>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 = 37.9 bits (89), Expect = 4e-04
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ Y E++E G V N +TI D ++G G AYI+F DKE+ +L
Sbjct: 14 VDYGATAEELEAHFHGCGSV-NRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Score = 30.9 bits (71), Expect = 0.11
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 21 SQFFKPIVPVN-ILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
F VN + +L D +G G A +EFS + + +L +S R I
Sbjct: 24 EAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQI 77
>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 = 37.8 bits (88), Expect = 4e-04
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
LP + ++V L+ ++ + Y R A++ ++ E A+ A+
Sbjct: 12 NLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64
Query: 207 KIGHRLV 213
G L+
Sbjct: 65 FRGKDLI 71
Score = 29.7 bits (67), Expect = 0.29
Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 11/74 (14%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYME 77
L + V R+ A V + + AQ A+Q H+ + + + + ++
Sbjct: 25 LLKDYDLKYCYV---------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75
Query: 78 EGTSSKEANGRGTG 91
T + +G +G
Sbjct: 76 P-TDALLCSGPSSG 88
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 38.0 bits (89), Expect = 4e-04
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 22 QFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGT 80
FK + ++ L+ D D + G VEF VD + AL + +GDR L ++
Sbjct: 34 AIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDR--SLRVDIAE 91
Query: 81 SSKEANGRGTGG 92
K+ + G
Sbjct: 92 GRKQDKSGPSSG 103
Score = 37.2 bits (87), Expect = 0.001
Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
LP+ + D++ + L I + + D + G Y++F + ++ ++AL
Sbjct: 22 NLPFNTVQGDIDAIFKDLSIR--SVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>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 = 37.3 bits (87), Expect = 8e-04
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIP--HDYAGRCTGVAYIQFVDKENAEKAL--LR 203
+P++ + ++ E F E+ + +P G G ++ F+ K++A+KA L
Sbjct: 22 NIPFQANQREIRELFSTFGELK--TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC 79
Query: 204 HKEKIGHRLVTLVMSGAQ 221
H + R LV+ A
Sbjct: 80 HSTHLYGR--RLVLEWAD 95
Score = 31.1 bits (71), Expect = 0.11
Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ--RHKSNMGDRYIELYMEEGTS 81
F + V + G G V+F + DA++A H +++ R L +E S
Sbjct: 39 FGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR--RLVLEWADS 96
Query: 82 SKEANGRGTGG 92
+ G
Sbjct: 97 EVTVQSGPSSG 107
>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 = 38.4 bits (90), Expect = 0.001
Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGT 80
+ ++ ++ G + V+F S +D ++AL+ + I+L +G
Sbjct: 32 VAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR 91
Query: 81 SSKEANGRGT 90
SK+ T
Sbjct: 92 DSKKVRAART 101
Score = 35.3 bits (82), Expect = 0.009
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L +++ + L N + + G Y+ F E+ EKAL
Sbjct: 20 NLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
Score = 33.0 bits (76), Expect = 0.059
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F+ + + + G+S G A +EF S DA++ L+
Sbjct: 118 EVFEDALEIRL---VSQDGKSKGIAYIEFKSEADAEKNLE 154
Score = 32.6 bits (75), Expect = 0.076
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNG-ITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + ++++++ E I + G+ G+AYI+F + +AEK L
Sbjct: 106 NLSFNITEDELKEVFE-----DALEIRLVSQ-DGKSKGIAYIEFKSEADAEKNL 153
>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 = 36.8 bits (86), Expect = 0.001
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
L Y +ED+EK G + + P D + G A++ F+ E+A KA
Sbjct: 15 NLSYTSSEEDLEKLFSAYG-PLS--ELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67
Score = 27.6 bits (62), Expect = 2.0
Identities = 7/33 (21%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ D + G A V F + A +A
Sbjct: 36 SELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 35.7 bits (83), Expect = 0.002
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 149 GLPYECKKEDVEK-FLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
GLP+ C KE++E+ + + + + AG+ G+AY+++ ++ A +A+
Sbjct: 24 GLPFSCTKEELEEICKAHGTVK--DLRLVTNRAGKPKGLAYVEYENESQASQAV 75
Score = 34.2 bits (79), Expect = 0.010
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
+ K V ++ L+T+ AG+ G A VE+ + A +A+ + + + I
Sbjct: 36 EICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENII 88
>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 = 35.9 bits (83), Expect = 0.003
Identities = 10/82 (12%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 138 SAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD--YAGRCTGVAYIQFVDKE 195
+ C + + G+P K+E++ + + + + + + G A++++
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 196 NAEKA---LLRHKEKIGHRLVT 214
A A L+ + ++ +
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIA 85
Score = 34.4 bits (79), Expect = 0.009
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRA---LQRHKSNMGDRYIE 73
++ + ++ V + D ++ G A VE+ S A A L + + I
Sbjct: 28 EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA 85
>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 = 34.9 bits (81), Expect = 0.005
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F+ + + + G+S G A +EF+S +DA+ AL
Sbjct: 34 EVFEKATFIKVP--QNQNGKSKGYAFIEFASFEDAKEALN 71
Score = 32.2 bits (74), Expect = 0.043
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L Y +E +++ E + I +P + G+ G A+I+F E+A++AL
Sbjct: 22 NLSYSATEETLQEVFE--KATF--IKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
>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 = 36.6 bits (85), Expect = 0.005
Identities = 14/39 (35%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
F P+ ++ DD GR++G+ VEF++ A++AL+R
Sbjct: 120 FGPVEKAVVV--VDDRGRATGKGFVEFAAKPPARKALER 156
Score = 27.7 bits (62), Expect = 3.9
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 178 DYAGRCTGVAYIQFVDKENAEKAL 201
D GR TG +++F K A KAL
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKAL 154
>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 = 35.0 bits (81), Expect = 0.006
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 36 TDDAGRSSGEADVEFSSVDDAQRALQR 62
D G+S G V F +A +A+
Sbjct: 49 EDKDGKSRGIGTVTFEQSIEAVQAISM 75
>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 = 34.5 bits (80), Expect = 0.007
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 21 SQFFKPIVPVNILLLTDDA-GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
+ N L + D G + V+F S +D ++AL+ + I+L
Sbjct: 35 KVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKL 89
Score = 33.8 bits (78), Expect = 0.011
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L +++ + L N + + G Y+ F E+ EKAL
Sbjct: 24 NLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
>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 = 34.6 bits (79), Expect = 0.007
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSS 82
F V + L+ +A V+ ++ DA A+ H+ +G + I + + G S
Sbjct: 34 FARHGKVKSVELSPHT-DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASG 92
Query: 83 KEA 85
+
Sbjct: 93 PSS 95
>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 = 35.6 bits (83), Expect = 0.008
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
Q+F+ P+ NI ++ D ++ A VE+ DA ALQ
Sbjct: 19 QYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Score = 29.4 bits (67), Expect = 0.80
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 160 EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ F G I I I D + A++++ +A AL
Sbjct: 19 QYFQVGGPIA--NIKIMIDKNNKNVNYAFVEYHQSHDANIAL 58
Score = 28.3 bits (64), Expect = 2.1
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQ 61
G S G V F+S DDAQ A+
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMD 147
Score = 26.3 bits (59), Expect = 9.5
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 181 GRCTGVAYIQFVDKENAEKAL 201
G G ++ F +++A+ A+
Sbjct: 126 GSSRGYGFVSFTSQDDAQNAM 146
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 34.3 bits (79), Expect = 0.009
Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
L ++ ++ G E+ + I + G+A + F A++ +
Sbjct: 13 RLNDNVRETFLKDMCRKYG-EVE--EVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Score = 33.9 bits (78), Expect = 0.016
Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 4/86 (4%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYME 77
+C ++ + V ILL + G A V F+S A+ ++ H +++ I ++
Sbjct: 26 MCRKY-GEVEEVEILL-HPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD 83
Query: 78 -EGTSSKEANGRGTGGFGGVKSTPYG 102
+G + G ++ P G
Sbjct: 84 IKGQQRMKYYELIVNGSYTPQTVPTG 109
>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 = 33.9 bits (78), Expect = 0.009
Identities = 7/58 (12%), Positives = 20/58 (34%), Gaps = 5/58 (8%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-----YAGRCTGVAYIQFVDKENAEKAL 201
+P+ +E + F + P + + A+++F + +A+
Sbjct: 13 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 70
Score = 28.5 bits (64), Expect = 0.63
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 7/54 (12%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
L P++ V I + A +EF SVD+ +A+ + +
Sbjct: 36 LTQAPGNPVLAVQI-------NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL 82
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 34.3 bits (79), Expect = 0.009
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 149 GLPY--ECKKEDVEKFLEGL-----EIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKA 200
G P K ++K L L ++V + P D A G+ G +++ +A+K
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVV--NMEFPIDEATGKTKGFLFVECGSMNDAKKI 70
Query: 201 L 201
+
Sbjct: 71 I 71
Score = 29.7 bits (67), Expect = 0.30
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 30 VNILLLTDDA-GRSSGEADVEFSSVDDAQRALQ 61
VN+ D+A G++ G VE S++DA++ ++
Sbjct: 40 VNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>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 = 34.1 bits (79), Expect = 0.010
Identities = 7/41 (17%), Positives = 14/41 (34%), Gaps = 1/41 (2%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F P+ + + D G+ V F + A+
Sbjct: 35 ELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Score = 30.7 bits (70), Expect = 0.14
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L ++E + E FL+ + +TI D G+ ++ F E+ A+
Sbjct: 23 NLEARVREEILYELFLQAGPLT--KVTICKDREGKPKSFGFVCFKHPESVSYAI 74
>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 = 36.0 bits (82), Expect = 0.016
Identities = 36/244 (14%), Positives = 71/244 (29%), Gaps = 66/244 (27%)
Query: 1 MRFSFYVIDIL---IHITYCLLCSQFFKPIVPVNILLLTDDAGRSSGEADVEFS--SVDD 55
R F + + HI LL +F I ++++ S E + S S+
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 56 AQRALQRHKSNMGD---RYIELYMEEGTSSKEANGRGTGGFGGVKSTPYGVGIFCISQFL 112
L+ N ++ Y + +++ PY F +
Sbjct: 431 IYLELKVKLENEYALHRSIVDHY--NIPKTFDSDD---------LIPPYLDQYFY--SHI 477
Query: 113 AKWMRRAKRSEM-----------DW---ALKRQGAVL--SGSAVDQCCMRLQGL----PY 152
++ + E + ++ SGS ++ LQ L PY
Sbjct: 478 GHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT----LQQLKFYKPY 533
Query: 153 ECKKE--------DVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKEN-----AEK 199
C + + FL +E + + T + I + ++ A K
Sbjct: 534 ICDNDPKYERLVNAILDFLPKIE--------ENLICSKYTDLLRIALMAEDEAIFEEAHK 585
Query: 200 ALLR 203
+ R
Sbjct: 586 QVQR 589
Score = 33.7 bits (76), Expect = 0.080
Identities = 22/150 (14%), Positives = 44/150 (29%), Gaps = 34/150 (22%)
Query: 32 ILLLTDDAG--RSSGEADVEFSSVDDAQRALQRHKS-NMGDRYIELYMEEGTSSKEANGR 88
ILL T A S+D L + ++ +Y++ +E
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD--CRPQDLPREV--- 322
Query: 89 GTGGFGGVKSTPYGVGIFCISQFLAKWMRRAKRSEM--DWALKRQGAVLSGSAVDQCCMR 146
+ + P + I I++ + + + L ++
Sbjct: 323 -------LTTNPRRLSI--IAESIRDGLATWDNWKHVNCDKLTT--------IIESSLNV 365
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIP 176
L+ P E +K + L + P IP
Sbjct: 366 LE--PAEYRK-----MFDRLSVFPPSAHIP 388
Score = 27.5 bits (60), Expect = 7.6
Identities = 27/249 (10%), Positives = 65/249 (26%), Gaps = 67/249 (26%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRAL-----------QRHKSNMGDRYI 72
+K I+ V + + + V D +++ + + R
Sbjct: 18 YKDILSVF---------EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF 68
Query: 73 ELYMEEGTSSKEANGRGTGGF-GGVKSTPYGVGIFCISQFLA-KWMRRAKRSEMDWALKR 130
+ + + F V Y FL ++ M
Sbjct: 69 WTLLSKQEEMVQK-------FVEEVLRINYK--------FLMSPIKTEQRQPSMM----- 108
Query: 131 QGAVLSGSAVDQCCMRLQGL-PYE-CKKEDVEKFLEGL-EIVPNGITIPH---------- 177
+ D+ Q Y + + K + L E+ P +
Sbjct: 109 --TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
Query: 178 ------DYAGRCT---GVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGAQWFLSPPL 228
Y +C + ++ N+ + +L +K+ +++ S + + L
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNL-KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 229 TNETPISRL 237
+ + L
Sbjct: 226 RIHSIQAEL 234
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 33.9 bits (78), Expect = 0.016
Identities = 19/75 (25%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANG 87
I L TD + G+ GEA V F A+ A+ I++ T + N
Sbjct: 43 PMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV--SFATRRADFNR 100
Query: 88 RGTGGFGGVKSTPYG 102
G G GG++ +
Sbjct: 101 GGGNGRGGLE--HHH 113
Score = 29.3 bits (66), Expect = 0.54
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 8/62 (12%)
Query: 148 QGLPYECKKEDVEKF-------LEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEK 199
QGL E V + + I + D G+ G A + F D +A+
Sbjct: 13 QGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKA 72
Query: 200 AL 201
A+
Sbjct: 73 AI 74
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 33.7 bits (77), Expect = 0.020
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 149 GLPYECKKEDVEKFLEGL-----EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ E KE ++ L L +I + I D + +G AYI F +E+A+ +
Sbjct: 36 NINPEVPKEKLQALLYALASSQGDI----LDIVVDLSDDNSGKAYIVFATQESAQAFV 89
Score = 29.1 bits (65), Expect = 0.94
Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRAL-QRHKSNMGDRYIEL 74
L S I+ + + D + +SG+A + F++ + AQ + + +
Sbjct: 53 LASSQ-GDILDIVV----DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI 104
>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 = 32.6 bits (75), Expect = 0.026
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + ++++ E F + LEI G+ G+AYI+F + +AEK L
Sbjct: 23 NLSFNITEDELKEVFEDALEIRLVSQD------GKSKGIAYIEFKSEADAEKNL 70
Score = 29.9 bits (68), Expect = 0.28
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F+ + + ++ G+S G A +EF S DA++ L+
Sbjct: 35 EVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLE 71
>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 = 33.1 bits (76), Expect = 0.026
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSS 82
PI V ++ D +S G A + F + DA+ A + + ++ + I++ + S
Sbjct: 31 HGPISEVLLI--KDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88
Query: 83 KEANGRGTGGFGGVKSTPYGVG 104
+ R +S +
Sbjct: 89 QSGGRRRPPASSRNRSPSGSLE 110
>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 = 34.1 bits (78), Expect = 0.029
Identities = 23/162 (14%), Positives = 47/162 (29%), Gaps = 26/162 (16%)
Query: 41 RSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTGGFGGVKST 99
A V+ + + AQ A+ + + + I + + + + G +
Sbjct: 39 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL---SKHQNVQLPREGQEDQGLTK 95
Query: 100 PYGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDV 159
YG + R K+ + L +P +ED+
Sbjct: 96 DYG----------NSPLHRFKKP--------GSKNFQNIFPPSATLHLSNIPPSVSEEDL 137
Query: 160 EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ G+ + + +A IQ E A +AL
Sbjct: 138 KVLFSSN----GGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 32.8 bits (75), Expect = 0.030
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+P + E ++ L +V + + D T V + + K+ A +AL
Sbjct: 22 NIPPHLQWEVLDSLLVQYGVVESCEQVNTD---SETAVVNVTYSSKDQARQAL 71
Score = 32.4 bits (74), Expect = 0.035
Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 22 QFFKPIVPVN--ILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL-YME 77
V + TD V +SS D A++AL + + + + +++ Y+
Sbjct: 34 SLLVQYGVVESCEQVNTDSETAVVN---VTYSSKDQARQALDKLNGFQLENFTLKVAYIP 90
Query: 78 EGTSSK 83
+ +++
Sbjct: 91 DEMAAQ 96
>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 = 32.7 bits (75), Expect = 0.031
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ + ++ V I+ + G +G VEF+ + A++ L
Sbjct: 29 AFATMGETVMSVKII--RNRLTGIPAGYCFVEFADLATAEKCLH 70
