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= psy1078
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 32/79 (40%), Positives = 50/79 (63%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG +PY+ +E + IFS+ G +V+ LV D+ TGK KG+ F Y+DQ + + ++ NL
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 96 NGVKVLSRTIRVDHVNDYK 114
NG + R +RVD+ K
Sbjct: 71 NGREFSGRALRVDNAASEK 89
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 51/80 (63%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S+ ++VG L ++++E + IF +G+I N+ L++D TG+SKG+ FI + D ++
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 93 DNLNGVKVLSRTIRVDHVND 112
+ LNG ++ R +RV HV +
Sbjct: 65 EQLNGFELAGRPMRVGHVTE 84
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 48/79 (60%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
D +FVGGL +D +E + +FS+YG+I + +V+D+ T +S+GF F+ +E+ +
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 92 VDNLNGVKVLSRTIRVDHV 110
+ +NG V R IRVD
Sbjct: 71 MMAMNGKSVDGRQIRVDQA 89
>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 = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 49/77 (63%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S +++G +PYD +E ++ + S G ++NL ++ D TG+SKG+ FI + D S+ +V
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 93 DNLNGVKVLSRTIRVDH 109
NLNG ++ SR ++ +
Sbjct: 64 RNLNGYQLGSRFLKCGY 80
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 49/77 (63%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S +++G +PYD +E ++ + S G ++NL ++ D TG+SKG+ FI + D S+ +V
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 93 DNLNGVKVLSRTIRVDH 109
NLNG ++ SR ++ +
Sbjct: 62 RNLNGYQLGSRFLKCGY 78
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 49/77 (63%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S +++G +PYD +E ++ + S G ++NL ++ D TG+SKG+ FI + D S+ +V
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 93 DNLNGVKVLSRTIRVDH 109
NLNG ++ SR ++ +
Sbjct: 63 RNLNGYQLGSRFLKCGY 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 57.0 bits (136), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 47/77 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L ++++E + IF +G I ++ L+ D TG+SKG+ FI + D +++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 96 NGVKVLSRTIRVDHVND 112
NG ++ R ++V HV +
Sbjct: 89 NGFELAGRPMKVGHVTE 105
>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 = 57.0 bits (136), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 48/75 (64%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ + +F GEI + LVRDKITG+S G+ F+ Y D + +++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NGVKVLSRTIRVDHV 110
NG+++ ++TI+V +
Sbjct: 65 NGLRLQTKTIKVSYA 79
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 41/66 (62%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A ++V GLP +++ ++ +FSQYG I+ ++ D++TG S+G FI ++ + ++
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 94 NLNGVK 99
LNG K
Sbjct: 149 GLNGQK 154
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 56.6 bits (135), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 47/75 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ + +F G+I + LVRDKITG+S G+ F+ Y D +++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 96 NGVKVLSRTIRVDHV 110
NG+K+ ++TI+V +
Sbjct: 67 NGLKLQTKTIKVSYA 81
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 41/68 (60%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A ++V GLP +S+ ++ +FSQYG I+ ++ D+ TG S+G FI ++ + ++
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 94 NLNGVKVL 101
LNG K L
Sbjct: 151 GLNGQKPL 158
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 47/75 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ + +F G+I + LVRDKITG+S G+ F+ Y D +++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 96 NGVKVLSRTIRVDHV 110
NG+K+ ++TI+V +
Sbjct: 67 NGLKLQTKTIKVSYA 81
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV + + E ++ F YGEI N++L D+ TG SKG+ + YE + + +
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG +++ +TI+VD
Sbjct: 132 EALNGAEIMGQTIQVD 147
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 47/75 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ ++ +FS GE+ + L+RDK+ G S G+ F+ Y + +++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 96 NGVKVLSRTIRVDHV 110
NG+++ S+TI+V +
Sbjct: 65 NGLRLQSKTIKVSYA 79
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 41/66 (62%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A +++ GLP +++ DV +FS++G I+N ++ D+ TG S+G FI ++ + ++
