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= 023559
(280 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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 52/79 (65%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
DE ++FVGGLS++ E+ LE F ++G+I E ++ +R++ R RGFGF+T+ + DA
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 65 IREMHGREFGDRVISVNKA 83
+ M+G+ R I V++A
Sbjct: 71 MMAMNGKSVDGRQIRVDQA 89
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
N+IFVGG+ N E +L F +FG + E ++ + + RPRGFGFIT+ D +++D A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 67 EMHGREFGDRVISVNKAQPK 86
MH + + + V +A+P+
Sbjct: 71 -MHFHDIMGKKVEVKRAEPR 89
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 50/82 (60%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FVG + + TE QL++ F G ++ +++ +R++G+P+G+GF Y D+ A+R +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 69 HGREFGDRVISVNKAQPKMGGE 90
+GREF R + V+ A + E
Sbjct: 71 NGREFSGRALRVDNAASEKNKE 92
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 64.7 bits (156), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 47/73 (64%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R++VG L +N+TE L F+ FG+I Q+M++ ++GR +G+GFIT++D A+ +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 68 MHGREFGDRVISV 80
++G E R + V
Sbjct: 88 LNGFELAGRPMKV 100
>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 = 64.3 bits (155), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 31/79 (39%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+IFVGG+ +V ++ E F ++G II+ Q+ML++D+G+ RGFGF+TY A+D +
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Query: 68 MHGREFGDRVISVNKAQPK 86
+F DR I + +A+P+
Sbjct: 149 KF-IDFKDRKIEIKRAEPR 166
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 51/83 (61%), Gaps = 2/83 (2%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
K+ ++F+GGL+W+ TE L F ++G + + +IM + +GR RGFGF+++ ++D+
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 64 AIREMHGREFGDRVISVNKAQPK 86
++ H + +VI +A P+
Sbjct: 61 VVKTQHILD--GKVIDPKRAIPR 81
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 4/88 (4%)
Query: 3 GKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
G ++F+GGLSW T+ L F +FG++ EC +M + + R RGFGF+T+ D+ +D
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 63 DAI----REMHGREFGDRVISVNKAQPK 86
+ E+ + +V +AQPK
Sbjct: 82 KVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 60.8 bits (146), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VG L +N+TE L F+ FGKI +M + D+GR +G+GFIT++D A+ ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 69 HGREFGDRVISVNKAQPKMGG 89
+G E R + V ++ G
Sbjct: 68 NGFELAGRPMRVGHVTERLDG 88
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 60.1 bits (144), Expect = 1e-09, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
I+VG L ++ T Q++ F +FGK+ +++ +R++ +P+GFGF+ + ++ +AI ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 69 HGREFGDRVISVNKAQPK 86
+F R I V +A PK
Sbjct: 63 DNTDFMGRTIRVTEANPK 80
>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 = 59.7 bits (143), Expect = 2e-09, Method: Composition-based stats.
Identities = 30/80 (37%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
+D + FVGGLSW+ +++ L++ F +FG++++C I + ++GR RGFGFI + D +++
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 64 AIREMHGREFGDRVISVNKA 83
+ + R G RVI KA
Sbjct: 69 VLDQKEHRLDG-RVIDPKKA 87
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 48/75 (64%), Gaps = 1/75 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
IFVGGLS N T +++ F++FGK+ + +M ++ + R RGFGF+T+ + + + + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 69 HGREFGDRVISVNKA 83
H E ++++ KA
Sbjct: 61 HFHEINNKMVECKKA 75
>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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 43/59 (72%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+F+GGLSW+ T++ L++ F +FG++++C + L+ +GR RGFGF+ + + ++D + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ TE L N ++++GK+ +C +M + S R RGFGF+T++ +D A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 57.4 bits (137), Expect = 8e-09, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 39/60 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
++F+GGLSW T+ L F +FG++ EC +M + + R RGFGF+T+ D+ +D + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 73
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 71
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 70
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++FVGGL W+ T+ L + F ++G++++C IM ++ + + RGFGF+ + D + +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 40/58 (68%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++F+GGLS+ T+ L + F+++G + +C +M + ++ R RGFGF+TYA +D A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+IFVGG+ + E L + F+++GKI +IM +R SG+ RGF F+T+ D ++D +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 40/61 (65%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+IFVGGL ++ T+ L F+ FG I E ++ +R +G+ RG+GF+T ADR A + A +
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 67 E 67
+
Sbjct: 78 D 78
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 48/79 (60%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+FVG LS +T +++AF FGKI + +++ + +G+ +G+GF+++ ++ ++AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 68 MHGREFGDRVISVNKAQPK 86
M G+ G R I N A K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIEC-QIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
IF+G L + E+ L + F FG I++ +IM + D+G +G+ FI +A A D AI
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 68 MHGREFGDRVISVNKAQPK 86
M+G+ +R I+V+ A K
Sbjct: 68 MNGQYLCNRPITVSYAFKK 86
>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 = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 49/79 (62%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+FVG LS +T ++ AF FG+I + +++ + +G+ +G+GF+++ ++ ++AI++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 68 MHGREFGDRVISVNKAQPK 86