>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 = 33.7 bits (77), Expect = 0.033
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
+ E +++++ EKF + EI I + D G G A +++ + A A
Sbjct: 79 SIHEEAQEDEIQEKFCDYGEIK--NIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Score = 29.0 bits (65), Expect = 1.3
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
NI L D G S G A VE+ + A A +
Sbjct: 100 KNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 32.9 bits (75), Expect = 0.034
Identities = 8/36 (22%), Positives = 13/36 (36%), Gaps = 1/36 (2%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
G +EF S + AL+R + I +
Sbjct: 64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 29.4 bits (66), Expect = 0.45
Identities = 9/57 (15%), Positives = 22/57 (38%), Gaps = 3/57 (5%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ ++ LP C +D++ + ++ G ++F +E +AL
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEAL 84
>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 = 33.7 bits (78), Expect = 0.035
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 5/55 (9%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ +C + D+ G +I I G G A++ F + A+ A+
Sbjct: 102 MISKKCTENDIRVMFSSFG-QIE--ECRILRGPDGLSRGCAFVTFTTRAMAQTAI 153
Score = 30.3 bits (69), Expect = 0.53
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 22 QFFKP---IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
F I IL G S G A V F++ AQ A++
Sbjct: 114 VMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIK 154
>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 = 32.2 bits (74), Expect = 0.037
Identities = 8/53 (15%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L +D+ + ++ G +G A++ + D+ A +A+
Sbjct: 15 NLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAI 61
Score = 26.8 bits (60), Expect = 3.1
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR--HKSNMGDRYIELYMEEGTSSKEANGRGTGG 92
SG A V++ + A RA++ K + + +E+ + S K + + G
Sbjct: 41 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV--DYSVSKKLRSSGPSSG 93
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 32.2 bits (74), Expect = 0.041
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTG 91
+ G+S G V+F S + A+RA + + + R E+ + + A+G +G
Sbjct: 43 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGR--EIDVRID---RNASGPSSG 92
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 32.0 bits (73), Expect = 0.044
Identities = 8/60 (13%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 149 GLPY--ECKKEDVEKFLEGL-----EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+P + E ++ + + +I P + G+ G ++++ +A A+
Sbjct: 8 NVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEE-DGKTKGYIFLEYASPAHAVDAV 64
Score = 31.2 bits (71), Expect = 0.070
Identities = 7/40 (17%), Positives = 18/40 (45%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F + ++ G++ G +E++S A A++
Sbjct: 26 KIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVK 65
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 32.8 bits (75), Expect = 0.045
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
GL E + + F+ +I I IP DY + G A+++F E+A A+
Sbjct: 70 GLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Score = 29.0 bits (65), Expect = 1.0
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+I + D + + G A VEF +DA A+
Sbjct: 91 TDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 32.4 bits (74), Expect = 0.049
Identities = 7/40 (17%), Positives = 18/40 (45%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F + ++ G++ G +E++S A A++
Sbjct: 40 KIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVK 79
Score = 32.0 bits (73), Expect = 0.067
Identities = 8/60 (13%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 149 GLPY--ECKKEDVEKFLEGL-----EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+P + E ++ + + +I P + G+ G ++++ +A A+
Sbjct: 22 NVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEE-DGKTKGYIFLEYASPAHAVDAV 78
>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 = 32.3 bits (74), Expect = 0.053
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
LP + + +D+E + + I + + G A+++F D +AE A+ +
Sbjct: 29 NLPPDIRTKDIEDVFYKYGAIRD-IDLKNRRGGP--PFAFVEFEDPRDAEDAVYGRDGYD 85
Query: 207 KIGHRL 212
G+RL
Sbjct: 86 YDGYRL 91
Score = 26.1 bits (58), Expect = 7.3
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 6/57 (10%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ-RHKSNMGDRYIELYMEEGTSSKEANGRGTGGFGG 95
A VEF DA+ A+ R + L +E + G G+G G
Sbjct: 58 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY--RLRVEF---PRSGRGTGSGPSSG 109
>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 = 31.9 bits (73), Expect = 0.056
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 9/57 (15%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNG----ITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + +EDV + + P G T+ G G A+++F A+ A+
Sbjct: 22 MLNKQQSEEDVLRLFQ-----PFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAI 73
Score = 31.1 bits (71), Expect = 0.14
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 22 QFFKP---IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ F+P I +L G S G A V+FSS +AQ A+
Sbjct: 34 RLFQPFGVIDECTVL--RGPDGSSKGCAFVKFSSHTEAQAAIH 74
>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 = 33.4 bits (77), Expect = 0.056
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHK 205
G+ + ++ + + E G +I I I D G+ G A++ F D ++ +K +++
Sbjct: 111 GIKEDTEEHHLRDYFEQYG-KIE--VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 167
Query: 206 EKIGHRLV 213
+
Sbjct: 168 HTVNGHNC 175
Score = 30.7 bits (70), Expect = 0.34
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 149 GLPYECKKEDVEKFLEGL-EIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHKE 206
GL +E E + E + + D R G ++ + E + A+
Sbjct: 20 GLSFETTDESLRSHFEQWGTLT--DCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH 77
Query: 207 KIGHRLV 213
K+ R+V
Sbjct: 78 KVDGRVV 84
Score = 29.6 bits (67), Expect = 1.0
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
I ++TD +G+ G A V F D + + + + E+
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 31.7 bits (72), Expect = 0.056
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LP + + D+++ L L VP +T A++ + D A++A+
Sbjct: 26 NLPRDARVSDLKRALRELGSVPLRLTW-----QGPRRRAFLHYPDSAAAQQAV 73
>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 = 32.2 bits (74), Expect = 0.058
Identities = 9/43 (20%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 22 QFFKP---IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
KP ++ IL D +G S G S + + +
Sbjct: 44 NMLKPFGQVISTRIL--RDSSGTSRGVGFARMESTEKCEAVIG 84
>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 = 32.9 bits (76), Expect = 0.060
Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHK 205
G+ + + ++ E+F G I+ + D G+ G ++ + + ++
Sbjct: 94 GIGPDVRPKEFEEFFSQWG-TII--DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF 150
Query: 206 EKIGHRLV 213
R +
Sbjct: 151 IDFKDRKI 158
Score = 29.4 bits (67), Expect = 0.80
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
++ L+ D D G+S G V + S D R Q + DR IE+
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEI 160
Score = 26.7 bits (60), Expect = 6.1
Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALL-RH 204
GL ++ ++++ ++ G + + I D A GR G ++ F + ++ + +H
Sbjct: 10 GLNWDTTEDNLREYFGKYG-TVT--DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
Query: 205 K 205
Sbjct: 67 I 67
Score = 26.7 bits (60), Expect = 6.7
Identities = 6/26 (23%), Positives = 10/26 (38%), Gaps = 1/26 (3%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ-RHK 64
GRS G + F ++ +H
Sbjct: 42 GRSRGFGFLSFEKPSSVDEVVKTQHI 67
>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 = 33.4 bits (76), Expect = 0.060
Identities = 25/172 (14%), Positives = 51/172 (29%), Gaps = 27/172 (15%)
Query: 41 RSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTGGFGGVKST 99
A V+ + + AQ A+ + + + I + + + + G +
Sbjct: 70 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL---SKHQNVQLPREGQEDQGLTK 126
Query: 100 PYGVGIFCISQFLAKWMRRAKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDV 159
YG + R K+ + L +P +ED+
Sbjct: 127 DYG----------NSPLHRFKKP--------GSKNFQNIFPPSATLHLSNIPPSVSEEDL 168