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 94 NLNGVK 99
+ NG K
Sbjct: 149 SFNGHK 154
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 47/75 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ ++ +FS GE+ + L+RDK+ G S G+ F+ Y + +++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 96 NGVKVLSRTIRVDHV 110
NG+++ S+TI+V +
Sbjct: 65 NGLRLQSKTIKVSYA 79
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 41/66 (62%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A +++ GLP +++ DV +FS++G I+N ++ D+ TG S+G FI ++ + ++
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 94 NLNGVK 99
+ NG K
Sbjct: 149 SFNGHK 154
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 47/75 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ ++ +FS GE+ + L+RDK+ G S G+ F+ Y + +++ L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 96 NGVKVLSRTIRVDHV 110
NG+++ S+TI+V +
Sbjct: 67 NGLRLQSKTIKVSYA 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV + + E ++ F YGEI N++L D+ TG SKG+ + YE + + +
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG +++ +TI+VD
Sbjct: 86 EALNGAEIMGQTIQVD 101
>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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 49/92 (53%)
Query: 16 QELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSK 75
Q++ GS + ++VG + Y+L E + F+ +G I ++++ D +T K K
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
Query: 76 GFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
GF F+ YE + L+++ +N V + R I+V
Sbjct: 71 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+V + DLS+ D+ +F +G+I + L RD TGK KG+ FI YE +S+ +V ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 96 NGVKVLSRTIRV 107
N + + +RV
Sbjct: 188 NLFDLGGQYLRV 199
>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 = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 93 DNLNGVKVLSRTIRVDHVNDYKPP 116
+ LNG ++ + I VD PP
Sbjct: 83 EGLNGQDLMGQPISVDWCFVRGPP 106
>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 = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 47/81 (58%)
Query: 30 YKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
Y + V LP + ++ ++ +FS GE+ + L+RDK+ G S G+ F+ Y +
Sbjct: 16 YFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 75
Query: 90 LSVDNLNGVKVLSRTIRVDHV 110
+++ LNG+++ S+TI+V +
Sbjct: 76 RAINTLNGLRLQSKTIKVSYA 96
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 53.5 bits (127), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 43/71 (60%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V LP+ L+ D+ IFS+YG++V + +++DK T KSKG FI + D+ S +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 96 NGVKVLSRTIR 106
N ++ R I+
Sbjct: 79 NNKQLFGRVIK 89
>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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 93 DNLNGVKVLSRTIRVDHVNDYKPP 116
+ LNG ++ + I VD PP
Sbjct: 67 EGLNGQDLMGQPISVDWCFVRGPP 90
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 54/100 (54%), Gaps = 5/100 (5%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITG--KSKGFCFICYEDQRSTV 89
D+ +FVG +P SE D+ +F QYG + +N++RD+ +SKG CF+ + +++ +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 90 LSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
+ + L+ +KVL + H KP K E +KL
Sbjct: 62 EAQNALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKL 98
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 13/66 (19%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G + +E D+ +FS +G+I ++R G S+G F+ + + ++ +
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 96 NGVKVL 101
+ + +
Sbjct: 157 HQAQTM 162
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 54/100 (54%), Gaps = 5/100 (5%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITG--KSKGFCFICYEDQRSTV 89
D+ +FVG +P SE D+ +F QYG + +N++RD+ +SKG CF+ + +++ +
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 90 LSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
+ + L+ +KVL + H KP K E +KL
Sbjct: 74 EAQNALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKL 110
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 13/66 (19%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G + +E D+ +FS +G+I ++R G S+G F+ + + ++ +
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 96 NGVKVL 101
+ + +
Sbjct: 169 HQAQTM 174
>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 = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG ++ + I VD
Sbjct: 82 EGLNGQDLMGQPISVD 97