M G+ G R I N A K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
++F+GGL+ E+ L+ F + G I E ++ +R S + RGF FIT+ + +A ++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 68 MHGREFGDRVISVNKAQ 84
M+G+ + I V +A+
Sbjct: 68 MNGKSLHGKAIKVEQAK 84
>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 = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 44/64 (68%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++V GL +T+++LE F ++G+II +I++++ +G RG GFI + R ++AI+ +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 69 HGRE 72
+G++
Sbjct: 151 NGQK 154
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 44/81 (54%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
+ + V L N+T+ + + F G+I C+++ ++ +G+ G+GF+ Y D + + A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 65 IREMHGREFGDRVISVNKAQP 85
I ++G + I V+ A+P
Sbjct: 61 INTLNGLRLQTKTIKVSYARP 81
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 42/77 (54%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL+ V ++ L AF FG I + QI L+ ++ + RGF F+ + AI M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 69 HGREFGDRVISVNKAQP 85
+ E R I VN A+P
Sbjct: 75 NESELFGRTIRVNLAKP 91
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 44/64 (68%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++V GL ++++++E F ++G+II +I+L++ +G RG GFI + R ++AI+ +
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 69 HGRE 72
+G++
Sbjct: 153 NGQK 156
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 45/80 (56%)
Query: 6 ENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+ + V L N+T+ + ++ F G I C+++ ++ +G+ G+GF+ Y+D D AI
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 66 REMHGREFGDRVISVNKAQP 85
++G + + I V+ A+P
Sbjct: 64 NTLNGLKLQTKTIKVSYARP 83
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 46/77 (59%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
NRI+V + ++++ +++ F+ FGKI C + + +G+ +G+GFI Y ++ DA+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 67 EMHGREFGDRVISVNKA 83
M+ + G + + V KA
Sbjct: 171 SMNLFDLGGQYLRVGKA 187
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R++VG + + + E + AF FG I + + + + +GF F+ Y A A+ +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 68 MHGREFGDRVISV------NKAQPKM 87
M+ G R I V +AQP +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPII 100
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV ++++ TE +L F+ +G I ++ + SG+PRG+ FI Y R M A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 69 HGREFGDRVISVN 81
G++ R + V+
Sbjct: 165 DGKKIDGRRVLVD 177
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
KD N +++ GL +T++ +E+ F RFG+II ++++++ +G RG FI + R ++
Sbjct: 87 KDAN-LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 64 AIREMHGRE 72
AI +G +
Sbjct: 146 AITSFNGHK 154
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 41/77 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L N+T+ +L + F G++ +++ ++ +G G+GF+ Y + + AI +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 HGREFGDRVISVNKAQP 85
+G + I V+ A+P
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
KD N +++ GL +T++ +E+ F RFG+II ++++++ +G RG FI + R ++
Sbjct: 87 KDAN-LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 64 AIREMHGRE 72
AI +G +
Sbjct: 146 AITSFNGHK 154
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 41/77 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L N+T+ +L + F G++ +++ ++ +G G+GF+ Y + + AI +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 HGREFGDRVISVNKAQP 85
+G + I V+ A+P
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 39/69 (56%)
Query: 1 MAGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRA 60
M D ++F+G + N+ E+ L+ F+ FGKI E ++ +R +G +G F+TY +R +
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 61 MDDAIREMH 69
A +H
Sbjct: 68 ALKAQSALH 76
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
KD N ++V L +T+ QL+ F ++G I++ I+ ++ +GRPRG F+ Y R +
Sbjct: 12 KDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 64 AIREMHGR--EFGDRVISVNKAQ 84
AI ++ E G + +SV A+
Sbjct: 71 AISALNNVIPEGGSQPLSVRLAE 93
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 45/77 (58%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
NRI+V + ++++ +++ F+ FGKI C + + +G+ +G+GFI Y ++ DA+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 67 EMHGREFGDRVISVNKA 83
+ + G + + V KA
Sbjct: 170 SXNLFDLGGQYLRVGKA 186
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R++VG + + + E + AF FG I + + + +GF F+ Y A A+ +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 68 MHGREFGDRVISV------NKAQPKM 87
+ G R I V +AQP +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPII 99
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 44/64 (68%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++V GL ++++++E F ++G+II +I+L++ +G RG GFI + R ++AI+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 69 HGRE 72
+G++
Sbjct: 64 NGQK 67
>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 = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 41/75 (54%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FVG L+ NV + L NAF F + +M + +G RG+GF+++ + +A+ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 69 HGREFGDRVISVNKA 83
G++ R + +N A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 46/79 (58%), Gaps = 8/79 (10%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
++F+G L TE+++ + F+++GK++EC I+ + +GF+ D+ A +DAIR
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 68 MHGREFGDRVISVNKAQPK 86
+H + I+V ++ K
Sbjct: 62 LHHYKLHGVNINVEASKNK 80
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 43/73 (58%)
Query: 6 ENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
++ ++V L +++T L F ++GK+++ IM ++D+ + +G FI + D+ + +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 66 REMHGREFGDRVI 78
R ++ ++ RVI
Sbjct: 76 RAINNKQLFGRVI 88
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
KD N ++V L +T+ QL+ F ++G I++ I+ ++ +GRPRG F+ Y R +
