BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 032812
(133 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 57/84 (67%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V GLSF T+ + L FS+YGQ+ E +V DR + +S+GFGFVTF + ++A+ A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSG 104
NGK++DGR I VD A + RSG
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSG 98
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 68.6 bits (166), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 40/98 (40%), Positives = 60/98 (61%), Gaps = 4/98 (4%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ GL+ T+ K L F ++G + E ++ DR S KS+GF F+TF + +A+ A +M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSGMPIARGPPESIADR 118
NGK+L G+ I V+ AK K SF+SG R PP S +R
Sbjct: 69 NGKSLHGKAIKVEQAK-KPSFQSGG--RRRPPASSRNR 103
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 50/76 (65%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V GLS YT+ + L + FS+YG + + +IV D+ S +S+GF FV F + ++A++A NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 83 KTLDGRVIVVDYAKPK 98
LDGR I VD++ K
Sbjct: 77 MELDGRRIRVDFSITK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 50/76 (65%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V GLS YT+ + L + FS+YG + + +IV D+ S +S+GF FV F + ++A++A NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 83 KTLDGRVIVVDYAKPK 98
LDGR I VD++ K
Sbjct: 80 MELDGRRIRVDFSITK 95
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 50/76 (65%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V GLS YT+ + L + FS+YG + + +IV D+ S +S+GF FV F + ++A++A NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 83 KTLDGRVIVVDYAKPK 98
LDGR I VD++ K
Sbjct: 111 MELDGRRIRVDFSITK 126
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 51/81 (62%), Gaps = 4/81 (4%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALS--- 78
++ GLS+ T+ +GL + F Q+G+V E ++ D ++ +S+GFGFVTF +K L+
Sbjct: 29 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 88
Query: 79 -EMNGKTLDGRVIVVDYAKPK 98
E++ KT+D +V A+PK
Sbjct: 89 HELDSKTIDPKVAFPRRAQPK 109
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 62.4 bits (150), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 31/70 (44%), Positives = 46/70 (65%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V GLS YT+ + L + FS+YG + + +IV D+ S +S+GF FV F + ++A++A NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 83 KTLDGRVIVV 92
LDGR I V
Sbjct: 80 MELDGRRIRV 89
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 62.0 bits (149), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 56/94 (59%), Gaps = 7/94 (7%)
Query: 15 NHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAE 74
NHF +V LS + + + AF+ +G++ +A +V D + KSKG+GFV+F + +AE
Sbjct: 14 NHFH--VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71
Query: 75 KALSEMNGKTLDGRVIVVDYAK-----PKTSFRS 103
A+ +M G+ L GR I ++A PK+++ S
Sbjct: 72 NAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 47/86 (54%), Gaps = 3/86 (3%)
Query: 13 CRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEE 72
R+ +V GLS T+ + L ++F V A IV DR + SKGFGFV F S E+
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 73 AEKALSEMNGKTLDGRVIVVDYAKPK 98
A+ A M +DG + +D+AKPK
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPK 92
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 33/90 (36%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 15 NHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAE 74
NHF +V LS + + + AF+ +G++ +A +V D + KSKG+GFV+F + +AE
Sbjct: 14 NHFH--VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAE 71
Query: 75 KALSEMNGKTLDGRVIVVDYAKPKTSFRSG 104
A+ M G+ L GR I ++A K SG
Sbjct: 72 NAIVHMGGQWLGGRQIRTNWATRKPPAPSG 101
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 60.1 bits (144), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 45/69 (65%), Gaps = 4/69 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE-- 79
++ GLS+ T+ K L D FS++G+VV+ + +D ++ +S+GFGFV F E +K + +
Sbjct: 3 FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 62
Query: 80 --MNGKTLD 86
+NGK +D
Sbjct: 63 HKLNGKVID 71
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 47/72 (65%), Gaps = 4/72 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALS--- 78
++ GLS+ T+ +GL + F Q+G+V E ++ D ++ +S+GFGFVTF +K L+
Sbjct: 4 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 63
Query: 79 -EMNGKTLDGRV 89
E++ KT+D +V
Sbjct: 64 HELDSKTIDPKV 75
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/97 (36%), Positives = 54/97 (55%), Gaps = 6/97 (6%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V GL ++T++ L F +G + EA ++ DR + KS+G+GFVT A AE+A + N
Sbjct: 21 FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN 80
Query: 82 GKTLDGRVIVVDY----AKPKTSFRSGMPIARGPPES 114
+DGR V+ AKP+ S ++G I P S
Sbjct: 81 -PIIDGRKANVNLAYLGAKPR-SLQTGFAIGVSGPSS 115
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 51/95 (53%), Gaps = 4/95 (4%)
Query: 18 CPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
C L YV LSFYT+ + + + FS+ G + + + +D++ + GF FV + S +AE A+
Sbjct: 40 CTL-YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 78 SEMNGKTLDGRVIVVDYAKPKTSFRSGMPIARGPP 112
+NG LD R+I D+ F+ G RG
Sbjct: 99 RYINGTRLDDRIIRTDW---DAGFKEGRQYGRGRS 130
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/69 (43%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V GLS+ TS K L D F+++G+VV+ I D + +S+GFGF+ F EK L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 82 GKTLDGRVI 90
+ LDGRVI
Sbjct: 75 HR-LDGRVI 82
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V L++ TS L F +YG+V + I DR + +S+GF FV F +AE A+ M+G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 83 KTLDGRVIVVD---YAKPKTSFRS 103
LDGR + V Y +P S S
Sbjct: 112 AVLDGRELRVQMARYGRPPDSHHS 135
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 50/83 (60%), Gaps = 2/83 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV L ++ L AFS +G + A ++M+ +SKGFGFV F+S EEA KA++EMN
Sbjct: 19 YVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G+ + + + V A+ K +SG
Sbjct: 77 GRIVATKPLYVALAQRKEERQSG 99
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV L F + L F +G++ ++MD + +SKG+GF+TF+ E A+KAL ++N
Sbjct: 30 YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN 89
Query: 82 GKTLDGRVIVVDYAKPKT 99
G L GR + V + +T
Sbjct: 90 GFELAGRPMKVGHVTERT 107
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV+GL + K L FSQYG+++ + I++D+V+ S+G GF+ F EAE+A+ +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 81 NGKTLDGRV--IVVDYA 95
NG+ G I V +A
Sbjct: 151 NGQKPSGATEPITVKFA 167
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 1/89 (1%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
F G++ +V D+++ +S G+GFV + ++AEKA++ +NG L + I V YA+P
Sbjct: 23 FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82
Query: 99 T-SFRSGMPIARGPPESIADRVKVNFFDE 126
+ S R G P+++ + F +
Sbjct: 83 SASIRDANLYVSGLPKTMTQKELEQLFSQ 111
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V L++ TS L F +YG+V + I DR + +S+GF FV F +AE A+ M+G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 83 KTLDGRVIVVD---YAKPKTSFRS 103
LDGR + V Y +P S S
Sbjct: 135 AVLDGRELRVQMARYGRPPDSHHS 158
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 40/69 (57%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV+ L F +N L FS+YG+VV+ I+ D+ + KSKG F+ F + A+ +N
Sbjct: 20 YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN 79
Query: 82 GKTLDGRVI 90
K L GRVI
Sbjct: 80 NKQLFGRVI 88
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+ + L + + Q+G++ + ++ D S +S+GFGFVTF+S E + A++
Sbjct: 31 FIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-AR 89
Query: 82 GKTLDGRVI 90
++DGRV+
Sbjct: 90 PHSIDGRVV 98
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 45/85 (52%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ YV GL+ +K L AF +G + + I +D ++K +GF FV F E+A A+
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 80 MNGKTLDGRVIVVDYAKPKTSFRSG 104
MN L GR I V+ AKP SG
Sbjct: 74 MNESELFGRTIRVNLAKPMRIKESG 98