Query: 160 EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR-HKEKIGH 210
+ G+ + + +A IQ E A +AL+ H +G
Sbjct: 169 KVLFSSN----GGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGE 216
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 32.1 bits (73), Expect = 0.066
Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 11/74 (14%)
Query: 149 GLPYECKKEDVEKFLEGL----EIVPNGITIPHDYAGRCT----GVAYIQFVDKENAEKA 200
GL +V K E +I + I + + + AY+ ++ E+A +A
Sbjct: 22 GLSQRLADPEVLKRPEYFGKFGKIH--KVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79
Query: 201 LLR-HKEKIGHRLV 213
+ + + R +
Sbjct: 80 IQCVNNVVVDGRTL 93
Score = 31.8 bits (72), Expect = 0.089
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 6 YVIDILIHITY--CLLCSQFFKP---IVPVNILLLTDDAG--RSSGEADVEFSSVDDAQR 58
+V+ + + L ++F I V I T AG S A V + +DA R
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78
Query: 59 ALQR-HKSNMGDRYI 72
A+Q + + R +
Sbjct: 79 AIQCVNNVVVDGRTL 93
>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 = 31.9 bits (73), Expect = 0.073
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ 61
GR G+A + F + + A +AL
Sbjct: 64 GRMRGQAFITFPNKEIAWQALH 85
Score = 26.5 bits (59), Expect = 6.1
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
L + D+ + G I GR G A+I F +KE A +AL
Sbjct: 32 NLSPRVTERDLVSLFARFQEK-KGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
>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 = 31.4 bits (72), Expect = 0.078
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 30 VNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIE 73
+ ++TD G S G V F + D Q+ ++ N + ++
Sbjct: 37 KEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI-NFHGKKLK 79
Score = 30.3 bits (69), Expect = 0.21
Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 5/66 (7%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
G+ + ++ F G + + I D G G ++ F + + +K +
Sbjct: 16 GIDVRMDETEIRSFFARYG-SVK--EVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQIN 72
Query: 207 KIGHRL 212
G +L
Sbjct: 73 FHGKKL 78
>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 = 31.1 bits (71), Expect = 0.078
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 10/70 (14%)
Query: 149 GLPYECKKEDVEK-FLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR--HK 205
GL + D+ F + EI IT+ A+IQF ++ AE A + +K
Sbjct: 19 GLGDTITETDLRNHFYQFGEIR--TITVVQR-----QQCAFIQFATRQAAEVAAEKSFNK 71
Query: 206 EKIGHRLVTL 215
+ R + +
Sbjct: 72 LIVNGRRLNV 81
>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 = 31.4 bits (72), Expect = 0.083
Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEK 199
D +R+ L + ++ D+++ + I + D G+ G A+I F +E+A +
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISR-IYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 200 AL 201
A+
Sbjct: 73 AI 74
Score = 30.7 bits (70), Expect = 0.16
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 22 QFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
+ F+P + I L D G+S G A + F +DA RA+
Sbjct: 34 ELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
>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 = 31.4 bits (72), Expect = 0.083
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
LP+ D+ + G ++V +TI D + GVA+I F+DK++A+
Sbjct: 23 NLPFSLTNNDLYRIFSKYG-KVV--KVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Score = 29.9 bits (68), Expect = 0.26
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
V + ++ D D +S G A + F D AQ +
Sbjct: 44 VKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
>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 = 31.5 bits (72), Expect = 0.085
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 22 QFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ F V I+ TD + G S G V+F+S +DA+ A +
Sbjct: 34 ESFDGSVRARIV--TDRETGSSKGFGFVDFNSEEDAKAAKE 72
Score = 26.5 bits (59), Expect = 4.7
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
GL + +E +++ +G I D G G ++ F +E+A+ A
Sbjct: 22 GLSEDTTEETLKESFDGSV----RARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
>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 = 31.5 bits (72), Expect = 0.088
Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
L ++ ++E + + L+ + + + G A+ QF+ +E A+K L
Sbjct: 22 NLSFDSEEEALGEVLQQFGDL-KYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 30.0 bits (68), Expect = 0.29
Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 22 QFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ + + + ++ D S G A +F + + AQ+ L
Sbjct: 34 EVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
>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 = 32.1 bits (73), Expect = 0.096
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANG 87
I++ D + G VE+ S DA+ A++ + + + DR I + G G
Sbjct: 67 KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYG 126
Query: 88 RGTGG 92
RG G
Sbjct: 127 RGRSG 131
Score = 28.6 bits (64), Expect = 1.5
Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 143 CCMRLQGLPYECKKEDV-EKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKA 200
C + + L + +E + E F + +I I + D G ++++ + +AE A
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKKTACGFCFVEYYSRADAENA 97
Query: 201 L 201
+
Sbjct: 98 M 98
>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 = 32.9 bits (74), Expect = 0.096
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 149 GLPYECKKEDVEKFLEGL-----EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + KK++++K L + +I+ I + R G A++ F + +A AL
Sbjct: 16 NLNEKIKKDELKKSLYAIFSQFGQIL--DILVSRSLKMR--GQAFVIFKEVSSATNAL 69
Score = 29.8 bits (66), Expect = 0.86
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 5/43 (11%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+ SQF I+ + + + + G+A V F V A AL+
Sbjct: 33 IFSQF-GQILDILVS----RSLKMRGQAFVIFKEVSSATNALR 70
Score = 29.5 bits (65), Expect = 1.3
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 5/60 (8%)
Query: 142 QCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ L LP E + + G GR +A+++F ++ A A
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFP----GFKEVRLVPGR-HDIAFVEFDNEVQAGAAR 261
>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 = 31.0 bits (71), Expect = 0.099
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 150 LPYECKKEDVEKFLEGL-----EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + KK++++K L + +I+ I + R G A++ F + +A AL
Sbjct: 16 LNEKIKKDELKKSLHAIFSRFGQIL--DILVSRSLKMR--GQAFVIFKEVSSATNAL 68
Score = 29.5 bits (67), Expect = 0.39
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
+ S+F I+ + + + + G+A V F V A AL+ D+ +
Sbjct: 32 IFSRF-GQILDILVS----RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM 81
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 31.1 bits (71), Expect = 0.10
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
NI L+ D ++ G A V+ SS DA + LQ
Sbjct: 39 NNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQI 72
Score = 30.8 bits (70), Expect = 0.14
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ + + L V N I + D + G A++Q +A + L
Sbjct: 16 NIAPHTVVDSIMTALSPYASLAVNN-IRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
>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 = 31.1 bits (71), Expect = 0.12
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
I L TD + G+ GEA V F A+ A+
Sbjct: 49 PMINLYTDRETGKLKGEATVSFDDPPSAKAAID 81
>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 = 30.6 bits (70), Expect = 0.13
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHD--YAGRCTGVAYIQFVDKENAEKAL 201
L K+ + E F +I I +P + + G AY++F + + AEKAL
Sbjct: 11 RLTRNVTKDHIMEIFSTYGKIK--MIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Score = 29.0 bits (66), Expect = 0.48
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 30 VNILLLTD--DAGRSSGEADVEFSSVDDAQRALQ 61
I + + S G A VEF + D+A++AL+
Sbjct: 32 KMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
>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 = 31.8 bits (73), Expect = 0.13
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIE 73
+ A +EF SVD+ +A+ + ++
Sbjct: 48 NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLK 81
Score = 29.9 bits (68), Expect = 0.56
Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 34 LLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIE 73