Sbjct: 99 KDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 157
Query: 64 AIREMHGR--EFGDRVISVNKAQ 84
AI ++ E G + +SV A+
Sbjct: 158 AISALNNVIPEGGSQPLSVRLAE 180
Score = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L + T+R+L F G I C+I + +G G+ F+ + AI+ +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 69 HGREFGDRVISVNKAQPKMGGE 90
+G ++ + V+ A+P GGE
Sbjct: 77 NGITVRNKRLKVSYARP--GGE 96
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 40/70 (57%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+++G + ++ TE Q+ + G +I ++M + +GR +G+ FI + D + A+R +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 69 HGREFGDRVI 78
+G + G R +
Sbjct: 66 NGYQLGSRFL 75
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 45/80 (56%)
Query: 6 ENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+ + V L N+T+ + ++ F G I C+++ ++ +G+ G+GF+ Y+D D AI
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 66 REMHGREFGDRVISVNKAQP 85
++G + + I V+ A+P
Sbjct: 64 NTLNGLKLQTKTIKVSYARP 83
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV ++++ TE +L F+ +G I ++ + SG+PRG+ FI Y R M A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 69 HGREFGDRVISVN 81
G++ R + V+
Sbjct: 165 DGKKIDGRRVLVD 177
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 40/70 (57%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+++G + ++ TE Q+ + G +I ++M + +GR +G+ FI + D + A+R +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 69 HGREFGDRVI 78
+G + G R +
Sbjct: 65 NGYQLGSRFL 74
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
D +FVG L+ NV + L NAF F + +M + +G RG+GF+++ + +A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 65 IREMHGREFGDRVISVNKA 83
+ M G++ R + +N A
Sbjct: 146 MDSMQGQDLNGRPLRINWA 164
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VG L +TE L+ F G I +IM+++++ + + F+ Y + A++ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 69 HGREFGDRVISVNKA 83
+G++ + ++ +N A
Sbjct: 62 NGKQIENNIVKINWA 76
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
KD N ++V L +T+ QL+ F ++G I++ I+ ++ +GRPRG F+ Y R +
Sbjct: 88 KDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 64 AIREMHG 70
AI ++
Sbjct: 147 AISALNN 153
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L ++T+R+L F G I C+IM + +G G+ F+ + AI+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 HGREFGDRVISVNKAQPKMGGE 90
+G ++ + V+ A+P GGE
Sbjct: 66 NGITVRNKRLKVSYARP--GGE 85
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 45/77 (58%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
NRI+V + ++++ +++ F+ FGKI + + +G+ +G+GFI Y ++ DA+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 67 EMHGREFGDRVISVNKA 83
M+ + G + + V KA
Sbjct: 186 SMNLFDLGGQYLRVGKA 202
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+R++VG + + + E + AF FG I + + + + +GF F+ Y A A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 67 EMHGREFGDRVISV------NKAQPKM 87
+M+ G R I V +AQP +
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPII 115
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++V L + + +L AF FG I ++M+E GR +GFGF+ ++ A+ EM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 69 HGREFGDRVISVNKAQPK 86
+GR + + V AQ K
Sbjct: 76 NGRIVATKPLYVALAQRK 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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
D+ ++VG + + T + LE F G I I+ ++ SG P+G+ +I +A+R ++D A
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 65 IREMHGREFGDRVISVNKAQPKMGG 89
+ M F R I V + M G
Sbjct: 95 V-AMDETVFRGRTIKVLPKRTNMPG 118
>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 = 47.4 bits (111), Expect = 9e-06, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 41/76 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL+ V ++ L AF FG I + QI L+ ++ + RGF F+ + AI M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 69 HGREFGDRVISVNKAQ 84
+ E R I VN A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 41/76 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL+ V ++ L AF FG I + QI L+ ++ + RGF F+ + AI M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 69 HGREFGDRVISVNKAQ 84
+ E R I VN A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
++ ++F+G +S TE + F FG+I EC+I+ D G RG F+T+ R A
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTA 152
Query: 65 IREMH 69
I+ MH
Sbjct: 153 IKAMH 157
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
IF+ L ++ + L + F FG I+ C+++ + + +G+GF+ + + A + AI +M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEKM 163
Query: 69 HGREFGDRVISV 80
+G DR + V
Sbjct: 164 NGMLLNDRKVFV 175
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
++ ++F+G +S TE + F FG+I EC+I+ D G RG F+T+ R A
Sbjct: 106 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTA 164
Query: 65 IREMH 69
I+ MH
Sbjct: 165 IKAMH 169
>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 = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 40/75 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL+ V ++ L AF FG I + QI L+ ++ + RGF F+ + AI M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 69 HGREFGDRVISVNKA 83
+ E R I VN A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R+FV LS+ +E LE F +G + E ++ + +P+GF F+T+ A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 68 MHGREFGDRVISV 80
+ G+ F R++ V
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 2 AGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAM 61
A + + + V GL W TE+ L+ F FG+++ Q+ + +G +GFGF+ + +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 62 DDAIREMH 69
+ + H
Sbjct: 71 VKVMSQRH 78
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 40/75 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL+ V ++ L AF FG I + QI L+ ++ + RGF F+ + AI M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 69 HGREFGDRVISVNKA 83
+ E R I VN A
Sbjct: 126 NESELFGRTIRVNLA 140
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
IF+ L ++ + L + F FG I+ C+++ D +G+GF+ + + A + AI +M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 65