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+VG L Y + V +FSQ+G++ N+ L+ D+ T K KGF F+ +++ S ++ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAKL 62
Query: 96 NGVKVLSRTIRVDHVN 111
+ + RTIRV N
Sbjct: 63 DNTDFMGRTIRVTEAN 78
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 1/93 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L +++ D+ F+ +G I + +V+D TGKSKG+ F+ + ++ ++ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKK 128
G + R IR + KPP + TK+
Sbjct: 78 GGQWLGGRQIRTNWAT-RKPPAPKSTYESNTKQ 109
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG ++ + I VD
Sbjct: 69 EGLNGQDLMGQPISVD 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG ++ + I VD
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 34 AWI-FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
WI FV G+ + +E D+ F++YGEI N++L D+ TG KG+ + YE + ++
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 93 DNLNGVKVLSRTIRVD 108
+ LNG ++ + I VD
Sbjct: 67 EGLNGQDLMGQPISVD 82
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITG--KSKGFCFICYEDQRSTV 89
D+ +FVG +P SE D+ +F QYG + +N++RD+ +SKG CF+ + +++ +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 90 LSVDNLNGVKVL 101
+ + L+ +KVL
Sbjct: 62 EAQNALHNMKVL 73
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 43/72 (59%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG + Y+L E + F+ +G I ++++ D +T K KGF F+ YE + L+++ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 96 NGVKVLSRTIRV 107
N V + R I+V
Sbjct: 76 NSVMLGGRNIKV 87
Score = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+V + DLS+ D+ +F +G+I + L RD TGK KG+ FI YE +S+ +V ++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 96 NGVKVLSRTIRV 107
N + + +RV
Sbjct: 173 NLFDLGGQYLRV 184
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 51/90 (56%), Gaps = 3/90 (3%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
GS S + D+ +F+G +P +L E D+ +F ++G+I L +++D+ TG KG F+
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 81 CYEDQRSTVLSVDNLNGVKVL---SRTIRV 107
Y ++ S + + L+ K L +R I+V
Sbjct: 61 TYCERESALKAQSALHEQKTLPGMNRPIQV 90
>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 = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 37/53 (69%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+F+GGL +D ++ D+ FS++GE+V+ L D ITG+S+GF F+ +++ S
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESV 54
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%)
Query: 38 VGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
V L Y S + +F +YG + ++ + RD+ T +S+GF F+ + D+R ++D ++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 98 VKVLSRTIRVDHVNDYKPP 116
+ R +RV +PP
Sbjct: 135 AVLDGRELRVQMARYGRPP 153
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL + +E + +F ++G I + L++D+ T KS+GF FI +E+ + ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 96 NGVKVLSRTIRVDHV 110
NG + + I+V+
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 38/58 (65%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+D+ FVGGL +D S+ D+ F+++GE+V+ + D TG+S+GF FI ++D S
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASV 66
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV + YD +E + F YG I +++V K +GK +G+ FI YE +R + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96 NGVKVLSRTIRVD 108
+G K+ R + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V LP +++ + IF +YG IV N++RDK+TG+ +G F+ Y + ++ L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 96 NGV 98
N V
Sbjct: 76 NNV 78
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 37/53 (69%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYE 83
K+S +F+GGL +D +E ++ F +YG + +L +++D TG+S+GF F+ +E
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 27 HDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYE 83
D+ + IFVGG+ D+ + FSQ+G I++ L+ DK TG+S+GF F+ Y+
Sbjct: 81 RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV + YD +E + F YG I +++V K +GK +G+ FI YE +R + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96 NGVKVLSRTIRVD 108
+G K+ R + VD
Sbjct: 165 DGKKIDGRRVLVD 177
>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 = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+V + DLS+ D+ +F +G+I + L RD TGK KG+ FI YE +S+ +V +
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 96 NGVKVLSRTIRV 107
N + + +RV
Sbjct: 172 NLFDLGGQYLRV 183
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 41/72 (56%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG + Y+L E + F+ +G I +++ D +T K KGF F+ YE + L+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 96 NGVKVLSRTIRV 107