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 43/72 (59%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V LS+ +S + L FS YG + E + +D ++ K KGF FVTF E A KA +E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 81 NGKTLDGRVIVV 92
+G+ GR++ V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 77 HK-VDGRVV 84
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K +
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 15 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 74
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 75 HK-VDGRVV 82
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K +
Sbjct: 106 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing
7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta
(Prn) Gg); A Human Telomeric Repeat Containing
Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(2pr) G); A Human Telomeric Repeat
Containing 2-Aminopurine
Length = 196
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 77 HK-VDGRVV 84
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K + +
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 167
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGMPIARG 110
T++G V A K S RG
Sbjct: 168 -HTVNGHNCEVRKALSKQEMASASSSQRG 195
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 7/79 (8%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L FS G+V A ++ D+V+ S G+GFV + + ++AE+A++ +NG L + I V Y
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 95 AKPKTS-------FRSGMP 106
A+P + + SG+P
Sbjct: 79 ARPSSEVIKDANLYISGLP 97
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 39/62 (62%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
Y++GL + K + D FS++G+++ + +++D+ + S+G F+ F EAE+A++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 81 NG 82
NG
Sbjct: 151 NG 152
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat
Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 16 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 75
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 76 HK-VDGRVV 83
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K + +
Sbjct: 107 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 166
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGMPIARG 110
T++G V A K S RG
Sbjct: 167 -HTVNGHNCEVRKALSKQEMASASSSQRG 194
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 10 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 70 HK-VDGRVV 77
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K +
Sbjct: 101 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 7/79 (8%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L FS G+V A ++ D+V+ S G+GFV + + ++AE+A++ +NG L + I V Y
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 95 AKPKTS-------FRSGMP 106
A+P + + SG+P
Sbjct: 79 ARPSSEVIKDANLYISGLP 97
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 39/62 (62%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
Y++GL + K + D FS++G+++ + +++D+ + S+G F+ F EAE+A++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 81 NG 82
NG
Sbjct: 151 NG 152
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L FS G+V A ++ D+V+ S G+GFV + + ++AE+A++ +NG L + I V Y
Sbjct: 21 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 80
Query: 95 AKP 97
A+P
Sbjct: 81 ARP 83
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GLSF T+++ L F Q+G + + ++ D + +S+GFGFVT+A+ EE + A++
Sbjct: 18 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 77
Query: 82 GKTLDGRVI 90
K +DGRV+
Sbjct: 78 HK-VDGRVV 85
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V G+ T L D F QYG++ I+ DR S K +GF FVTF H+ +K + +
Sbjct: 109 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 168
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGMPIARG 110
T++G V A K S RG
Sbjct: 169 -HTVNGHNCEVRKALSKQEMASASSSQRG 196
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ L NK L D FS +G ++ +V D + SKG+GFV F + E AE+A+ +MN
Sbjct: 102 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 82 GKTLDGRVIVV 92
G L+ R + V
Sbjct: 160 GMLLNDRKVFV 170
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV+GL S K + FSQYG+++ + I++D+ + S+G GF+ F EAE+A+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 81 NGK 83
NG+
Sbjct: 64 NGQ 66
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 45/92 (48%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V + + + + L D FS+ G VV +V DR + K KG+GF + E A A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSGMPIARGPP 112
NG+ GR + VD A + + + G P
Sbjct: 71 NGREFSGRALRVDNAASEKNKEELKSLGTGAP 102
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L FS G+V A ++ D+V+ S G+GFV + + ++AE+A++ +NG L + I V Y
Sbjct: 36 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 95
Query: 95 AKP 97
A+P
Sbjct: 96 ARP 98
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ L NK L D FS +G ++ +V D + SKG+GFV F + E AE+A+ +MN
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 82 GKTLDGRVIVV 92
G L+ R + V
Sbjct: 165 GMLLNDRKVFV 175
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV+GL S K + FSQYG+++ + I++D+ + S+G GF+ F EAE+A+ +
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 81 NGK 83
NG+
Sbjct: 153 NGQ 155
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 48/89 (53%), Gaps = 1/89 (1%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
F G + +V D+++ +S G+GFV ++ +A+KA++ +NG L + I V YA+P
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
Query: 99 T-SFRSGMPIARGPPESIADRVKVNFFDE 126
+ S R G P++++ + F +
Sbjct: 85 SASIRDANLYVSGLPKTMSQKEMEQLFSQ 113
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ L NK L D FS +G ++ +V D + SKG+GFV F + E AE+A+ +MN
Sbjct: 15 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 82 GKTLDGRVIVVDYAKPK 98
G L+ R + V K +
Sbjct: 73 GMLLNDRKVFVGRFKSR 89
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 A Ph 9.0
Length = 115
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ L NK L D FS +G ++ +V D + SKG+GFV F + E AE+A+ +MN
Sbjct: 9 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 82 GKTLDGRVIVVDYAKPK 98
G L+ R + V K +
Sbjct: 67 GMLLNDRKVFVGRFKSR 83
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V GL + T+ + L FSQYG+VV+ I+ D+ +++S+GFGFV F L+
Sbjct: 20 FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP 79
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
TLDGR I P+ SG
Sbjct: 80 -HTLDGRNIDPKPCTPRGMQPSG 101
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 38/57 (66%)
Query: 42 YGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
+G++ +A +V D + KSKG+GFV+F + +AE A+ +M G+ L GR I ++A K
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 42/77 (54%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ YV GL+ +K L AF +G + + I +D ++K +GF FV F E+A A+
Sbjct: 7 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 80 MNGKTLDGRVIVVDYAK 96
MN L GR I V+ AK
Sbjct: 67 MNESELFGRTIRVNLAK 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 42/77 (54%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ YV GL+ +K L AF +G + + I +D ++K +GF FV F E+A A+
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 80 MNGKTLDGRVIVVDYAK 96
MN L GR I V+ AK
Sbjct: 69 MNESELFGRTIRVNLAK 85
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L + +++ + + FSQ+G+V ++ DR + K KGFGFV E +A++++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 81 NGKTLDGRVIVVDYAKPKTSF 101
+ GR I V A PK S
Sbjct: 63 DNTDFMGRTIRVTEANPKKSL 83
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 52.8 bits (125), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 45/75 (60%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V L+ ++ L +AF + + +++ D + S+G+GFV+F S ++A+ A+ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 81 NGKTLDGRVIVVDYA 95
G+ L+GR + +++A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 18 CPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
C L YV LSFYT+ + + + FS+ G + + + +D++ + GF FV + S +AE A+
Sbjct: 19 CTL-YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAM 76
Query: 78 SEMNGKTLDGRVIVVDY 94
+NG LD R+I D+
Sbjct: 77 RYINGTRLDDRIIRTDW 93
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 11/93 (11%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 80 MNGKTLDGRVIVVDYAKPKTSFRSGMPIARGPP 112
+NG+ L G+ I VD+ RGPP