Query: 69 HGREFGDRVISV 80
+G DR + V
Sbjct: 66 NGMLLNDRKVFV 77
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 40/70 (57%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+++G + ++ TE Q+ + G +I ++M + +GR +G+ FI + D + A+R +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 69 HGREFGDRVI 78
+G + G R +
Sbjct: 67 NGYQLGSRFL 76
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
IF+ L ++ + L + F FG I+ C+++ D +G+GF+ + + A + AI +M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 71
Query: 69 HGREFGDRVISV 80
+G DR + V
Sbjct: 72 NGMLLNDRKVFV 83
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
IF+ L ++ + L + F FG I+ C+++ D +G+GF+ + + A + AI +M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 158
Query: 69 HGREFGDRVISV 80
+G DR + V
Sbjct: 159 NGMLLNDRKVFV 170
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+++F+GGL + + Q++ FG + ++ + +G +G+ F Y D D AI
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
Query: 67 EMHGREFGDRVISVNKA 83
++G + GD+ + V +A
Sbjct: 175 GLNGMQLGDKKLLVQRA 191
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+++F+GGL + + Q++ FG + ++ + +G +G+ F Y D D AI
Sbjct: 97 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 67 EMHGREFGDRVISVNKA 83
++G + GD+ + V +A
Sbjct: 157 GLNGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+++F+GGL + + Q++ FG + ++ + +G +G+ F Y D D AI
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 67 EMHGREFGDRVISVNKA 83
++G + GD+ + V +A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 10/84 (11%)
Query: 6 ENRIFVGGLSWNVTERQ-LENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
+R+F+G L+ V ++ +E F ++GKI+ C + +GF F+ Y + R A
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAA 66
Query: 65 IREMHGREFGDRVISVN-KAQPKM 87
+ GR +V+ +N A+PK+
Sbjct: 67 VAGEDGRMIAGQVLDINLAAEPKV 90
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
++ ++F+G +S TE + F FG+I EC+I+ D G RG F+T+ R A
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTA 152
Query: 65 IREMH 69
I+ H
Sbjct: 153 IKAXH 157
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 41/77 (53%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+++F+GGL + + Q++ FG + ++ + +G +G+ F Y D D AI
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 67 EMHGREFGDRVISVNKA 83
++G + GD+ + V +A
Sbjct: 62 GLNGMQLGDKKLLVQRA 78
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
+++++F+ GL ++ T+ +LE G + + +++ R +G+P+G ++ Y + A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQA 74
Query: 65 IREMHGREFGDRVISV 80
+ +M G + +I V
Sbjct: 75 VMKMDGMTIKENIIKV 90
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%)
Query: 1 MAGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRA 60
M D ++FVG + + E+ L+ F+ FG+I E ++ +R +G +G F+TY R +
Sbjct: 10 MKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDS 69
Query: 61 MDDAIREMH 69
A +H
Sbjct: 70 ALKAQSALH 78
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV GLS + TE L+ +FD + +I+ +R++G +GFGF+ + A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 69 HGREFGDRVISVNKAQPK 86
E ++++ A+PK
Sbjct: 75 EDGEIDGNKVTLDWAKPK 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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V GLS TER L F ++G I + I+ ++ S R RGF F+ + + +A +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 71 REFGDRVISVNKAQPK 86
E R I V+ + K
Sbjct: 80 MELDGRRIRVDFSITK 95
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V L++ + L F+++G++ + I E + PRGF F+ + DRR DA M G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 71 REFGDRVISVNKAQ 84
E R + V A+
Sbjct: 78 AELDGRELRVQVAR 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 36/71 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V GLS TER L F ++G I + I+ ++ S R RGF F+ + + +A +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 71 REFGDRVISVN 81
E R I V+
Sbjct: 80 MELDGRRIRVS 90
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V GLS TER L F ++G I + I+ ++ S R RGF F+ + + +A +G
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 71 REFGDRVISVNKAQPK 86
E R I V+ + K
Sbjct: 77 MELDGRRIRVDFSITK 92
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VGGL V+E L F + G ++ + +R +G+ +G+GF+ + D AI+ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 69 HGREFGDRVISVNKA 83
+ + I VNKA
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
R+FV +V E +L F FG + E +I+ GF F+ + + + AI
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIE 83
Query: 67 EMHGREFGDRVISV 80
E+HG+ F ++ + V
Sbjct: 84 EVHGKSFANQPLEV 97
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V GLS TER L F ++G I + I+ ++ S R RGF F+ + + +A +G
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 71 REFGDRVISVNKAQPK 86
E R I V+ + K
Sbjct: 111 MELDGRRIRVDFSITK 126
>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 = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 42/83 (50%)
Query: 3 GKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
G + V L N+T+ +L + F G++ +++ ++ +G G+GF+ Y + +
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 63 DAIREMHGREFGDRVISVNKAQP 85
AI ++G + I V+ A+P
Sbjct: 61 RAINTLNGLRLQSKTIKVSYARP 83
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 40/77 (51%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L N T+ +L + F G++ +++ ++ +G G+GF+ Y + + AI +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 69 HGREFGDRVISVNKAQP 85
+G + I V+ A+P
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 48/79 (60%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+FVG LS +T + AF FG+I + +++ + +G+ +G+GF+++ ++ ++AI++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 68 MHGREFGDRVISVNKAQPK 86
M G+ G R I N A K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
++FVG L+ +E + F+ FG I EC I+ D G +G F+ Y+ AI
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
Query: 68 MHGRE 72
+HG +
Sbjct: 76 LHGSQ 80
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 42/80 (52%)
Query: 1 MAGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRA 60