N V + R I+V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 50.1 bits (118), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A ++V GLP +S+ ++ +FSQYG I+ ++ D+ TG S+G FI ++ + ++
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 94 NLNGVKVL--SRTIRVDHVND 112
LNG K L + I V N+
Sbjct: 62 GLNGQKPLGAAEPITVKFANN 82
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%)
Query: 41 LPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKV 100
L Y S + +F +YG + ++ + RD+ T +S+GF F+ + D+R ++D ++G +
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 101 LSRTIRVDHVNDYKPP 116
R +RV +PP
Sbjct: 115 DGRELRVQMARYGRPP 130
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 51/100 (51%), Gaps = 5/100 (5%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITG--KSKGFCFICYEDQRSTV 89
D+ FVG +P SE D+ +F QYG + +N++RD+ +SKG CF+ + +++ +
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 90 LSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
+ + L+ KVL H KP K E +KL
Sbjct: 62 EAQNALHNXKVLPGX---HHPIQXKPADSEKNNAVEDRKL 98
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICY 82
+F+G + +E D+ FS +G+I ++R G S+G F+ +
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTF 143
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 32 DSAW-IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
DSA +F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 91 SVDNLNGVKVLSRTIRVDHVN 111
++ LNG+++ + + V +
Sbjct: 172 AIAGLNGMQLGDKKLLVQRAS 192
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V LP +++ + IF +YG IV N++RDK+TG+ +G F+ Y + ++ L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 96 NGV 98
N V
Sbjct: 163 NNV 165
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T ++ L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 96 NGVKVLSRTIRVDHVN 111
NG+++ + + V +
Sbjct: 159 NGMQLGDKKLLVQRAS 174
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E ++DN+
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 96 NGVKVLSRTIRVD 108
N ++ RTIRV+
Sbjct: 75 NESELFGRTIRVN 87
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSG HD K +FVG +P L E D+ +F ++G I L +++D++TG KG
Sbjct: 5 SSGVPMKDHDAIK----LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCA 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVL---SRTIRV 107
F+ Y + S + + L+ K L +R I+V
Sbjct: 61 FLTYCARDSALKAQSALHEQKTLPGMNRPIQV 92
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L +++ D+ F+ +G+I + +V+D TGKSKG+ F+ + ++ ++ ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 96 NGVKVLSRTIRVDHVNDYKPP 116
G + R IR + KPP
Sbjct: 78 GGQWLGGRQIRTNWAT-RKPP 97
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V LP +++ + IF +YG IV N++RDK+TG+ +G F+ Y + ++ L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 96 NGV 98
N V
Sbjct: 152 NNV 154
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP D+++ ++ +F G I ++RD TG S G+ F+ + + + ++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGVKVLSRTIRVDHV 110
NG+ V ++ ++V +
Sbjct: 66 NGITVRNKRLKVSYA 80
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T ++ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 96 NGVKVLSRTIRVDHVN 111
NG+++ + + V +
Sbjct: 157 NGMQLGDKKLLVQRAS 172
>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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E ++DN+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 96 NGVKVLSRTIRVD 108
N ++ RTIRV+
Sbjct: 70 NESELFGRTIRVN 82
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E ++DN+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 96 NGVKVLSRTIRVD 108
N ++ RTIRV+
Sbjct: 68 NESELFGRTIRVN 80
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T ++ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 96 NGVKVLSRTIRV 107
NG+++ + + V
Sbjct: 64 NGMQLGDKKLLV 75
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E ++DN+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 96 NGVKVLSRTIRVD 108
N ++ RTIRV+
Sbjct: 65 NESELFGRTIRVN 77
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 46/75 (61%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
A ++VGGL +SE + +F Q G +VN ++ +D++TG+ +G+ F+ + + ++
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 94 NLNGVKVLSRTIRVD 108
++ +K+ + IRV+
Sbjct: 76 IMDMIKLYGKPIRVN 90
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 9/81 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVGGL + ++ + FSQYGE+V+ +++DK T +S+GF F+ ++D N
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP--------NC 70
Query: 96 NGVKVLSRTIRVDHVN-DYKP 115
G + SR +D N D KP
Sbjct: 71 VGTVLASRPHTLDGRNIDPKP 91