Sbjct: 69 LNGQDLMGQPISVDWC-----------FVRGPP 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 45/75 (60%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V L+ ++ L +AF + + +++ D + S+G+GFV+F S ++A+ A+ M
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 81 NGKTLDGRVIVVDYA 95
G+ L+GR + +++A
Sbjct: 150 QGQDLNGRPLRINWA 164
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 40/74 (54%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV GL+ +K L AF +G + + I +D ++K +GF FV F E+A A+ MN
Sbjct: 67 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 126
Query: 82 GKTLDGRVIVVDYA 95
L GR I V+ A
Sbjct: 127 ESELFGRTIRVNLA 140
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 11/93 (11%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 80 MNGKTLDGRVIVVDYAKPKTSFRSGMPIARGPP 112
+NG+ L G+ I VD+ RGPP
Sbjct: 85 LNGQDLMGQPISVDWC-----------FVRGPP 106
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 2/84 (2%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V+ + F + L F Q+G++++ I+ + SKGFGFVTF + +A++A ++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSG 104
+G ++GR I V+ A + SG
Sbjct: 76 HGTVVEGRKIEVNNATARVMTNSG 99
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ YV GL+ +K L AF +G + + I +D ++K +GF FV F E+A A+
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 80 MNGKTLDGRVIVVDYA 95
MN L GR I V+ A
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 44/84 (52%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV GL S L + F Q G VV ++ DRV+ + +G+GFV F S E+A+ A+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSG 104
+ L G+ I V+ A SG
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V+ + F + L F Q+G++++ I+ + SKGFGFVTF + +A++A ++
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 81 NGKTLDGRVIVVDYAKPK 98
+G ++GR I V+ A +
Sbjct: 90 HGTVVEGRKIEVNNATAR 107
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 46/75 (61%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 11 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 80 MNGKTLDGRVIVVDY 94
+NG+ L G+ I VD+
Sbjct: 71 LNGQDLMGQPISVDW 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 46/75 (61%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 80 MNGKTLDGRVIVVDY 94
+NG+ L G+ I VD+
Sbjct: 69 LNGQDLMGQPISVDW 83
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 46/75 (61%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 80 MNGKTLDGRVIVVDY 94
+NG+ L G+ I VD+
Sbjct: 69 LNGQDLMGQPISVDW 83
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 46/75 (61%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V G+ + + + D F++YG++ ++ +DR + KG+ V + +++EA+ A+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 80 MNGKTLDGRVIVVDY 94
+NG+ L G+ I VD+
Sbjct: 84 LNGQDLMGQPISVDW 98
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
F G + +V D+++ +S G+GFV ++ +A+KA++ +NG L + I V YA+P
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
Query: 99 TS 100
++
Sbjct: 85 SA 86
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 44/83 (53%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV L F + L F +G++ ++ D + +SKG+GF+TF+ E A +AL ++N
Sbjct: 9 YVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLN 68
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G L GR + V + + SG
Sbjct: 69 GFELAGRPMRVGHVTERLDGGSG 91
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V L F + K L D F++ G V+ A+I M+ + KSKG G V F S E AE+A MN
Sbjct: 12 FVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G L GR I V + + SG
Sbjct: 70 GMKLSGREIDVRIDRNASGPSSG 92
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 34/83 (40%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V L F + K L D F++ G V+ A+I M+ + KSKG G V F S E AE+A MN
Sbjct: 9 FVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMN 66
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G L GR I V + + SG
Sbjct: 67 GMKLSGREIDVRIDRNASGPSSG 89
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKA----L 77
+V GLS T+ + + F Q+G+V +A ++ D+ +++ +GFGFVTF S + EK
Sbjct: 3 FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62
Query: 78 SEMNGKTLD 86
E+N K ++
Sbjct: 63 HEINNKMVE 71
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVM-DRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ L K L D FS +G +++ +M D + SKG+ F+ FAS + ++ A+ M
Sbjct: 9 FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 68
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSG 104
NG+ L R I V YA K S SG
Sbjct: 69 NGQYLCNRPITVSYAFKKDSKGSG 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L ++ L F +YG +V+ NI+ D+++ + +G FV + EEA++A+S +
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 81 NGKTLDG 87
N +G
Sbjct: 152 NNVIPEG 158
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 31 SNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVI 90
+++ L F G + I+ D + S G+ FV F S ++++A+ +NG T+ + +
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 91 VVDYAKP 97
V YA+P
Sbjct: 76 KVSYARP 82
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+VA +++ T+ L F YG + ++V + S K +G+ F+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 81 NGKTLDGRVIVVDYAKPKT 99
+GK +DGR ++VD + +T
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L ++ L F +YG +V+ NI+ D+++ + +G FV + EEA++A+S +
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 81 NGKTLDG 87
N +G
Sbjct: 163 NNVIPEG 169
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 31 SNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVI 90
+++ L F G + I D + S G+ FV F S ++++A+ +NG T+ + +
Sbjct: 27 TDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRL 86
Query: 91 VVDYAKP 97
V YA+P
Sbjct: 87 KVSYARP 93
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L ++ L F +YG +V+ NI+ D+++ + +G FV + EEA++A+S +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 81 NGKTLDG 87
N +G
Sbjct: 76 NNVIPEG 82
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V LS T L + F +G + + D+ + +SKGF F++F E+A +A++ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 83 KTLDGRVIVVDYAKPKTS 100
D ++ V++AKP T+
Sbjct: 80 FGYDHLILNVEWAKPSTN 97
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
Y G++ +++ + FS +GQ++E + + KG+ FV F++HE A A+ +N
Sbjct: 29 YCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVN 82
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G T++G V+ + K SG
Sbjct: 83 GTTIEGHVVKCYWGKESPDMTSG 105
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GL++ T+ L + F +YG V + I+ D + +S+GFGF++F ++ + +
Sbjct: 7 FIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
Query: 82 GKTLDGRVIVVDYAKPK 98
LDG+VI A P+
Sbjct: 67 --ILDGKVIDPKRAIPR 81
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 35/54 (64%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEK 75
+V G+ K + FSQ+G +++A +++D+ + +S+GFGFVT+ S + ++
Sbjct: 91 FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 46.6 bits (109), Expect = 4e-06, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 41/78 (52%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+VA +++ T+ L F YG + ++V + S K +G+ F+ + + A +
Sbjct: 106 FVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD 165
Query: 82 GKTLDGRVIVVDYAKPKT 99
GK +DGR ++VD + +T
Sbjct: 166 GKKIDGRRVLVDVERGRT 183
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+VA L + K L + FS G VV A+I+ D+ KS+G G VTF EA +A+S
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 81 NGKTLDGRVIVV---DYAKPKTSF 101
NG+ L R + V + A PK F
Sbjct: 77 NGQLLFDRPMHVKMDERALPKGDF 100
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 18 CPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
+ +V L+ + + L AFSQ+G+ ++RV K K + F+ F + A KA+
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGK-------LERVK-KLKDYAFIHFDERDGAVKAM 62
Query: 78 SEMNGKTLDGRVIVVDYAKP 97
EMNGK L+G I + +AKP
Sbjct: 63 EEMNGKDLEGENIEIVFAKP 82
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V L++ TS L F +YG+V + I + + +GF FV F +A+ A + M+G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 83 KTLDGRVIVVDYAK 96
LDGR + V A+
Sbjct: 78 AELDGRELRVQVAR 91
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V GL + T+ + L + FS +G+V+ + D + SKGFGFV F +E K +S+ +
Sbjct: 20 VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH- 78