+ G + +F+ L T+ L + F FG +I ++ +++ + + FGF+++ + +
Sbjct: 35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 61 MDDAIREMHGREFGDRVISV 80
AI+ M+G + G + + V
Sbjct: 95 AQVAIKAMNGFQVGTKRLKV 114
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIML-ERDSGRPRGFGFITYADRRAMDDAIR 66
R+ V + + + L F +FGKI++ +I+ ER S +GFGF+T+ + D A
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRARE 73
Query: 67 EMHGREFGDRVISVNKAQPKM 87
++HG R I VN A ++
Sbjct: 74 KLHGTVVEGRKIEVNNATARV 94
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 5/90 (5%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V + V E QL F+R+G I +I+ +R++ + RG+GF+ + + AI +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 69 HGREFGDRVISVNKA-----QPKMGGEVSD 93
+G ++ + V A +P + G V D
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGAVGD 134
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIML-ERDSGRPRGFGFITYADRRAMDDAIR 66
R+ V + + + L F +FGKI++ +I+ ER S +GFGF+T+ + D A
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRARE 87
Query: 67 EMHGREFGDRVISVNKAQPKM 87
++HG R I VN A ++
Sbjct: 88 KLHGTVVEGRKIEVNNATARV 108
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
D I+VG + + T +LE F G + I+ ++ SG P+GF +I ++D+ ++ +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 65 I 65
+
Sbjct: 65 L 65
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R+FV +V E +L F FG + E +I+ GF F+ + + + AI E
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 57
Query: 68 MHGREFGDRVISV 80
+HG+ F ++ + V
Sbjct: 58 VHGKSFANQPLEV 70
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV L+ VTE LE AF +FGK LER + + + FI + +R A+ EM
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGK-------LER-VKKLKDYAFIHFDERDGAVKAMEEM 65
Query: 69 HGREFGDRVISVNKAQP 85
+G++ I + A+P
Sbjct: 66 NGKDLEGENIEIVFAKP 82
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSG---RPRGFGFITYADRRAMDDAI 65
+F+ L+++ TE L+ F + G I C I +++ GFGF+ Y A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 66 REMHGR 71
+++ G
Sbjct: 68 KQLQGH 73
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
D I+VG + + T +LE F G + I+ ++ SG P+GF +I ++D+ ++ +
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 65 I 65
+
Sbjct: 64 L 64
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 2 AGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAM 61
AG+ + +FV L + V ++L+ F G ++ I+ ++D G+ RG G +T+
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEA 69
Query: 62 DDAIREMHGREFGDRVISVN---KAQPK 86
AI +G+ DR + V +A PK
Sbjct: 70 VQAISMFNGQLLFDRPMHVKMDERALPK 97
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITY---ADRRAMDD 63
N +FVGG+ + E ++ + F R+G + E +I+ +R +G +G+GF+++ D + + +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 64 AIREMHGREF 73
+ HG++
Sbjct: 69 SQINFHGKKL 78
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++VG LS +VTE + F + G C+++ E S P + F+ + + R A+ M
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75
Query: 69 HGREFGDRVISVNKA 83
+GR+ + + VN A
Sbjct: 76 NGRKILGKEVKVNWA 90
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 38/73 (52%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+F+ L ++ L F FG ++ ++ +++ + + FGF++Y + + AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 68 MHGREFGDRVISV 80
M+G + G + + V
Sbjct: 87 MNGFQIGMKRLKV 99
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYAD 57
+IFVGGLS + E ++ F FG++ ++ ++ + + RGF FIT+ +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE 52
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L++ + L F+++G++ + I +R + RGF F+ + D+R +DA+ M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 69 HGREFGDRVISVNKAQ 84
G R + V A+
Sbjct: 110 DGAVLDGRELRVQMAR 125
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
D I V LS + E L+ F FG I + ++ +G+ +GF FI++ R A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 65 IREMHGREFGDRVISVNKAQPKM 87
I + G + +++V A+P
Sbjct: 74 IAGVSGFGYDHLILNVEWAKPST 96
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 86 NGQDLMGQPISVD 98
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
N ++V G ++T L AF FG II+ + PR F+TY + D A+
Sbjct: 16 NTLYVYG--EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 67
Query: 67 EMHGREFGDRVISVNKA--QPKM 87
E++G + + VN A QP +
Sbjct: 68 ELNGTQVESVQLKVNIARKQPML 90
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV L+ VTE LE +F FGK LER + + + F+ + DR A A+ EM
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGK-------LER-VKKLKDYAFVHFEDRGAAVKAMDEM 69
Query: 69 HGR 71
+G+
Sbjct: 70 NGK 72
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 8 RIFVGGLSWNVTERQ-LENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
R+F+G L+ + ++ +E F ++G++ C + +G+ F+ Y++ R A+
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80
Query: 67 EMHGREFGDRVISVNKA-QPK 86
+GR + + +N A +PK
Sbjct: 81 GENGRVLAGQTLDINMAGEPK 101
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITY---ADRRAMDD 63
N +FVGG+ + E ++ + F R+G + E +I+ +R +G +G+GF+++ D + + +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 64 AIREMHGREF 73
+ HG++
Sbjct: 69 SQINFHGKKL 78
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGK--IIECQIMLERDSGRPRGFGFI---TYADRRAMDD 63
+++G L+W T+ L A G I+E + R +G+ +GF + + A + + D
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 64 AI--REMHGREFGDRVISVNK 82
+ RE+HG+ V VNK
Sbjct: 131 LLPKRELHGQN--PVVTPVNK 149
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L ++T+R+L F G I C+IM + +G G+ F+ + AI+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 HGREFGDRVISVNKAQPKMGGE 90
+G ++ + V+ A+P GGE
Sbjct: 66 NGITVRNKRLKVSYARP--GGE 85
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 17/98 (17%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
R+FVG L ++TE + F+R+G+ ++ + RD RGFGFI R + A E
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGE--PSEVFINRD----RGFGFIRLESRTLAEIAKAE 77
Query: 68 MHGREFGDR-----------VISVNKAQPKMGGEVSDH 94
+ G R ++V P + E+ +
Sbjct: 78 LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQ 115