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 54/94 (57%), Gaps = 1/94 (1%)
Query: 16 QELSSGSKTSWHDQYKD-SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKS 74
Q++ GS+ + D + + V GL +E D+ +FS+YG I ++++V D+ + +S
Sbjct: 28 QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 87
Query: 75 KGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
+GF F+ +E+ + + NG+++ R IRVD
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E ++DN+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96 NGVKVLSRTIRVD 108
N ++ RTIRV+
Sbjct: 126 NESELFGRTIRVN 138
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 46/78 (58%)
Query: 38 VGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
V GL +E D+ +FS+YG I ++++V D+ + +S+GF F+ +E+ + + NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 98 VKVLSRTIRVDHVNDYKP 115
+++ R IRVD +P
Sbjct: 77 MELDGRRIRVDFSITKRP 94
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 46/78 (58%)
Query: 38 VGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
V GL +E D+ +FS+YG I ++++V D+ + +S+GF F+ +E+ + + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 98 VKVLSRTIRVDHVNDYKP 115
+++ R IRVD +P
Sbjct: 80 MELDGRRIRVDFSITKRP 97
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 37 FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLN 96
+VG LP++ +GD+ IF I ++ LVRDK T K KGFC++ + D+ ++ +
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYD 76
Query: 97 GVKVLSRTIRVD 108
G + R++RVD
Sbjct: 77 GALLGDRSLRVD 88
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
D+A I V L D E D+ +F +G I + L +DK TG+SKGF FI + + +
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 92 VDNLNGV 98
+ ++G
Sbjct: 74 IAGVSGF 80
>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 = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 157
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 68
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 11/90 (12%)
Query: 18 LSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
L G KT Y +FVG LP D++E D +F +YGE + + RD +GF
Sbjct: 12 LKPGEKT-----YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGF 60
Query: 78 CFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
FI E + ++ L+G + SR +R+
Sbjct: 61 GFIRLESRTLAEIAKAELDGTILKSRPLRI 90
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 69
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 159
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 70
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 156
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 67
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 69
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D S
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y +TV VD
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY----ATVEEVD 62
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 48/85 (56%), Gaps = 5/85 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVGG+P++ E ++ F ++G + + ++ D + +GF FI +ED++S +V N+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNK 120
+ ++ + + V P+D+K
Sbjct: 72 HFHDIMGKKVEVKRAE----PRDSK 92
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 31 KDSAW--IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
KD+ + IFVGGLPY ++ + F +G+I ++ D+ TGKS+G+ F+ D+ +
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 43/70 (61%)
Query: 38 VGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
V GL +E D+ +FS+YG I ++++V D+ + +S+GF F+ +E+ + + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 98 VKVLSRTIRV 107
+++ R IRV
Sbjct: 80 MELDGRRIRV 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L + E + +F Q G + + + +D+ GK K F F+C++ S ++ L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77
Query: 96 NGVKVLSRTIRVD 108
NG+++ R I V
Sbjct: 78 NGIRLYGRPINVS 90
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
K S ++VG L + +E + +FS+ G+I + + DK+ + GFCF+ Y +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 91 SVDNLNGVKVLSRTIRVDHVNDYKPPK 117
++ +NG ++ R IR D +K +
Sbjct: 97 AMRYINGTRLDDRIIRTDWDAGFKEGR 123
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 32/50 (64%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
+F+GGL + ++ + F Q+GE+ ++RD +T +S+GF F+ + DQ
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
IFVGGL D E + F +GE+ ++ L D T K +GFCFI ++++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 53
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV L Y SE D+ +FS YG + L+ D +T K KGF F+ + V + +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 96 NGVKVLSRTIRV 107