Query: 83 KTLDGRVIVVDYAKPKTSFRSG 104
+DGR K S SG
Sbjct: 79 -MIDGRWCDCKLPNSKQSQDSG 99
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDK-SKGFGFVTFASHEEAEKALSE 79
++ L+ + + + FS YG++ ++ ++R+ SKG+ +V F + +EAEKAL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 80 MNGKTLDGRVIV 91
M+G +DG+ I
Sbjct: 67 MDGGQIDGQEIT 78
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 36/59 (61%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
Y+ GL T+++ L YG++V ++D+ ++K KG+GFV F S A+KA++ +
Sbjct: 9 YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir
In The Complex With Fbp Nbox Peptide
Length = 199
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 7/92 (7%)
Query: 1 MLQQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSK 60
M Q+ L + +CR YV + + + AF+ +G + ++ D V+ K K
Sbjct: 3 MAQRQRALAI-MCR------VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 55
Query: 61 GFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
GF FV + E A+ AL +MN L GR I V
Sbjct: 56 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YVA + S+ + F +G++ + D + K KG+GF+ + + ++ A+S MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Query: 82 GKTLDGRVIVVDYA 95
L G+ + V A
Sbjct: 174 LFDLGGQYLRVGKA 187
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL---- 77
++ LSF + + L + Q+G + +V+ ++ SKG F F + E A+K L
Sbjct: 19 FIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS 78
Query: 78 --SEMNGKTLDGRVIVVDYAKPKTSFRSG 104
+E G LDGR + VD A + SG
Sbjct: 79 LEAEGGGLKLDGRQLKVDLAVTRDEAASG 107
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
L F +YG + IV DR + +S+G+GFV F S A++A++ +NG
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV + + + AF+ +G + ++ D V+ K KGF FV + E A+ AL +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 81 NGKTLDGRVIVV 92
N L GR I V
Sbjct: 91 NSVMLGGRNIKV 102
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YVA + S+ + F +G++ A + D + K KG+GF+ + + ++ A+S M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 81 NGKTLDGRVIVVDYA 95
N L G+ + V A
Sbjct: 188 NLFDLGGQYLRVGKA 202
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 4/82 (4%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
++ LS+ + + L + F + + V + KSKG+ F+ FAS E+A++AL+ N
Sbjct: 20 LSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 83 KTLDGRVIVVDYAKPKTSFRSG 104
+ ++GR I ++ P+ S SG
Sbjct: 76 REIEGRAIRLELQGPRGSPNSG 97
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDK---SKGFGFVTFASHEEAEKALS 78
++ L+F T+ + L FS+ G + I + S GFGFV + E+A+KAL
Sbjct: 9 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
Query: 79 EMNGKTLDGRVIVVDYAKPKTSFRSG 104
++ G T+DG + V ++ T SG
Sbjct: 69 QLQGHTVDGHKLEVRISERATKPASG 94
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V G+ L + F ++G V E ++ D + +GFGF+TF + ++A++ M+
Sbjct: 14 FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MH 72
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
+ G+ + V A+P+ S SG
Sbjct: 73 FHDIMGKKVEVKRAEPRDSKSSG 95
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V + + + F YG++ ++ +DR + SKG+ V + +H++A A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 80 MNGKTLDGRVIVVDY 94
+NG + G+ I VD+
Sbjct: 88 LNGAEIMGQTIQVDW 102
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V + + + F YG++ ++ +DR + SKG+ V + +H++A A
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 80 MNGKTLDGRVIVVDY 94
+NG + G+ I VD+
Sbjct: 134 LNGAEIMGQTIQVDW 148
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 45/85 (52%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ Y+ LS + + L F+++ + I ++ + +G F+TF + E A +AL
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 80 MNGKTLDGRVIVVDYAKPKTSFRSG 104
+NG L G+++V+++ K K SG
Sbjct: 87 VNGYKLYGKILVIEFGKNKKQRSSG 111
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV + + + AF+ +G + + D V+ K KGF FV + E A+ AL +
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 81 NGKTLDGRVIVV 92
N L GR I V
Sbjct: 75 NSVXLGGRNIKV 86
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YVA + S+ + F +G++ + D + K KG+GF+ + + ++ A+S N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Query: 82 GKTLDGRVIVVDYA 95
L G+ + V A
Sbjct: 173 LFDLGGQYLRVGKA 186
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLD 86
K L+ FS+ G+VV +D + K+KGF FV S +A+K + +GK LD
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQ-VVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ L Y +S AF+ G+ V+ I+ +R++ G+ FV FA AEK L ++
Sbjct: 13 WMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKI 72
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSGMPIARGP 111
NGK L G A P F+ GP
Sbjct: 73 NGKPLPG-------ATPAKRFKLNYATYSGP 96
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLD 86
K L+ FS+ G+VV +D + K+KGF FV S +A+K + +GK LD
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
L+ F +G V+ A + +D+ + SK FGFV+F + + A+ A+ MNG
Sbjct: 57 LASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V LS SN+ L AFSQ+G V +A +V+D ++ G GFV FA+ A KAL
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCG- 158
Query: 83 KTLDGRVIVVDYAKP 97
DG ++ +P
Sbjct: 159 ---DGAFLLTTTPRP 170
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V L + + F +YG+ E I DR GFGF+ S AE A +E+
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 81 NGKTLDGRVIVVDYA 95
+G L R + + +A
Sbjct: 79 DGTILKSRPLRIRFA 93
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSD--KSKGFGFVTFASHE---EAEKA 76
+V + S K L + F QYG V E N++ DR + +SKG FVTF + + EA+ A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 77 LSEMNGKTLDG 87
L M K L G
Sbjct: 67 LHNM--KVLPG 75
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
F +G VV A + +D+ ++ SK FGFV++ + A+ A+ MNG + + + V + K
Sbjct: 46 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 105
Query: 99 TSFRSG 104
+SG
Sbjct: 106 NDSKSG 111
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSD--KSKGFGFVTFASHE---EAEKA 76
+V + S K L + F QYG V E N++ DR + +SKG FVTF + + EA+ A
Sbjct: 19 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 78
Query: 77 LSEMNGKTLDG 87
L M K L G
Sbjct: 79 LHNM--KVLPG 87
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDK-SKGFGFVTFASHEEAEKALSEM 80
++ +S + + FS +GQ+ E I+ R D S+G FVTF + A+ A+ M
Sbjct: 111 FIGMISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 81 N-GKTLDG 87
+ +T++G
Sbjct: 169 HQAQTMEG 176
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSD--KSKGFGFVTFASHE---EAEKA 76
+V + S K L + F QYG V E N++ DR + +SKG FVTF + + EA+ A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 77 LSEMNGKTLDG 87
L M K L G
Sbjct: 67 LHNM--KVLPG 75
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDK-SKGFGFVTFASHEEAEKALSEM 80
++ +S + + FS +GQ+ E I+ R D S+G FVTF + A+ A+ M
Sbjct: 99 FIGMISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 81 N-GKTLDG 87
+ +T++G
Sbjct: 157 HQAQTMEG 164
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSD--KSKGFGFVTFASHEEAEKALSE 79
+V + S K L + F QYG V E N++ DR + +SKG FVTF + + A +A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 80 M-NGKTLDG 87
+ N K L G
Sbjct: 67 LHNXKVLPG 75
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDK-SKGFGFVTFASHEEAEKAL-SE 79
++ +S + + FS +GQ+ E I+ R D S+G FVTF + A+ A+ +
Sbjct: 99 FIGXISKKCTENDIRVXFSSFGQIEECRIL--RGPDGLSRGCAFVTFTTRAXAQTAIKAX 156
Query: 80 MNGKTLDG 87
+T +G
Sbjct: 157 HQAQTXEG 164
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYG--QVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALS 78
YV S++T+++ L G VVE +R + +SKG+ V AS K L
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 79 EMNGKTLDGRVIVVDYA 95
+ GK L+G + V A
Sbjct: 118 LLPGKVLNGEKVDVRPA 134
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALS 78
+V GLS T + + + F +G+V + MD ++K +GF F+TF E +K +
Sbjct: 3 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 44/88 (50%), Gaps = 12/88 (13%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANI---VMDRVSDKSKGFGFVTFASHEEAEKA 76
+ YV L TS + + F+ NI ++RV K + + FV F++ E+A +A
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFN--------NIKPGAVERVK-KIRDYAFVHFSNREDAVEA 67
Query: 77 LSEMNGKTLDGRVIVVDYAKPKTSFRSG 104
+ +NGK LDG I V AKP SG
Sbjct: 68 MKALNGKVLDGSPIEVTLAKPVDKDSSG 95