L+ D G S G A E+ ++ +A+ + +GD+ +
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Score = 27.2 bits (61), Expect = 4.3
Identities = 7/70 (10%), Positives = 22/70 (31%), Gaps = 5/70 (7%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-----YAGRCTGVAYIQFVDKENAEKALLR 203
+P+ +E + F + P + + A+++F + +A+
Sbjct: 11 NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 70
Query: 204 HKEKIGHRLV 213
+ +
Sbjct: 71 DGIIFQGQSL 80
Score = 26.4 bits (59), Expect = 8.1
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
GLP + V++ L G + + D A G G A+ ++VD ++A+
Sbjct: 101 GLPNYLNDDQVKELLTSFG-PLK--AFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
>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 = 31.2 bits (71), Expect = 0.14
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 9/69 (13%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRH 204
LPY+ E++ G I I + + G AY+ + D +A+ A+ L
Sbjct: 15 NLPYKITAEEMYDIFGKYG-PIR--QIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSG 69
Query: 205 KEKIGHRLV 213
LV
Sbjct: 70 FNVSNRYLV 78
Score = 29.6 bits (67), Expect = 0.40
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ-RHKSNMGDRYI 72
+ G A V + + DA+ A+ N+ +RY+
Sbjct: 44 PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYL 77
>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 = 31.2 bits (71), Expect = 0.14
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
I + D + G+ G+A V + A+ A++
Sbjct: 51 PMIHIYLDKETGKPKGDATVSYEDPPTAKAAVE 83
>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 = 30.7 bits (70), Expect = 0.15
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDVEK-FLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
L Y + + + F + + + IP + + G A+++F D+ +A+ A
Sbjct: 20 NLTYRTSPDSLRRVFEKYGRVG--DVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72
Score = 28.3 bits (64), Expect = 1.1
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
++ + + G A V F DAQ A
Sbjct: 41 GDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
>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 = 31.2 bits (71), Expect = 0.16
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
G+ E +ED+ +KF E EI I + D G G +++ + A+ A+
Sbjct: 29 GVHEEATEEDIHDKFAEYGEIK--NIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Score = 28.9 bits (65), Expect = 0.98
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANG 87
NI L D G G VE+ + +AQ A++ + ++ + I + + G
Sbjct: 50 KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV--DWCFVRGPPKG 107
Query: 88 RGTGGFGGVKSTP 100
+ GG +S
Sbjct: 108 KRRGGRRRSRSPD 120
>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 = 31.3 bits (71), Expect = 0.19
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ 61
GR G+A + + A +AL+
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALK 110
Score = 29.4 bits (66), Expect = 0.75
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 150 LPYECKKEDVEKFLE-----GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L +++D++ E I GR G A+I +++ A KAL
Sbjct: 53 LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
>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 = 30.3 bits (69), Expect = 0.20
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 22 QFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ F PV N + D G+ G VEF S +DA A++
Sbjct: 34 ELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
>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 = 30.2 bits (69), Expect = 0.20
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
NI+L+ D D GRS G + FS + A+RAL+
Sbjct: 33 DNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Score = 29.1 bits (66), Expect = 0.61
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
L + ++ + E + N I + D GR G +I F D E A +AL
Sbjct: 12 SLHFNITEDMLRGIFEPFGKIDN-IVLMKDSDTGRSKGYGFITFSDSECARRAL 64
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 30.4 bits (69), Expect = 0.22
Identities = 7/54 (12%), Positives = 18/54 (33%), Gaps = 8/54 (14%)
Query: 149 GLPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+P+ + D+ + I+ + G +I++ E A +
Sbjct: 34 NIPHFATEADLIPLFQNFGFIL--DFKHYPEK-----GCCFIKYDTHEQAAVCI 80
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 30.3 bits (69), Expect = 0.22
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
NI L D G G VE+ + +AQ A++
Sbjct: 51 KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
>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 = 29.8 bits (68), Expect = 0.23
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 3 FSFYVIDILIHITYCLLCSQF--FKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRA 59
F +V D+ IT + + F F I ++ D G+S G V F + DA+ A
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVV--KDMATGKSKGYGFVSFFNKWDAENA 64
Query: 60 LQ 61
+Q
Sbjct: 65 IQ 66
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 30.0 bits (68), Expect = 0.24
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGV-AYIQFVDKENAEKALLRHK 205
G P + ++ G + + + D GV A ++ D E L + +
Sbjct: 15 GFPRGVDSAQLSEYFLAFG-PV--ASVVMDKD-----KGVFAIVEMGDVGAREAVLSQSQ 66
Query: 206 EKI-GHRL 212
+ GHRL
Sbjct: 67 HSLGGHRL 74
>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 = 31.0 bits (70), Expect = 0.25
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
L Y + + + E V + + IP D Y G A+++F DK +AE A+
Sbjct: 77 NLTYRTSPDTLRRVFEKYGRVGD-VYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Score = 27.5 bits (61), Expect = 3.3
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
++ + D S G A V F DA+ A+
Sbjct: 98 GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
>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 = 30.4 bits (69), Expect = 0.25
Identities = 8/54 (14%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 149 GLPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
G+ + + + +I+ I + + G ++++F E+A A+
Sbjct: 32 GIASGLTDQLMRQTFSPFGQIM--EIRVFPEK-----GYSFVRFSTHESAAHAI 78
>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 = 31.2 bits (70), Expect = 0.25
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 5 FYVIDILIHITYCLLCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ-RH 63
V ++ +T +L Q F V ++ + +A ++++ AQ A
Sbjct: 49 IIVENLFYPVTLDVLH-QIFSKFGTVLKIITFTKNNQ--FQALLQYADPVSAQHAKLSLD 105
Query: 64 KSNMGDRYIEL 74
N+ + L
Sbjct: 106 GQNIYNACCTL 116
>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 = 29.9 bits (68), Expect = 0.26
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
++ ++ D + RS G A V F +VDDA+ A +R
Sbjct: 43 ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
>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 = 31.5 bits (72), Expect = 0.26
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 4 SFYVIDILIHITYCLLCSQF--FKPIVPVNILLLTDDA-GRSSGEADVEFSSVDDAQRAL 60
S YV D+ +T +L +F PI+ + + D RS G A V F DA+RAL
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVC--RDMITRRSLGYAYVNFQQPADAERAL 74
Query: 61 Q 61
Sbjct: 75 D 75
Score = 27.2 bits (61), Expect = 5.4
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
D S G V F + + A+RA+++ + + DR +
Sbjct: 138 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 29.9 bits (68), Expect = 0.28
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 3 FSFYVIDILIHITYCLLCSQFFKP---IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRA 59
+S +V D+ + +L F K ++ D G S G V+F+ + +RA
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV--LDQTGVSKGYGFVKFTDELEQKRA 67
Query: 60 LQ 61
L
Sbjct: 68 LT 69
>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 = 31.2 bits (70), Expect = 0.30
Identities = 13/90 (14%), Positives = 26/90 (28%), Gaps = 5/90 (5%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI--EL 74
+ + I + G+S G A V S +++ + K + +
Sbjct: 88 AVHSLGVNDI-LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP 146
Query: 75 YMEEGTSSKEANGRGTGGFGGVKSTPYGVG 104
++ S E R T G +
Sbjct: 147 VNKQFLSQFEMQSRKTTQSGQMSGEGKAGP 176
>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 = 30.0 bits (68), Expect = 0.32
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 11/55 (20%)
Query: 149 GLPYE-CKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L KK DVE + G ++ YA ++Q+ ++ +A A+
Sbjct: 34 NLNTALVKKSDVETIFSKYGRVA--GCSVHKGYA-------FVQYSNERHARAAV 79