+G R + V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
IFVGGL D E + F +GE+ ++ L D T K +GFCFI ++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNL-NLVRDKITGKSKGFCFICYEDQRSTVLS 91
S+ IF+G L ++ E + FS +G I+ ++RD TG SKG+ FI + ++ +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 92 VDNLNGVKVLSRTIRVDHV 110
++ +NG + +R I V +
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 32/50 (64%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
+F+GGL + ++ + F Q+GE+ ++RD +T +S+GF F+ + DQ
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP D+++ ++ +F G I ++RD TG S G+ F+ + + + ++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGVKVLSRTIRVDHV 110
NG+ V ++ ++V +
Sbjct: 66 NGITVRNKRLKVSYA 80
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
+ V GLP+ +E D+ FS +GE++ + + +D TG SKGF F+ + + + V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 42/72 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V +P + E + +F +YG I ++ +V D+ T +S+G+ F+ ++ S ++ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 96 NGVKVLSRTIRV 107
NG +L++ ++V
Sbjct: 105 NGFNILNKRLKV 116
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
IFVGGL + + DV F Q+G++ + L+ DK T + +GF F+ +E +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ LPY ++ ++ IF +YG I +R T +++G ++ YED +VD+L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 96 NGVKVLSRTIRVDHVN 111
+G V +R + V + N
Sbjct: 68 SGFNVSNRYLVVLYYN 83
>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 = 7e-04, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 5/82 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYE---DQRSTVLSV 92
+FVGG+ + E ++ F++YG + + ++ D+ TG SKG+ F+ + D + V S
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 93 DNLNGVKV-LSRTIRVDHVNDY 113
N +G K+ L IR +++ Y
Sbjct: 71 INFHGKKLKLGPAIRKQNLSTY 92
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+ GLP+ ++ ++ I +G + +L LV ++ GK KG ++ YE++ +V +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 96 NGVKVLSRTIRVDHVND 112
+G+ + I+V N
Sbjct: 79 DGMTIKENIIKVAISNS 95
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL ++ +E + + Q+G++ + ++RD + +S+GF F+ + S++ VD
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF----SSMAEVDAA 85
Query: 96 NGVK 99
+
Sbjct: 86 MAAR 89
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
K S ++VG L + +E + +FS+ G+I + + DK+ + GFCF+ Y +
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAEN 74
Query: 91 SVDNLNGVKVLSRTIRVD 108
++ +NG ++ R IR D
Sbjct: 75 AMRYINGTRLDDRIIRTD 92
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 50/100 (50%), Gaps = 9/100 (9%)
Query: 17 ELSSGSKTSWHDQYKDSAWIFVGGLPYDL-SEGDVICIFSQYGEIVNLNLVRDKITGKSK 75
+L + + T+ +D ++ +F+G L L + DV IFS+YG + ++ K
Sbjct: 11 KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HK 62
Query: 76 GFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKP 115
G+ F+ Y ++R +V NG + +T+ ++ + KP
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYE---DQRSTVLSV 92
+FVGG+ + E ++ F++YG + + ++ D+ TG SKG+ F+ + D + V S
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 93 DNLNGVKV-LSRTIR 106
N +G K+ L IR
Sbjct: 71 INFHGKKLKLGPAIR 85
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ LPY ++ ++ IF +YG I +R T +++G ++ YED + D+L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 96 NGVKVLSRTIRVDHVNDYKPPK--DNKYTDEETKKLR 130
+G V +R + V + N + + D K +E+ K L+
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 114
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V +P+ + D+ +F Q+G+I+++ ++ ++ SKGF F+ +E+ + + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 96 NGVKVLSRTIRVDHV 110
+G V R I V++
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V +P+ + D+ +F Q+G+I+++ ++ ++ SKGF F+ +E+ + + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 96 NGVKVLSRTIRVDHV 110
+G V R I V++
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYE---DQRSTVLSV 92
+FVGG+ + E ++ F++YG + + ++ D+ TG SKG+ F+ + D + V S
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 93 DNLNGVKV-LSRTIR 106
N +G K+ L IR
Sbjct: 72 INFHGKKLKLGPAIR 86
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G LP + +E ++ +F QYG+++ +++++ + F+ ED+ + ++ NL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 96 NGVKVLSRTIRVD 108
+ K+ I V+
Sbjct: 63 HHYKLHGVNINVE 75
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D + ++VG L D++E ++ +FSQ G + ++ + + +C
Sbjct: 2 SSGSSGMMEDDGQPRT-LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YC 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