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+V GLS T + + + F +G+V + MD ++K +GF F+TF E +K + +
Sbjct: 5 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 31 SNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVI 90
+++ L F G + I+ D + S G+ FV F S ++++A+ +NG T+ + +
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 91 VVDYAKP 97
V YA+P
Sbjct: 76 KVSYARP 82
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V+ L F S+ + + F+++G + +A + DR S +S G V F +A KA+ + NG
Sbjct: 33 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG 91
Query: 83 KTLDGR 88
LDGR
Sbjct: 92 VPLDGR 97
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ Y+ + + + + + D S G V+ ++ D + +SKG+ F+ F E + A+
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 80 MNGKTLDGRVIVVDYA 95
+NG L R + Y+
Sbjct: 66 LNGYQLGSRFLKCGYS 81
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 6/91 (6%)
Query: 14 RNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEA 73
R FC L+ + L D FS G+V + I+ DR S +SKG +V F +
Sbjct: 26 RTVFC-----MQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 74 EKALSEMNGKTLDGRVIVVDYAKPKTSFRSG 104
A+ + G+ L G I+V ++ + + SG
Sbjct: 81 PLAIG-LTGQRLLGVPIIVQASQAEKNRLSG 110
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 10/84 (11%)
Query: 21 CYVAGLSF-----YTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEK 75
C+ A L+ Y SN+ L +AFS +GQV A +++D S G G V F+ A K
Sbjct: 94 CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPS-GKGIVEFSGKPAARK 152
Query: 76 ALSEMNGKTLDGRVIVVDYAKPKT 99
AL + +G ++ + +P T
Sbjct: 153 ALD----RCSEGSFLLTTFPRPVT 172
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
+V L + + + F +YG+ E I K KGFGF+ + AE A E+
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVEL 78
Query: 81 NGKTLDGRVIVVDYA 95
+ L G+ + V +A
Sbjct: 79 DNMPLRGKQLRVRFA 93
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V L + L + F Q G + + I DR K K FGFV F E A++ +N
Sbjct: 20 FVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 82 GKTLDGRVIVV 92
G L GR I V
Sbjct: 79 GIRLYGRPINV 89
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ Y+ + + + + + D S G V+ ++ D + +SKG+ F+ F E + A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 80 MNGKTLDGRVIVVDYA 95
+NG L R + Y+
Sbjct: 64 LNGYQLGSRFLKCGYS 79
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL-SE 79
+V G+ + F++YG V E I+ DR + SKG+GFV+F + + +K + S+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 80 MN--GKTL 85
+N GK L
Sbjct: 71 INFHGKKL 78
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ Y+ + + + + + D S G V+ ++ D + +SKG+ F+ F E + A+
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 80 MNGKTLDGRVIVVDYA 95
+NG L R + Y+
Sbjct: 65 LNGYQLGSRFLKCGYS 80
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL-SE 79
+V G+ + F++YG V E I+ DR + SKG+GFV+F + + +K + S+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 80 MN--GKTL 85
+N GK L
Sbjct: 71 INFHGKKL 78
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 58 KSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPKTSFR 102
KSKG ++ F S +AEK L E G +DGR + + Y K R
Sbjct: 51 KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V+ L F S+ + + F+++G + +A + DR S +S G V F +A KA + NG
Sbjct: 34 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQYNG 92
Query: 83 KTLDGR 88
LDGR
Sbjct: 93 VPLDGR 98
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 14 RNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEA 73
++H ++ + K L F ++G++ E ++ DR + KG F+T+ E A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 74 EKALSEMN-GKTLDG 87
KA S ++ KTL G
Sbjct: 69 LKAQSALHEQKTLPG 83
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL-SE 79
+V G+ + F++YG V E I+ DR + SKG+GFV+F + + +K + S+
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 80 MN--GKTL 85
+N GK L
Sbjct: 72 INFHGKKL 79
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 38/75 (50%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ GL Y ++ + + + +G + N+V D + SKG+ F + ++A++ +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 81 NGKTLDGRVIVVDYA 95
NG L + ++V A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 38/75 (50%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ GL Y ++ + + + +G + N+V D + SKG+ F + ++A++ +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 81 NGKTLDGRVIVVDYA 95
NG L + ++V A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 38/75 (50%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
++ GL Y ++ + + + +G + N+V D + SKG+ F + ++A++ +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 81 NGKTLDGRVIVVDYA 95
NG L + ++V A
Sbjct: 177 NGMQLGDKKLLVQRA 191
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKS-KGFGFVTFASHEEAEKALSEMN 81
V + F + + + + FS +G++ + + +GFGFV F + ++A+KA + +
Sbjct: 20 VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC 79
Query: 82 GKT-LDGRVIVVDYAKPKTSFRSG 104
T L GR +V+++A + + +SG
Sbjct: 80 HSTHLYGRRLVLEWADSEVTVQSG 103
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+++GL F + + L + +G V + +V +R + K KG +V + + +A +A+ +M+
Sbjct: 21 FISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMD 79
Query: 82 GKTLDGRVIVV 92
G T+ +I V
Sbjct: 80 GMTIKENIIKV 90
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
Y++ L + L + +GQV+ I+ D S S+G GF S E+ E + N
Sbjct: 29 YISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 82 GK 83
GK
Sbjct: 88 GK 89
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V+ L F S+ + + F+++G + +A + DR S +S G V F +A KA+ + G
Sbjct: 93 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 151
Query: 83 KTLDGRVIVV 92
LDGR + +
Sbjct: 152 VPLDGRPMDI 161
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
+ +V L+ + + L +FS++G+ ++RV K K + FV F A KA+ E
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGK-------LERVK-KLKDYAFVHFEDRGAAVKAMDE 68
Query: 80 MNGKTLDGRVIVVDYAKPKTSFRSG 104
MNGK ++G I + AKP RSG
Sbjct: 69 MNGKEIEGEEIEIVLAKPPDKKRSG 93
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 7/85 (8%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV + + ++ + L FS G + I+ D+ S KG+ ++ FA + A++ M+
Sbjct: 40 YVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MD 98
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGMP 106
GR I V PK R+ MP
Sbjct: 99 ETVFRGRTIKV---LPK---RTNMP 117
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 58 KSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
KSKG ++ F S +AEK L E G +DGR + + Y K
Sbjct: 134 KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 51 VMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPKTS 100
V+D + ++ FG+V F S E+ EKAL E+ G + G I ++ K + S
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDS 93
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L AFS +G +++ ++ D + FVT+ E A++A++E+NG ++ + V+
Sbjct: 30 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 95 AKPKTSFRSG 104
A+ + SG
Sbjct: 84 ARKQPMLDSG 93
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV LS + + FSQ G ++ + S+ + FV F H +A AL+ MN
Sbjct: 19 YVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAMN 76
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G+ + G+ + V++A +S +SG
Sbjct: 77 GRKILGKEVKVNWATTPSSQKSG 99
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ GL Y ++ + + + +G + N+V D + SKG+ F + ++A++ +N
Sbjct: 5 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64
Query: 82 GKTLDGRVIVVDYA 95
G L + ++V A
Sbjct: 65 GMQLGDKKLLVQRA 78
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 14 RNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEA 73
++H +V + + L F ++G++ E ++ DR++ KG F+T+ + + A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 74 EKALSEMN-GKTLDG--RVIVVDYAKPKTSFRSG 104
KA S ++ KTL G R I V A + SG
Sbjct: 71 LKAQSALHEQKTLPGMNRPIQVKPAASEGRGESG 104
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 9/69 (13%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L++ F +G + E I+ GF FV F E A KA+ E++GK+ + + V Y
Sbjct: 48 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Query: 95 AK-PKTSFR 102
+K P +R
Sbjct: 100 SKLPAKRYR 108
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
LC VA L + + + +G + +V + +SKG+GF + + A +A S+
Sbjct: 98 LC-VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 80 MNGKTLDGRVIVVDY 94