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADR 58
+ V LS V+ LE AF +FG + E +++ D GR G GF+ +A +
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPV-EKAVVVVDDRGRATGKGFVEFAAK 147
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYAD 57
IFVGGLS + E ++ F FG++ ++ ++ + + RGF FIT+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE 50
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+++VG L N + +LE AF +G + + + P GF F+ + D R DA+RE
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 129
Query: 68 MHGREF 73
+ GR
Sbjct: 130 LDGRTL 135
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FVG L V E L F + G + + I +R+ G+P+ FGF+ + ++ AI +
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 69 HGREFGDRVISVN 81
+G R I+V+
Sbjct: 78 NGIRLYGRPINVS 90
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
N ++V G ++T L AF FG II+ + PR F+TY + D A+
Sbjct: 40 NTLYVYG--EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 91
Query: 67 EMHGREFGDRVISVNKA--QPKM 87
E++G + + VN A QP +
Sbjct: 92 ELNGTQVESVQLKVNIARKQPML 114
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
++FVG L+ +E + F FG I EC ++ D G +G F+ ++ AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 68 MHGRE 72
+HG +
Sbjct: 76 LHGSQ 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITY---ADRRAMDD 63
N +FVGG+ + E ++ + F R+G + E +I+ +R +G +G+GF+++ D + + +
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
Query: 64 AIREMHGREF 73
+ HG++
Sbjct: 70 SQINFHGKKL 79
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 85 NGQDLMGQPISVD 97
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 37/73 (50%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L ++T++Q E FG + C ++ +G+ +G+GF Y + + A ++
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 69 HGREFGDRVISVN 81
G+ G R + V+
Sbjct: 156 LGKPLGPRTLYVH 168
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
+D +++ L ++ E++LEN FG++I +I L SG RG GF +
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI-LRDSSGTSRGVGFARMESTEKCEA 81
Query: 64 AIREMHGR 71
I +G+
Sbjct: 82 VIGHFNGK 89
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 37/73 (50%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L ++T++Q E FG + C ++ +G+ +G+GF Y + + A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69 HGREFGDRVISVN 81
G+ G R + V+
Sbjct: 158 LGKPLGPRTLYVH 170
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 37/73 (50%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ V L ++T++Q E FG + C ++ +G+ +G+GF Y + + A ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69 HGREFGDRVISVN 81
G+ G R + V+
Sbjct: 158 LGKPLGPRTLYVH 170
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 3 GKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
G+ +++ LS VTER L + F RF + I +GR RG FIT+ ++
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81
Query: 63 DAIREMHGREFGDRVISV----NKAQ 84
A+ ++G + +++ + NK Q
Sbjct: 82 QALHLVNGYKLYGKILVIEFGKNKKQ 107
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKI--------IECQIMLERDSGRPRGFGFITYA 56
D + I+V GL+ +VT L + F + G + I L++++G+P+G ++Y
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 57 DRRAMDDAIREMHGREF-GDRV-ISVNKAQPKM 87
D A+ G++F G ++ +S+ + +P M
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 11/84 (13%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+IFVG +S T ++L + F+R G++IEC ++ + + F+ AI +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQ 62
Query: 68 MHGREFGDRVISV---NKAQPKMG 88
++G+E + I+V K Q K G
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKSG 86
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%)
Query: 11 VGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 70
V L++ + L F+++G++ + I +R + RGF F+ + D+R +DA+ M G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 71 REFGDRVISVNKA 83
R + V A
Sbjct: 135 AVLDGRELRVQMA 147
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+++VG L N + +LE AF +G + + + P GF F+ + D R DA+R+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRD 129
Query: 68 MHGREF 73
+ GR
Sbjct: 130 LDGRTL 135
>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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 70 NGQDLMGQPISVD 82
>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 = 36.6 bits (83), Expect = 0.014, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 72 NGQDLMGQPISVD 84
>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 = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV G+ TE + + F +G+I + L+R +G +G+ + Y + A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 HGREFGDRVISVN 81
+G++ + ISV+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 2 AGKDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAM 61
AG ++ RI+VG L ++ + +E+ F ++G I + + R G P F F+ + D R
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPP--FAFVEFEDPRDA 74
Query: 62 DDAI 65
+DA+
Sbjct: 75 EDAV 78
>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 = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 45/80 (56%), Gaps = 7/80 (8%)
Query: 9 IFVGGLSWNVTERQLENA----FDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + + +L+ + F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 63
Query: 65 IREMHGREFGDRVISVNKAQ 84
+R M G F D+ + + A+
Sbjct: 64 LRSMQGFPFYDKPMRIQYAK 83
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
++ ++FVG L T+ + F+ FG I EC ++ D G +G F+ + A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAA 69
Query: 65 IREMH 69
I +H
Sbjct: 70 INTLH 74
>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 = 35.8 bits (81), Expect = 0.027, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 45/80 (56%), Gaps = 7/80 (8%)
Query: 9 IFVGGLSWNVTERQLENA----FDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + + +L+ + F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 62
Query: 65 IREMHGREFGDRVISVNKAQ 84
+R M G F D+ + + A+
Sbjct: 63 LRSMQGFPFYDKPMRIQYAK 82
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