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 30.4 bits (68), Expect = 0.32
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 5 FYVIDILIHITYCLLCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRAL-QRH 63
V ++ +T +L Q F V ++ + +A ++++ AQ A
Sbjct: 31 IIVENLFYPVTLDVLH-QIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLD 87
Query: 64 KSNMGDRYIEL 74
N+ + L
Sbjct: 88 GQNIYNACCTL 98
>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 = 31.6 bits (71), Expect = 0.35
Identities = 27/161 (16%), Positives = 48/161 (29%), Gaps = 56/161 (34%)
Query: 135 LSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNG-------ITIP--------HDY 179
L + +D + QGL ++ ++LE P+ I+ P H Y
Sbjct: 198 LIRTTLDAEKVFTQGL-------NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAH-Y 249
Query: 180 --AGRCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGAQ-W--FLSPPLTNETPI 234
+ G + K H + + + + ++ W F
Sbjct: 250 VVTAKLLGFTPGELRSYL---KGATGHSQGL---VTAVAIAETDSWESFFV--------S 295
Query: 235 SRLDLT-----GSPVRSTICVLCHPLTPR-SVRPRSVRQSE 269
R +T G VR C+ P S+ P + S
Sbjct: 296 VRKAITVLFFIG--VR------CYEAYPNTSLPPSILEDSL 328
>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 = 30.0 bits (68), Expect = 0.36
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 34 LLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
L+ D + GRS G + FS + A++AL+
Sbjct: 58 LMMDSETGRSKGYGFITFSDSECAKKALE 86
Score = 28.0 bits (63), Expect = 1.5
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
L + ++ + F I I + D GR G +I F D E A+KAL
Sbjct: 33 SLHFNITEDMLRGIFEPFGRIE--SIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 30.1 bits (68), Expect = 0.38
Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 6/89 (6%)
Query: 116 MRRAKRSEMDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLE--GLEIVPNGI 173
M + +++ L Y + + + E G + +
Sbjct: 21 MASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG-RVG--DV 77
Query: 174 TIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
IP D Y G A+++F DK +AE A+
Sbjct: 78 YIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Score = 27.0 bits (60), Expect = 4.9
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
++ + D S G A V F DA+ A+
Sbjct: 75 GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
>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 = 29.0 bits (66), Expect = 0.39
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHK 205
GL + +E + ++ G E+ I +P D + G +I F ++E +K + +
Sbjct: 6 GLSPDTPEEKIREYFGGFG-EVE--SIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62
Query: 206 EKIGHRLV 213
+G
Sbjct: 63 HNVGLSKC 70
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 30.7 bits (70), Expect = 0.40
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 22 QFFKPIVPV-NILLLTDDA-GRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
Q F P P+ +I + D + G A VE+ + AQ AL++ + +G R I
Sbjct: 47 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100
Score = 28.4 bits (64), Expect = 2.3
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 34 LLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
L D G+ G +E+ +Q A+ + ++G +Y+ +
Sbjct: 157 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Score = 28.0 bits (63), Expect = 3.4
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ YE ++ + + F I I + D + G A++++ E A+ AL
Sbjct: 35 SIYYELGEDTIRQAFAPFGPIK--SIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
>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 = 28.6 bits (65), Expect = 0.53
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+I + D + + G A VEF +DA A+
Sbjct: 35 TDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
>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 = 29.2 bits (66), Expect = 0.56
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
NI L D G S G A VE+ + A A +
Sbjct: 54 KNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86
>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 = 29.1 bits (66), Expect = 0.56
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQ 61
+ GRS G V FSS ++A +A+
Sbjct: 50 EGGRSKGFGFVCFSSPEEATKAVT 73
>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 = 28.7 bits (65), Expect = 0.66
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 34 LLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTG 91
++ D + RS G V F ++DDA+ A+ + ++ R I + ++ S + +
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV--DQAGKSSDNRSGPSS 101
Query: 92 G 92
G
Sbjct: 102 G 102
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 28.8 bits (65), Expect = 0.70
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
L K ++E+ + + I + G A+++F D +AE A+ L K
Sbjct: 7 NLGTGAGKGELERAFSYYGPLRT-VWIARNP----PGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 207 KIGHRL 212
G R+
Sbjct: 62 ICGSRV 67
>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 = 28.7 bits (65), Expect = 0.74
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
LCS P++ + ++ D GRS G A +EF ++ + A++
Sbjct: 22 LCSNV-GPVINLK--MMFDPQTGRSKGYAFIEFRDLESSASAVR 62
>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 = 29.5 bits (67), Expect = 0.74
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
L PI I+ D G S G A V+F+S D+QRA++
Sbjct: 23 LFRAI-GPINTCRIM--RDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Score = 26.8 bits (60), Expect = 6.4
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 181 GRCTGVAYIQFVDKENAEKAL 201
GR GVA++++ +E A++A+
Sbjct: 128 GRPRGVAFVRYNKREEAQEAI 148
Score = 26.8 bits (60), Expect = 6.5
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 22 QFFKP---IVPVNILLLTDDA-GRSSGEADVEFSSVDDAQRALQ 61
F IV NIL D GR G A V ++ ++AQ A+
Sbjct: 108 TIFGKYGSIVQKNIL--RDKLTGRPRGVAFVRYNKREEAQEAIS 149
Score = 26.8 bits (60), Expect = 7.8
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
LP + ++ F I I DY G G A++ F + ++++A+
Sbjct: 10 YLPQDMTDRELYALFRAIGPIN--TCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 29.3 bits (65), Expect = 0.76
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 5 FYVIDILIHITYCLLCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-H 63
+ + L IT +L P+ V +++ G +A VEF SV AQ+A +
Sbjct: 28 LSIQNPLYPITVDVLY-TVCNPVGKVQRIVIFKRNG---IQAMVEFESVLCAQKAKAALN 83
Query: 64 KSNMGDRYIELYME 77
+++ L +E
Sbjct: 84 GADIYAGCCTLKIE 97
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 28.8 bits (65), Expect = 0.79
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIE 73
+ S G V F + DA RA ++ H + + R IE
Sbjct: 64 NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
>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 = 28.9 bits (65), Expect = 0.85
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 3 FSFYVIDILIHITYCLLCSQF--FKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRA 59
F +V D+ IT + + F F I ++ D G+S G V F + DA+ A
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVV--KDMATGKSKGYGFVSFFNKWDAENA 73
Query: 60 LQ 61
+Q
Sbjct: 74 IQ 75
>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 = 29.1 bits (65), Expect = 0.93
Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
L K ++E+ + + + + + G A+++F D +A A+ L +
Sbjct: 80 NLGNNGNKTELERAFGYYGPLRS-VWVARNP----PGFAFVEFEDPRDAADAVRELDGRT 134
Query: 207 KIGHRL 212
G R+
Sbjct: 135 LCGCRV 140
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 29.1 bits (65), Expect = 0.95
Identities = 7/55 (12%), Positives = 18/55 (32%), Gaps = 2/55 (3%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ + + + + G+ V + G+ G A + + + K L
Sbjct: 62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Score = 28.3 bits (63), Expect = 1.9
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
V + + G+S G A+V +S + + L+ + +
Sbjct: 85 VELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
>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 = 28.6 bits (64), Expect = 0.96
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
++GL + D+ + LE G TI + A ++F + ++A++ +
Sbjct: 20 VRGLCESVVEADLVEALE-----KFG-TICYVMMMPFKRQALVEFENIDSAKECV 68
Score = 26.7 bits (59), Expect = 4.0
Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 8/48 (16%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSN 66
+F I V + +A VEF ++D A+ +
Sbjct: 35 ALEKF-GTICYVMM-------MPFKRQALVEFENIDSAKECVTFAADV 74