+ GK L R + V +
Sbjct: 157 LLGKPLGPRTLYVHW 171
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
DK KG FVT + E+AE A++ + L R + V
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 89
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
LC VA L + + + +G + +V + +SKG+GF + + A +A S+
Sbjct: 98 LC-VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 80 MNGKTLDGRVIVVDY 94
+ GK L R + V +
Sbjct: 157 LLGKPLGPRTLYVHW 171
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
DK KG FVT + E+AE A++ + L R + V
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 89
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 20 LCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE 79
LC VA L + + + +G + +V + +SKG+GF + + A +A S+
Sbjct: 96 LC-VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
Query: 80 MNGKTLDGRVIVVDY 94
+ GK L R + V +
Sbjct: 155 LLGKPLGPRTLYVHW 169
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
DK KG FVT + E+AE A++ + L R + V
Sbjct: 52 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 87
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V+ L F S+ + + F+++G + +A + DR S +S G V F +A KA+ + G
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 98
Query: 83 KTLDGR 88
LDGR
Sbjct: 99 VPLDGR 104
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.0 bits (79), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 23 VAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNG 82
V+ L F S+ + + F+++G + +A + DR S +S G V F +A KA+ + G
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 98
Query: 83 KTLDGR 88
LDGR
Sbjct: 99 VPLDGR 104
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 35.0 bits (79), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L AFS +G +++ ++ D + FVT+ E A++A++E+NG ++ + V+
Sbjct: 54 LRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Query: 95 AK 96
A+
Sbjct: 108 AR 109
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
++ L + + + F QYG+V+E +I+ K +GFV AE A+ ++
Sbjct: 12 FIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLH 63
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
L G I V+ +K K+ SG
Sbjct: 64 HYKLHGVNINVEASKNKSKASSG 86
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L F T +G DA + + +V D+ +DK KGF +V F + ++AL+
Sbjct: 18 AYVGNLPFNTV-QGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSG 104
+G L R + VD A+ + +SG
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDKSG 99
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 41 QYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVI 90
+YG+V E N V D + D G +V F E+AEKA+ ++N + +G+ I
Sbjct: 50 KYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
FS+YG++V ++ KGF FV + + A A++ +G+ + G+V+ ++ A
Sbjct: 37 FSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88
Query: 99 TSFRSG 104
RSG
Sbjct: 89 KVNRSG 94
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L++ F +G + E I+ GF FV F E A KA+ E++GK+ + + V Y
Sbjct: 21 LNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 72
Query: 95 AK 96
+K
Sbjct: 73 SK 74
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 35 LSDAFSQYGQV--VEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
+ D S+YG V +E +D V G FV F S + +KA+ + G+ RV+V
Sbjct: 31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90
Query: 93 DYAKPKTSFR 102
Y P + R
Sbjct: 91 KYCDPDSYHR 100
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 34.7 bits (78), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 35 LSDAFSQYGQV--VEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
+ D S+YG V +E +D V G FV F S + +KA+ + G+ RV+V
Sbjct: 31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90
Query: 93 DYAKPKTSFR 102
Y P + R
Sbjct: 91 KYCDPDSYHR 100
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 36/86 (41%), Gaps = 12/86 (13%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEM 80
YV L L AFS YG + I + GF FV F +AE A+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 81 NGKTLDGRVIVVDYAKPKTSFRSGMP 106
+GK + G + V+ + +GMP
Sbjct: 58 DGKVICGSRVRVELS-------TGMP 76
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 58 KSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY-AKPK 98
KSKG ++ F + +AEK E G +DGR I + Y +PK
Sbjct: 128 KSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPK 169
Score = 32.7 bits (73), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 12/85 (14%)
Query: 21 CYVAGLSFYTS----NKGLSDAFSQYG-QVVEANIVMDRVSDKSKGFGFVTFASHEEAEK 75
+V L+F S G+SD F++ VV+ I M R FG+V F S E+ EK
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRK------FGYVDFESAEDLEK 63
Query: 76 ALSEMNGKTLDGRVIVVDYAKPKTS 100
AL E+ G + G I ++ K K S
Sbjct: 64 AL-ELTGLKVFGNEIKLEKPKGKDS 87
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FSQ+GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 28 KSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Query: 93 DYAK 96
YAK
Sbjct: 85 QYAK 88
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FSQ+GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 28 KSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Query: 93 DYAK 96
YAK
Sbjct: 85 QYAK 88
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V L + + + F +YG+ E I K KGFGF+ + AE A E++
Sbjct: 19 FVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELD 72
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
L G+ + V +A S SG
Sbjct: 73 NMPLRGKQLRVRFACHSASLTSG 95
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 18 CPL---CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAE 74
CPL YV L + L AF YG + V+ GF FV F +A
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAA 124
Query: 75 KALSEMNGKTLDGRVIVVD 93
A+ E++G+TL G + V+
Sbjct: 125 DAVRELDGRTLCGCRVRVE 143
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 5/96 (5%)
Query: 10 VYICRNHFCPLCYVAG-LSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFA 68
V I +N F P+ + L + L S++GQ+ + ++ DR D G V+F
Sbjct: 17 VVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKL-LLFDRHPD---GVASVSFR 72
Query: 69 SHEEAEKALSEMNGKTLDGRVIVVDYAKPKTSFRSG 104
EEA+ + ++G+ GR I T ++SG
Sbjct: 73 DPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSG 108
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V +S +N+ L F +YG V+E +IV D + FV E+A +A+ ++
Sbjct: 14 HVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLD 65
Query: 82 GKTLDGRVIVVDYAKPKTSFRSG 104
G+ + V + + SG
Sbjct: 66 NTEFQGKRMHVQLSTSRLRTASG 88
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPK 98
FS+YG+V ++ KG+ FV +++ A A+ NG+ L G+ + ++ A
Sbjct: 49 FSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100
Query: 99 TSFRSG 104
RSG
Sbjct: 101 KPDRSG 106
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV + + + + L F G V I+ D+ S KGF ++ F+ E +L+ ++
Sbjct: 9 YVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LD 67
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGM 105
GR I V PK + R G+
Sbjct: 68 ESLFRGRQIKV---IPKRTNRPGI 88
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 33.1 bits (74), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 35 LSDAFSQYGQV--VEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
+ D S+YG V +E +D V G FV F S + +KA + G+ RV+V
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVT 91
Query: 93 DYAKPKTSFR 102
Y P + R
Sbjct: 92 KYCDPDSYHR 101
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 35 LSDAFSQYGQV--VEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
+ D S+YG V +E +D V G FV F S + +KA + G+ RV+V
Sbjct: 33 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVT 92
Query: 93 DYAKPKTSFR 102
Y P + R
Sbjct: 93 KYCDPDSYHR 102
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 15 NHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAE 74
N+ C + YV L K + D F +YG + + ++ R F FV F +AE
Sbjct: 20 NNDCRI-YVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAE 75
Query: 75 KALSEMNGKTLDGRVIVVDYAKPKTSFRSGMPIARGP 111
A+ +G DG + V++ RSG GP
Sbjct: 76 DAVYGRDGYDYDGYRLRVEFP------RSGRGTGSGP 106
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FSQ+GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 27 KSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Query: 93 DYAK 96