++ GG++ +T++ + F FG+I+E ++ E +G+ F+ ++ + AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 69 HGREFGDRVI 78
+G V+
Sbjct: 82 NGTTIEGHVV 91
>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 = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+R+FVG L ++TE ++ F+++GK E + + +D +GFGFI R + A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGE--VFIHKD----KGFGFIRLETRTLAEIAKV 69
Query: 67 EM 68
E+
Sbjct: 70 EL 71
>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 = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 65
Query: 65 IREMHGREFGDRVISVNKAQ 84
+R M G F D+ + + A+
Sbjct: 66 LRSMQGFPFYDKPMRIQYAK 85
>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 = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 67
Query: 65 IREMHGREFGDR 76
+R M G F D+
Sbjct: 68 LRSMQGFPFYDK 79
>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 = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 68
Query: 65 IREMHGREFGDR 76
+R M G F D+
Sbjct: 69 LRSMQGFPFYDK 80
>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 = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 67
Query: 65 IREMHGREFGDR 76
+R M G F D+
Sbjct: 68 LRSMQGFPFYDK 79
>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 = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIE--------CQIMLERDSGRPRGFGFITYA 56
D N IFV GL NVT + + F + G I + +R++G+ +G +++
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 57 DRRAMDDAIREMHGREFGDRVISVNKA 83
D + AI G+EF I V+ A
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 7 NRIFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
+ I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + +
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSAT 65
Query: 63 DAIREMHGREFGDR 76
+A+R M G F D+
Sbjct: 66 NALRSMQGFPFYDK 79
>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 = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 68
Query: 65 IREMHGREFGDR 76
+R M G F D+
Sbjct: 69 LRSMQGFPFYDK 80
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 7 NRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
+R+FVG L ++TE ++ F+++GK E + + +D +GFGFI R + A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGE--VFIHKD----KGFGFIRLETRTLAEIAKV 76
Query: 67 EM 68
E+
Sbjct: 77 EL 78
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITY----ADRRAMD 62
+ V L V+ LE AF FG++ E +++ D GRP G G + + A R+A+D
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQV-ERAVVIVDDRGRPSGKGIVEFSGKPAARKALD 155
>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 = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 9 IFVGGLSWNV----TERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + ++ L F RFG+I++ I++ R S + RG F+ + + + +A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 64
Query: 65 IREMHGREFGDR 76
+R M G F D+
Sbjct: 65 LRSMQGFPFYDK 76
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+++VG L + +LE AF +G + I + P GF F+ + D R +DA+R
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 68 MHGREF-GDRV-ISVNKAQPK 86
+ G+ G RV + ++ P+
Sbjct: 57 LDGKVICGSRVRVELSTGMPR 77
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 5 DENRIFVGGLSWNVTERQLENAFDRFGKIIE--------CQIMLERDSGRPRGFGFITYA 56
D N IFV GL NVT + + F + G I + +R++G+ +G +++
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 57 DRRAMDDAIREMHGREFGDRVISVNKA 83
D + AI G+EF I V+ A
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>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 = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 46/82 (56%), Gaps = 7/82 (8%)
Query: 7 NRIFVGGLSWNVTERQLENA----FDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
+ I++ L+ + + +L+ + F +FG+I++ I++ R S + RG F+ + + +
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSAT 66
Query: 63 DAIREMHGREFGDRVISVNKAQ 84
+A+R M G F D+ + + A+
Sbjct: 67 NALRSMQGFPFYDKPMRIQYAK 88
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 34.7 bits (78), Expect = 0.066, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 9 IFVGGLSWNVTERQLENAFDRFG--KIIECQIMLERDSGRPRGFGFI---TYADRRAMDD 63
+++G L+W T+ L A G I+E + R +G+ +GF + + A + + D
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 64 AI--REMHGR 71
+ RE+HG+
Sbjct: 64 LLPKRELHGQ 73
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 45/80 (56%), Gaps = 7/80 (8%)
Query: 9 IFVGGLSWNVTERQLENA----FDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDA 64
I++ L+ + + +L+ + F +FG+I++ I++ R S + RG F+ + + + +A
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSATNA 67
Query: 65 IREMHGREFGDRVISVNKAQ 84
+R M G F D+ + + A+
Sbjct: 68 LRSMQGFPFYDKPMRIQYAK 87
>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 = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGK--IIECQIMLERDSGRPRGFGFITYADRRAMDDAIR 66
++VG SW T++QL G ++E + R +G+ +G+ + A ++ +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 67 EMHGREF-GDRV 77
+ G+ G++V
Sbjct: 118 LLPGKVLNGEKV 129
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 7/74 (9%)
Query: 7 NRIFVGGLSWNVTERQLENA----FDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMD 62
+ I++ L+ + + +L+ + F +FG+I++ I++ R S + RG F+ + + +
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILD--ILVSR-SLKMRGQAFVIFKEVSSAT 66
Query: 63 DAIREMHGREFGDR 76
+A+R M G F D+
Sbjct: 67 NALRSMQGFPFYDK 80
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV + E +++ F +G+I + L+R +G +G+ + Y + A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 69 HGREFGDRVISVN 81
+G E + I V+
Sbjct: 135 NGAEIMGQTIQVD 147
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 6 ENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
R++VGGL N + L FDRFG I D + F +I Y A A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSFAYIQYESLDAAQAAC 70
Query: 66 REMHGREFG--DRVISVNKAQ 84
+M G G DR + V+ A+
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAK 91
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 13/81 (16%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRP-RGFGFITYADRRAMDDAIRE 67