>3guv_A Site-specific recombinase, resolvase family prote; structural
genomics, PSI-2, protein structure initiative; 2.20A
{Streptococcus pneumoniae}
Length = 167
Score = 29.1 bits (66), Expect = 1.00
Identities = 10/48 (20%), Positives = 18/48 (37%)
Query: 41 RSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTSSKEANGR 88
R S +E S++ + ++ + Y + G S K GR
Sbjct: 12 RVSTSIQIEGYSLEAQKSRMKAFAIYNDYEIVGEYEDAGKSGKSIEGR 59
>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 = 27.8 bits (63), Expect = 1.0
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 3 FSFYVIDILIHITYCLLCSQF--FKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRA 59
F+ +V D+ +++ L + F F + +++ D G S G V F+S DDAQ A
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM--WDMQTGSSRGYGFVSFTSQDDAQNA 59
Query: 60 LQ 61
+
Sbjct: 60 MD 61
>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 = 28.9 bits (65), Expect = 1.1
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
++ ++ D + RS G A V F +VDDA+ A +R
Sbjct: 74 ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Score = 26.2 bits (58), Expect = 8.6
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
GL + D+ + G I ++I +D + R G A++ F + ++A++A
Sbjct: 53 GLSLYTTERDLREVFSKYG-PIA--DVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 28.4 bits (63), Expect = 1.1
Identities = 7/35 (20%), Positives = 12/35 (34%)
Query: 41 RSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
R + F DA+R L + + + L
Sbjct: 45 RLGCGGVLTFREPADAERVLAQADHELHGAQLSLR 79
>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 = 28.4 bits (64), Expect = 1.1
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 7/72 (9%)
Query: 24 FKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTSS 82
F I + +L D G G A + + + A +A + ++ M
Sbjct: 37 FGKIYELTVL--KDRFTGMHKGCAFLTYCERESALKAQS----ALHEQKTLPGMNRPIQV 90
Query: 83 KEANGRGTGGFG 94
K A+ GG G
Sbjct: 91 KPADSESRGGSG 102
Score = 26.1 bits (58), Expect = 5.9
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKA 200
+P ++D++ E G +I +T+ D + G G A++ + ++E+A KA
Sbjct: 20 QIPRNLDEKDLKPLFEEFG-KIY--ELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 27.9 bits (63), Expect = 1.1
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 149 GLPYE-CKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRH 204
LP + KED+ + I+ I I + + +IQF + ++ A+
Sbjct: 17 NLPLKNVSKEDLFRIFSPYGHIM--QINIKNAFG-------FIQFDNPQSVRDAIECESQ 67
Query: 205 KEKIGHRL 212
+ G +L
Sbjct: 68 EMNFGKKL 75
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 28.5 bits (64), Expect = 1.1
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQ 61
S V F + D AQ A++
Sbjct: 77 QTSLSKCFGFVSFDNPDSAQVAIK 100
>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 = 28.3 bits (64), Expect = 1.2
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+I + D + + G A VEF +DA A+
Sbjct: 40 TDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
>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 = 27.9 bits (63), Expect = 1.2
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHK 205
G+P+ C + ++ ++ + G + + + +D R G +I F D+++ ++A+ H
Sbjct: 17 GIPHNCGETELREYFKKFG-VVT--EVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHF 73
Query: 206 EKIGHRLVT 214
I + V
Sbjct: 74 HDIMGKKVE 82
>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 = 28.4 bits (64), Expect = 1.3
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQ 61
S V + + AQ A+Q
Sbjct: 62 QTNLSKCFGFVSYDNPVSAQAAIQ 85
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 28.0 bits (63), Expect = 1.4
Identities = 8/54 (14%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 149 GLPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
P + ++ ++ + + + I + +A +++F + E+A KA+
Sbjct: 38 PFPLDVQESELNEIFGPFGPMK--EVKILNGFA-------FVEFEEAESAAKAI 82
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 27.8 bits (62), Expect = 1.4
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 8/48 (16%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSN 66
+F PI V ++ +A VEF V A A+ N
Sbjct: 41 ALQEF-GPISYVVVM-------PKKRQALVEFEDVLGACNAVNYAADN 80
>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 = 28.7 bits (65), Expect = 1.5
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 4/44 (9%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
L I ++ D G+S G V + DA++A+
Sbjct: 22 LFGSI-GEIESCKLV--RDKITGQSLGYGFVNYIDPKDAEKAIN 62
Score = 27.5 bits (62), Expect = 3.7
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL 201
LP +E+ F EI + D G+ G ++ ++D ++AEKA+
Sbjct: 9 YLPQNMTQEEFRSLFGSIGEIE--SCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>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 = 28.0 bits (63), Expect = 1.6
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTGG 92
+ S G V F + DA RA ++ H + + R IE+ T+ N + G
Sbjct: 50 NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV--NNATARVMTNSGPSSG 103
>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 = 27.7 bits (62), Expect = 1.6
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 149 GLPYE-CKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRH 204
LP + KED+ + I+ I I + + +IQF + ++ A+
Sbjct: 29 NLPLKNVSKEDLFRIFSPYGHIM--QINIKNAFG-------FIQFDNPQSVRDAIEXESQ 79
Query: 205 KEKIGHRL 212
+ G +L
Sbjct: 80 EMNFGKKL 87
>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 = 27.5 bits (62), Expect = 1.7
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 19 LCSQFFKPIVPVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
LC + K IV + D + G V+F S AQ+A+
Sbjct: 25 LCQPYGK-IVSTKAI--LDKTTNKCKGYGFVDFDSPSAAQKAVT 65
>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 = 27.6 bits (62), Expect = 1.8
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 36 TDDAGRSSGEADVEFSSVDDAQRALQ 61
S G VE+ + AQ+AL+
Sbjct: 43 KAGVLLSMGFGFVEYKKPEQAQKALK 68
>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 = 27.8 bits (62), Expect = 1.8
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)
Query: 152 YECKKEDVEKFLEGLEIVPNGITIPH---DYAGRCTGVAYIQFVDKENAEKAL 201
YE EDV +V I IP G +++F + +KA+
Sbjct: 25 YEEIVEDVRDECSKYGLV-KSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAM 76
>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 = 27.5 bits (62), Expect = 1.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQ 61
D G S G A + F+S D + A++
Sbjct: 43 DTGNSKGYAFINFASFDASDAAIE 66
>3giw_A Protein of unknown function DUF574; rossmann-fold protein,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE UNL; 1.45A {Streptomyces
avermitilis} PDB: 3go4_A*
Length = 277
Score = 28.7 bits (64), Expect = 2.1
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 145 MRLQGLPYE-CKKEDVEKFLEGLEIVPNGITIPHD 178
+ +P + E+F EGLE+V GI H
Sbjct: 217 YAARNMPMRLRTHAEAEEFFEGLELVEPGIVQVHK 251
>3g13_A Putative conjugative transposon recombinase; resolvase, PSI-II,
target 11223F, structural genomics, prote structure
initiative; 2.00A {Clostridium difficile}
Length = 169
Score = 28.3 bits (64), Expect = 2.2
Identities = 8/49 (16%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 41 RSSGEADVEFSSVDDAQRALQRH-KSNMGDRYIELYMEEGTSSKEANGR 88
R S +++ + +S + K N ++Y +E + + R
Sbjct: 13 RVSTDSEDQLNSYKSQVQYYTDMIKKNKEWVLADIYADEAITGTQVTKR 61
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 27.4 bits (60), Expect = 2.5
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 42 SSGEADVEFSSVDDAQRALQR 62
+ A + F + D A+RA +R
Sbjct: 45 TGCSAILRFINQDSAERAQKR 65
>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 = 27.1 bits (60), Expect = 2.7
Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 173 ITIPHDYAGRCTGVAYIQFVDKENAEKALLR-HKEKIGHRLVT 214
+ + + G Y++F +E+AEKA++ + + +
Sbjct: 57 MNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
>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 = 27.1 bits (60), Expect = 2.8
Identities = 12/61 (19%), Positives = 21/61 (34%), Gaps = 6/61 (9%)
Query: 41 RSSGEADVEFSSVDDAQRALQR-HKSNMGDR-----YIELYMEEGTSSKEANGRGTGGFG 94
G VEF +D A+++ + YI + ++ S R +G
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107
Query: 95 G 95
G
Sbjct: 108 G 108
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 27.1 bits (60), Expect = 3.2
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 156 KEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