YAK
Sbjct: 84 QYAK 87
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
YV + + + + L F G V I+ D+ S KGF ++ F+ E +L+ ++
Sbjct: 10 YVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LD 68
Query: 82 GKTLDGRVIVVDYAKPKTSFRSGM 105
GR I V PK + R G+
Sbjct: 69 ESLFRGRQIKV---IPKRTNRPGI 89
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 27 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 84 QYAKTDSDIIAKM 96
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 28 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 85 QYAKTDSDIIAKM 97
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 32.7 bits (73), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 25 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 81
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 82 QYAKTDSDIIAKM 94
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 32.7 bits (73), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 27 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 84 QYAKTDSDIIAKM 96
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.7 bits (73), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 48 ANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKT-LDGRVIVVDYAKPKTSFRSGMP 106
+V+D+ + SKG+GFV F E ++AL+E G L + + + A PK S P
Sbjct: 40 GKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK--P 96
Query: 107 IARGP 111
+ GP
Sbjct: 97 VESGP 101
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 27 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 84 QYAKTDSDIIAKM 96
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 28 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 85 QYAKTDSDIIAKM 97
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 24 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 80
Query: 93 DYAKPKTSFRSGM 105
YAK + + M
Sbjct: 81 QYAKTDSDIIAKM 93
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 32.3 bits (72), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 44 QVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLD--GRVIVVDYAKPK 98
Q E ++ ++ S +S+GF FV F+ ++A + + E N +L+ G+ + + Y+ PK
Sbjct: 28 QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM-EANQHSLNILGQKVSMHYSDPK 83
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 32.3 bits (72), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 23 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 79
Query: 93 DYAK 96
YAK
Sbjct: 80 QYAK 83
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 32.3 bits (72), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 33 KGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
K L FS++GQ+++ I++ R S K +G FV F A AL M G + + +
Sbjct: 22 KSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 78
Query: 93 DYAK 96
YAK
Sbjct: 79 QYAK 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 18 CPL---CYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAE 74
CPL YV L + L AF YG + V+ GF FV F +A
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV-----WVARNPPGFAFVEFEDPRDAA 124
Query: 75 KALSEMNGKTLDGRVIVVD 93
A+ +++G+TL G + V+
Sbjct: 125 DAVRDLDGRTLCGCRVRVE 143
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.0 bits (71), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVEA--------NIVMDRVSDKSKGFGFVTFASHEE 72
+V GL + + ++D F Q G + N+ DR + K KG V+F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 73 AEKALSEMNGKTLDGRVIVVDYAKPKTSF 101
A+ A+ +GK G I V +A + F
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRADF 98
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 6/61 (9%)
Query: 39 FSQYGQVVEANIVMDRVSD-KSKGFGFVTFASHEEAEKALSEMNG-KTLDG--RVIVVDY 94
F +G + E I+ R D SKG FV ++SH EA+ A++ ++G +T+ G +VV +
Sbjct: 36 FEAFGNIEECTIL--RGPDGNSKGCAFVKYSSHAEAQAAINALHGSQTMPGASSSLVVKF 93
Query: 95 A 95
A
Sbjct: 94 A 94
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMN 81
+V L+ S + + F +G V++ V+ SKG FV F+SH EA+ A+ ++
Sbjct: 19 FVGMLNKQQSEEDVLRLFQPFG-VIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 82 G-KTLDG--RVIVVDYA 95
G +T+ G +VV +A
Sbjct: 78 GSQTMPGASSSLVVKFA 94
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 58 KSKGFGFVTFASHEEAEKALSE-MNGKT-LDGRVIVVDYAKPK 98
K++GF FV + SH A A + M G+ L G I VD+A+P+
Sbjct: 50 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 92
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 21 CYVAGLSFYTSNKGLSDAFSQYGQVVE--------ANIVMDRVSDKSKGFGFVTFASHEE 72
+V GL + + ++D F Q G + N+ DR + K KG V+F
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 73 AEKALSEMNGKTLDGRVIVVDYA 95
A+ A+ +GK G I V +A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1QGH|A Chain A, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|B Chain B, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|C Chain C, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|D Chain D, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|E Chain E, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|F Chain F, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|G Chain G, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|H Chain H, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|I Chain I, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|J Chain J, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|K Chain K, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site.
pdb|1QGH|L Chain L, The X-Ray Structure Of The Unusual Dodecameric Ferritin
From Listeria Innocua, Reveals A Novel Intersubunit
Iron Binding Site
Length = 156
Score = 29.3 bits (64), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 3 QQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGF 62
Q+ L+V+ + H Y+ G +F+T ++ + D +S++G+ MD V+++
Sbjct: 15 HQVANLNVFTVKIHQIH-WYMRGHNFFTLHEKMDDLYSEFGE------QMDEVAERLLAI 67
Query: 63 GFVTFASHEE 72
G F++ +E
Sbjct: 68 GGSPFSTLKE 77
>pdb|2IY4|A Chain A, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|B Chain B, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|C Chain C, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|D Chain D, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|E Chain E, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|F Chain F, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|G Chain G, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|H Chain H, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|I Chain I, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|J Chain J, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|K Chain K, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|L Chain L, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|M Chain M, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|N Chain N, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|O Chain O, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|P Chain P, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|Q Chain Q, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|R Chain R, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|S Chain S, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|T Chain T, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|U Chain U, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|V Chain V, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|X Chain X, X-ray Structure Of Dps From Listeria Monocytogenes
pdb|2IY4|Y Chain Y, X-ray Structure Of Dps From Listeria Monocytogenes
Length = 156
Score = 29.3 bits (64), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 3 QQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGF 62
Q+ L+V+ + H Y+ G +F+T ++ + D +S++G+ MD V+++
Sbjct: 15 HQVANLNVFTVKIHQIH-WYMRGHNFFTLHEKMDDLYSEFGE------QMDEVAERLLAI 67
Query: 63 GFVTFASHEE 72
G F++ +E
Sbjct: 68 GGSPFSTLKE 77
>pdb|2BK6|A Chain A, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant.
pdb|2BK6|B Chain B, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant.
pdb|2BK6|C Chain C, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant.
pdb|2BK6|D Chain D, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant.
pdb|2BK6|E Chain E, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant.