+FVG + ++TE +L F ++G +++ I +P R F F+T+AD D +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFI------PKPFRAFAFVTFAD----DQIAQS 57
Query: 68 MHGREFGDRVISVN--KAQPK 86
+ G + + ISV+ A+PK
Sbjct: 58 LCGEDLIIKGISVHISNAEPK 78
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 27/54 (50%)
Query: 18 VTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR 71
V ++ L + F + GK++ + ++ +G+ +GF F+ I+ HG+
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 120 CFKCGRPGHWARDCP 134
CF+CG+PGH+ ++CP
Sbjct: 10 CFRCGKPGHYIKNCP 24
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+FV + E +++ F +G+I + L+R +G +G+ + Y + A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 69 HGREFGDRVISVN 81
+G E + I V+
Sbjct: 89 NGAEIMGQTIQVD 101
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ LS+N+TE +L+ F+ +I L G+ +G +I + + + E
Sbjct: 19 LLAKNLSFNITEDELKEVFED-----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 69 HGREFGDRVISV 80
G E R +S+
Sbjct: 74 QGAEIDGRSVSL 85
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGK-IIECQIMLERDSGRPRGFGFITYADRRAMDDAIRE 67
+++G L + E + AF G+ ++ +I+ R +G P G+ F+ +AD + + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 68 MHGREF 73
++G+
Sbjct: 72 INGKPL 77
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIE--CQIMLERDSGRPRGFGFITYADR---RAMD 62
++FVGGL ++ E ++ +F RFG ++ + P+G+ F+ + + +A+
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 63 DAIREMHGREF 73
DA E G+ +
Sbjct: 70 DACLEEDGKLY 80
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.0 bits (71), Expect = 0.39, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 4 KDENRIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
K ++ VG +S T ++L F+ +G +IEC I+ + + F+ +
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59
Query: 64 AIREMHGREFGDRVISVNKAQPKM 87
AIR + EF + + V + ++
Sbjct: 60 AIRGLDNTEFQGKRMHVQLSTSRL 83
>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 = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREM 68
+ LS+N+TE +L+ F+ +I L G+ +G +I + + + E
Sbjct: 102 LLAKNLSFNITEDELKEVFED-----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 69 HGREFGDRVISV 80
G E R +S+
Sbjct: 157 QGAEIDGRSVSL 168
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 13/88 (14%)
Query: 6 ENRIFVGGLSWNVTERQLENAFDRF------GKIIECQIMLERDSGRPRGFGFITYADRR 59
E +FVG L+ +V + L F + GK++ Q +G +G+GF+ + D
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ------TGVSKGYGFVKFTDEL 62
Query: 60 AMDDAIREMHGRE-FGDRVISVNKAQPK 86
A+ E G G + + ++ A PK
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVAIPK 90
>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 = 31.6 bits (70), Expect = 0.55, Method: Composition-based stats.
Identities = 12/56 (21%), Positives = 27/56 (48%)
Query: 18 VTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF 73
V ++ L + F + GK++ + ++ +G+ +GF F+ I+ HG+
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.8 bits (68), Expect = 0.87, Method: Composition-based stats.
Identities = 13/57 (22%), Positives = 31/57 (54%)
Query: 9 IFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAI 65
+++ GL T++ L +GKI+ + +L++ + + +G+GF+ + A A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 2 AGKDEN--RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRR 59
+G+D+ ++VGGL +TE L N F +FG+I ++ + FI +A R+
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQ 59
Query: 60 AMDDA 64
A + A
Sbjct: 60 AAEVA 64
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 8 RIFVGGLSWNVTERQLENAFDRFGKIIECQIMLER-DSGRPRGFGFITYADRRAMDDAIR 66
++ +G L+ NVT+ + F +GKI + +ER +G+ ++ + + + A++
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 67 EMHGREFGDRVIS 79
M G + + I+
Sbjct: 66 HMDGGQIDGQEIT 78
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 118 DDCFKCGRPGHWARDCP 134
D C C GHWA+DCP
Sbjct: 24 DQCAYCKEKGHWAKDCP 40
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 120 CFKCGRPGHWARDC 133
CFKCG+ GH+A++C
Sbjct: 4 CFKCGKKGHFAKNC 17
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 28.5 bits (62), Expect = 3.8, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 120 CFKCGRPGHWARDC 133
CF CG+PGH AR C
Sbjct: 3 CFNCGKPGHTARMC 16
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 23 LENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR 76
L F +FG+I++ ++ + + RG F+ + + + +A+R M G F D+
Sbjct: 27 LYAIFSQFGQILD---IVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDK 77
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 5 DENRI-FVGGLSWNVTERQLENAFDRFGKIIECQIMLERDSGRPRGFGFITYADRRAMDD 63
+ NRI ++ L + +T ++ + F ++G I + ++ ++ RG ++ Y D +
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62
Query: 64 AIREMHGREFGDRVISV-----NKAQPKM 87
A+ + G +R + V N+A KM
Sbjct: 63 AVDHLSGFNVSNRYLVVLYYNANRAFQKM 91
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 28.1 bits (61), Expect = 5.5, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 120 CFKCGRPGHWARDC 133
CFKC +PGH+++ C
Sbjct: 22 CFKCKQPGHFSKQC 35
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 118 DDCFKCGRPGHWARDCP 134
D C C GHWA+DCP
Sbjct: 11 DQCAYCKEKGHWAKDCP 27
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 120 CFKCGRPGHWARDC 133
CF CG+ GH AR+C
Sbjct: 3 CFNCGKEGHIARNC 16
>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 = 27.3 bits (59), Expect = 8.6, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 35 ECQIMLERDSGRPRGFGFITYADRRAMDDAIREM----HGREFGDRVISVNKAQPK 86
E ++M + SG+ RGF F+ ++ + DA R M H + +S++ + PK
Sbjct: 31 EVRLMRNKSSGQSRGFAFVEFSH---LQDATRWMEANQHSLNILGQKVSMHYSDPK 83
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
0.319 0.141 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,762,268
Number of Sequences: 62578
Number of extensions: 305923
Number of successful extensions: 742
Number of sequences better than 100.0: 197
Number of HSP's better than 100.0 without gapping: 155
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 529
Number of HSP's gapped (non-prelim): 232
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)