KE+ EK+ + + V I +++F E+A KA+
Sbjct: 31 KEECEKYGKVGKCV---IFEIPGAPDDEAVRIFLEFERVESAIKAV 73
Score = 26.3 bits (58), Expect = 4.8
Identities = 6/32 (18%), Positives = 12/32 (37%)
Query: 30 VNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
I + + +EF V+ A +A+
Sbjct: 43 CVIFEIPGAPDDEAVRIFLEFERVESAIKAVV 74
>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 = 27.1 bits (60), Expect = 3.4
Identities = 15/94 (15%), Positives = 30/94 (31%), Gaps = 19/94 (20%)
Query: 150 LPYECKKEDV----EKF--LEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
LP ++ +F L + + G A ++F++ A KA
Sbjct: 18 LPAGTLAAEIQETFSRFGSLGRVLLPEGG------------ITAIVEFLEPLEARKAFRH 65
Query: 204 -HKEKIGHRLVTLVMSGAQWFLSPPLTNETPISR 236
K H + L + F + P ++ +
Sbjct: 66 LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQ 99
>3mk7_B Cytochrome C oxidase, CBB3-type, subunit O; TM helices,
oxidoreductase; HET: HEM HEC FC6; 3.20A {Pseudomonas
stutzeri}
Length = 203
Score = 28.0 bits (62), Expect = 3.5
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 212 LVTLVMSGAQWFLSPPLTNETPISRLDLTGSPV-RSTICVLCHPLTPRSVRPRSVR 266
L +V Q ++ P+ P + L L G + CV CH R R + R
Sbjct: 27 LTQIVPLFFQDSVNEPVEGMKPYTALQLEGRDLYIREGCVGCHSQMIRPFRAETER 82
>1whs_B Serine carboxypeptidase II; HET: NAG FUC; 2.00A {Triticum aestivum}
SCOP: c.69.1.5 PDB: 1wht_B* 1bcs_B* 1bcr_B* 3sc2_B*
Length = 153
Score = 27.4 bits (61), Expect = 3.7
Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 2/61 (3%)
Query: 182 RCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGAQWFLSPPLTNETPISRLDLTG 241
C+ + D + + R G R+ V SG + P I L L
Sbjct: 37 TCSDTINTHWHDAPRSMLPIYRELIAAGLRI--WVFSGDTDAVVPLTATRYSIGALGLPT 94
Query: 242 S 242
+
Sbjct: 95 T 95
>2pmp_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; plant enzymes,
MEP pathway, isoprenoid proteins, CMP, zinc IONS, lyase;
HET: C5P; 2.30A {Arabidopsis thaliana}
Length = 160
Score = 27.4 bits (62), Expect = 3.7
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 158 DVEKFLEGLEIVPNGITIPHDY 179
D+ + G ++ GI IPHD
Sbjct: 11 DLHRLEPGYPLIIGGIVIPHDR 32
>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 = 26.4 bits (59), Expect = 3.9
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
+ I + G+S G A V S +++ +
Sbjct: 31 LEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
>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 = 26.8 bits (60), Expect = 4.0
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 38 DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
D S G V F + + A+RA+++ + + DR +
Sbjct: 40 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 75
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 25.9 bits (58), Expect = 4.1
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALLRHK 205
GL EDV+ + E G ++ + D R G ++ F ++ EK H
Sbjct: 6 GLSVNTTVEDVKHYFEQFG-KVD--DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62
Query: 206 EKIGHRLV 213
+I +++V
Sbjct: 63 HEINNKMV 70
>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 = 26.8 bits (60), Expect = 4.2
Identities = 6/54 (11%), Positives = 19/54 (35%), Gaps = 4/54 (7%)
Query: 149 GLPYECKKEDV-EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L + + + + F + + ++ +++F + +A AL
Sbjct: 22 NLSRDVTEVLILQLFSQIGPCK--SCKMITEHTSN-DPYCFVEFYEHRDAAAAL 72
>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 = 26.5 bits (59), Expect = 4.2
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 149 GLPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LP + +E++ K E + + I D G +I+ + AE A
Sbjct: 22 NLPPDITEEEMRKLFEKYGKAG--EVFIHKD-----KGFGFIRLETRTLAEIAK 68
>1iv3_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; isoprenoid,
non-mevalonate, riken structural genomics/proteomics
initiative, RSGI; 1.52A {Thermus thermophilus} SCOP:
d.79.5.1 PDB: 1iv2_A 1iv4_A* 1iv1_A
Length = 152
Score = 27.0 bits (61), Expect = 4.3
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 158 DVEKFLEGLEIVPNGITIPHD 178
D + EG + G+ IP
Sbjct: 8 DSHRLEEGRPLYLCGLLIPSP 28
>1t0a_A 2C-methyl-D-erythritol 2,4-cyclodiphosphate synth; mixed alpha
beta, homotrimer, synthase, lyase; HET: FPP; 1.60A
{Shewanella oneidensis} SCOP: d.79.5.1 PDB: 1vh8_A*
1vha_A* 1jn1_A 3fpi_A* 3f6m_A*
Length = 159
Score = 27.0 bits (61), Expect = 4.9
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 158 DVEKFLEGLEIVPNGITIPHDY 179
DV KF E ++ G+ +P++
Sbjct: 10 DVHKFGEPRPLILCGVEVPYET 31
>1gx1_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; isoprenoid,
lyase, isoprene biosynthesis; HET: CDP; 1.8A
{Escherichia coli} SCOP: d.79.5.1 PDB: 1h47_A* 1h48_A*
3ern_A* 3eor_A* 3elc_A* 3esj_A* 3fba_A* 2amt_A* 1knj_A*
1knk_A 1u3l_A* 1u3p_A 1u40_A* 1u43_A* 1jy8_A* 2gzl_A*
1yqn_A* 3ghz_A* 3t80_A*
Length = 160
Score = 27.0 bits (61), Expect = 5.1
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 158 DVEKFLEGLEIVPNGITIPHDY 179
DV F I+ G+ IP++
Sbjct: 9 DVHAFGGEGPIIIGGVRIPYEK 30
>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 = 26.7 bits (59), Expect = 5.1
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 41 RSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
G VEF +D A+++ + E
Sbjct: 49 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET 83
>3f0d_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; ssgcid, niaid,
isoprene biosynthe lyase, metal-binding, structural
genomics; 1.20A {Burkholderia pseudomallei} PDB: 3f0e_A
3f0f_A* 3f0g_A* 3ieq_A* 3iew_A* 3jvh_A* 3k14_A* 3k2x_A*
3ke1_A* 3mbm_A* 3p0z_A* 3p10_A* 3q8h_A* 3qhd_A* 3ikf_A*
3ike_A*
Length = 183
Score = 27.2 bits (61), Expect = 5.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 158 DVEKFLEGLEIVPNGITIPHDY 179
DV + + G ++ G+TIP++
Sbjct: 31 DVHQLVPGRPLIIGGVTIPYER 52
>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 = 26.1 bits (58), Expect = 5.5
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 149 GLPYECKKEDVEK-FLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
L +E +EK F + DYA ++ F ++E+A +A+
Sbjct: 22 NLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYA-------FVHFSNREDAVEAM 68
>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 = 26.6 bits (59), Expect = 5.7
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ 61
+S G V+F S AQ+A+
Sbjct: 81 RQSRGYGFVKFQSGSSAQQAIA 102
>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 = 26.6 bits (59), Expect = 6.2
Identities = 4/17 (23%), Positives = 11/17 (64%)
Query: 185 GVAYIQFVDKENAEKAL 201
A++ + E+A++A+
Sbjct: 74 NCAFVTYEKMESADQAV 90
>1sz7_A BET3 homolog, trafficking protein particle complex subunit 3;
alpha-beta plait, trapp complex, palmitoylated,
transport PR; HET: PLM; 1.55A {Homo sapiens} PDB:
2cfh_A* 2pwn_A* 3kxc_A* 1wc8_A* 2j3w_D* 2j3r_A* 2j3t_A*
1wc9_A* 2c0j_A*
Length = 200
Score = 26.8 bits (59), Expect = 7.3
Identities = 9/45 (20%), Positives = 20/45 (44%)
Query: 49 EFSSVDDAQRALQRHKSNMGDRYIELYMEEGTSSKEANGRGTGGF 93
++ + +D + L + N+G R IE ++ + + R T
Sbjct: 42 DYENDEDVNKQLDKMGFNIGVRLIEDFLARSNVGRCHDFRETADV 86
>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 = 26.1 bits (58), Expect = 7.4
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
V+ L+ D + G+ G E+ + A A++
Sbjct: 36 VSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
>2qe6_A Uncharacterized protein TFU_2867; putative methyltransferase,
structural genomics, joint cente structural genomics,
JCSG; HET: NEP SAM; 1.95A {Thermobifida fusca}
Length = 274
Score = 26.8 bits (59), Expect = 9.7
Identities = 6/35 (17%), Positives = 11/35 (31%), Gaps = 1/35 (2%)
Query: 145 MRLQGLPYE-CKKEDVEKFLEGLEIVPNGITIPHD 178
R E++E+ E+V G+
Sbjct: 212 TRENLGEGWARTPEEIERQFGDFELVEPGVVYTAL 246
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
0.323 0.138 0.430
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,774,867
Number of extensions: 282670
Number of successful extensions: 1069
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1038
Number of HSP's successfully gapped: 289
Length of query: 304
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 211
Effective length of database: 4,105,140
Effective search space: 866184540
Effective search space used: 866184540
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 (21.9 bits)
S2: 57 (25.7 bits)