pdb|2BK6|F Chain F, The X-Ray Crystal Structure Of The Listeria Innocua H31g
Dps Mutant
Length = 156
Score = 29.3 bits (64), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 3 QQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGF 62
Q+ L+V+ + H Y+ G +F+T ++ + D +S++G+ MD V+++
Sbjct: 15 HQVANLNVFTVKIHQIG-WYMRGHNFFTLHEKMDDLYSEFGE------QMDEVAERLLAI 67
Query: 63 GFVTFASHEE 72
G F++ +E
Sbjct: 68 GGSPFSTLKE 77
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 29.3 bits (64), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSD-KSKGFGFVTFASHEEAEKALSEM 80
+V L +++ + F +G + E ++ R D SKG FV F +H EA+ A++ +
Sbjct: 16 FVGMLGKQQTDEDVRKMFEPFGTIDECTVL--RGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 81 N-GKTLDG--RVIVVDYA 95
+ +TL G +VV +A
Sbjct: 74 HSSRTLPGASSSLVVKFA 91
>pdb|2BJY|A Chain A, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|B Chain B, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|C Chain C, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|D Chain D, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|E Chain E, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|F Chain F, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|G Chain G, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|H Chain H, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|I Chain I, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|J Chain J, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|K Chain K, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant.
pdb|2BJY|L Chain L, The X-Ray Crystal Structure Of Listeria Innocua Dps
H31g- H43g Mutant
Length = 156
Score = 28.9 bits (63), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 3 QQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGF 62
Q+ L+V+ + H Y+ G +F+T + + D +S++G+ MD V+++
Sbjct: 15 HQVANLNVFTVKIHQIG-WYMRGHNFFTLGEKMDDLYSEFGE------QMDEVAERLLAI 67
Query: 63 GFVTFASHEE 72
G F++ +E
Sbjct: 68 GGSPFSTLKE 77
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 28.9 bits (63), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 17 FCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKA 76
FC Y+ GL F NK + D F + V ++ + + K+ G GFV F + + + A
Sbjct: 26 FC--VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83
Query: 77 L 77
L
Sbjct: 84 L 84
>pdb|2BKC|A Chain A, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|B Chain B, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|C Chain C, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|D Chain D, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|E Chain E, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|F Chain F, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|G Chain G, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|H Chain H, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|I Chain I, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|J Chain J, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|K Chain K, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|L Chain L, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|M Chain M, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|N Chain N, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|O Chain O, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|P Chain P, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|Q Chain Q, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|R Chain R, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|S Chain S, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|T Chain T, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|U Chain U, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|V Chain V, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|X Chain X, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
pdb|2BKC|Y Chain Y, The X-Ray Structure Of The H43g Listeria Innocua Dps
Mutant
Length = 156
Score = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 3 QQLLTLHVYICRNHFCPLCYVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGF 62
Q+ L+V+ + H Y+ G +F+T + + D +S++G+ MD V+++
Sbjct: 15 HQVANLNVFTVKIHQIH-WYMRGHNFFTLGEKMDDLYSEFGE------QMDEVAERLLAI 67
Query: 63 GFVTFASHEE 72
G F++ +E
Sbjct: 68 GGSPFSTLKE 77
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A
Fragment Of U6 Rna
Length = 92
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 22/41 (53%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKP 97
+ S+ F ++ S E+A + ++NG ++G +V + P
Sbjct: 42 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 82
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 49 NIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAK 96
+IV+D +SD + G ++ FA+ E A+ + G G +V+ +++
Sbjct: 62 DIVVD-LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 22/41 (53%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKP 97
+ S+ F ++ S E+A + ++NG ++G +V + P
Sbjct: 119 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 159
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 51 VMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKPKTSFR 102
V+D + ++ FG+V F S E+ EKAL E+ G + G I ++ K + R
Sbjct: 49 VVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 99
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 22 YVAGLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSE-M 80
YV GL + L + F Q+G++ +V + + F+ FA+ + AE A +
Sbjct: 16 YVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKSF 69
Query: 81 NGKTLDGRVIVVDYAK 96
N ++GR + V + +
Sbjct: 70 NKLIVNGRRLNVKWGR 85
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAK 96
FSQ+GQ+++ ++ + K +G FV F A AL M G + + + Y+K
Sbjct: 31 FSQFGQILD---IVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 22/41 (53%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDYAKP 97
+ S+ F ++ S E+A + ++NG ++G +V + P
Sbjct: 156 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 196
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY 94
L QYG VVE+ ++ +D VT++S ++A +AL ++NG L+ + V Y
Sbjct: 32 LDSLLVQYG-VVESCEQVN--TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY 88
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
DK KG FVT + E+AE A++ + L R + V
Sbjct: 34 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 69
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 24/53 (45%)
Query: 25 GLSFYTSNKGLSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKAL 77
GL F S + + FS V + +S G FV FAS E AEKAL
Sbjct: 22 GLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74
>pdb|3SY7|A Chain A, Improved Crystal Structure Of Pseudomonas Aeruginosa Oprd
Length = 428
Score = 26.2 bits (56), Expect = 5.8, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGK--------TLD 86
L D + QY + +N + SD+S GF F + +++E + +++ TLD
Sbjct: 206 LEDIYRQY--YLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLD 263
Query: 87 GRVIVVDYAK 96
+ Y K
Sbjct: 264 AHTFTLAYQK 273
>pdb|2ODJ|A Chain A, Crystal Structure Of The Outer Membrane Protein Oprd From
Pseudomonas Aeruginosa
pdb|2ODJ|B Chain B, Crystal Structure Of The Outer Membrane Protein Oprd From
Pseudomonas Aeruginosa
Length = 428
Score = 26.2 bits (56), Expect = 6.2, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 35 LSDAFSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGK--------TLD 86
L D + QY + +N + SD+S GF F + +++E + +++ TLD
Sbjct: 206 LEDIYRQY--YLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLD 263
Query: 87 GRVIVVDYAK 96
+ Y K
Sbjct: 264 AHTFTLAYQK 273
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 57 DKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVV 92
DK KG FVT + E+AE A++ + L R + V
Sbjct: 37 DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSV 72
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 64 FVTFASHEEAEKALSEMNGKTLDGRVIVVD 93
FV F+ E KA+ +NG+ GR +V +
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAE 208
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 25.8 bits (55), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 64 FVTFASHEEAEKALSEMNGKTLDGRVI 90
F+ F E A KA+ ++NG+ GRV+
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVV 86
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of
Fbp- Interacting Repressor, Siahbp1
Length = 119
Score = 25.8 bits (55), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 64 FVTFASHEEAEKALSEMNGKTLDGRVIVVD 93
FV F+ E KA+ +NG+ GR +V +
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVAE 99
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 64 FVTFASHEEAEKALSEMNGKTLDGRVIVVD 93
FV F+ E KA+ +NG+ GR +V +
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAE 104
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLD 86
FS++G++ N K+KG+ F+ +AS A A+ +G LD
Sbjct: 28 FSKFGKI--TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 32/113 (28%), Positives = 52/113 (46%), Gaps = 12/113 (10%)
Query: 3 QQLLTLHVYICRNHFCPLC--YVAGLSFYTSNKGLSDAFSQY------GQVVEANIVMDR 54
+++ TL V+ P C YV L+ + K L F +Y Q + +I + +
Sbjct: 28 EEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK 87
Query: 55 VSDKSKGFGFVTFASHEEAEKALSEMNGKTLDGRVIVVDY---AKPKTSFRSG 104
+ KG F+ + + A KAL E NG L G+ +VV + A+PK + G
Sbjct: 88 -EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEG 139
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 25.4 bits (54), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 39 FSQYGQVVEANIVMDRVSDKSKGFGFVTFASHEEAEKALSEMNGKTLD 86
FS++G++ N K+KG+ F+ +AS A A+ +G LD
Sbjct: 42 FSKFGKI--TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,875,141
Number of Sequences: 62578
Number of extensions: 142466
Number of successful extensions: 643
Number of sequences better than 100.0: 210
Number of HSP's better than 100.0 without gapping: 175
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 428
Number of HSP's gapped (non-prelim): 237
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)