F+ + + R ++ +NG K+L + ++V+
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVN 88
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 41 LPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKV 100
L Y S + +F +YG + ++ + R+ T +GF F+ + D+R + ++G ++
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80
Query: 101 LSRTIRV 107
R +RV
Sbjct: 81 DGRELRV 87
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 5/97 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ + LPY ++ ++ IF +YG I +R T +++G ++ YED + D+L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 96 NGVKVLSRTIRVDHVNDYKPPK--DNKYTDEETKKLR 130
+G V +R + V + N + + D K +E+ K L+
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 114
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 40/73 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L +++ + F+ +G I + +V+D TGKSKG+ F+ + ++ ++ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 96 NGVKVLSRTIRVD 108
G + R IR +
Sbjct: 69 GGQWLGGRQIRTN 81
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 51/110 (46%), Gaps = 3/110 (2%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + S +FV L Y + + +FS G +V +++ DK GKS+G
Sbjct: 2 SSGSSGALQAGRLGST-VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKK 128
+ +E V ++ NG + R + V +++ PK + + E ++
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLLFDRPMHV-KMDERALPKGDFFPPERPQQ 108
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 53/108 (49%), Gaps = 19/108 (17%)
Query: 1 MNPLT-NVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGE 59
M LT ++KN +K E+ + S+ +FVG LP D++E ++ +F +YG+
Sbjct: 1 MEGLTIDLKNFRKPGEKTFTQRSR------------LFVGNLPPDITEEEMRKLFEKYGK 48
Query: 60 IVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
+ + +D KGF FI E + ++ L+ + + + +RV
Sbjct: 49 AGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV 90
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
D ++VG + Y + D+ FS G I + ++ DK +G KG+ +I + +R++V +
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDA 93
Query: 92 VDNLNGVKVLSRTIRV 107
++ RTI+V
Sbjct: 94 AVAMDETVFRGRTIKV 109
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ LPY ++ ++ IF +YG I +R T +++G ++ YED + D+L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 96 NGVKVLSRTIRVDHVN 111
+G V +R + V + N
Sbjct: 72 SGFNVCNRYLVVLYYN 87
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVN--LNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+FVGGLP D+ E ++ F ++G +V + K KG+ F+ ++++ S +D
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+VG LP D+ D+ +F +YG I +++L +++ G F F+ +ED R +V
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 96 NGVKVLSRTIRVD 108
+G +RV+
Sbjct: 82 DGYDYDGYRLRVE 94
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S+ +++ GL ++ D++ + YG+IV+ + DK T K KG+ F+ ++ + +V
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 93 DNLNGVKVLSRTIR 106
L V ++ +
Sbjct: 65 TALKASGVQAQMAK 78
>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 = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 30 YKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
+ + +FVG LP D++E ++ +F +YG+ + + +D KGF FI E +
Sbjct: 12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 65
Query: 90 LSVDNLNGVKVLSRTIRV 107
++ L+ + + + +RV
Sbjct: 66 IAKVELDNMPLRGKQLRV 83
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L +G++ FS YG + + + R+ GF F+ +ED R +V L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 96 NGVKVLSRTIRVD 108
+G + +RV+
Sbjct: 58 DGKVICGSRVRVE 70
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.0 bits (79), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 13/103 (12%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGL-PYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
SSGS + D ++ +F+G L + + DV IFS+YG+IV ++ KGF
Sbjct: 2 SSGS-SGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGF 52
Query: 78 CFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
F+ Y ++R+ +V +G + + + +N PK N+
Sbjct: 53 AFVQYVNERNARAAVAGEDGRMIAGQVL---DINLAAEPKVNR 92
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 35.0 bits (79), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 37 FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLN 96
++G +P+ +E D+I +F +G I++ + KG CFI Y+ + + L
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALA 84
Query: 97 GVKVLSRTIR 106
R +R
Sbjct: 85 NFPFQGRNLR 94
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.0 bits (79), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L SE DV +F +G I ++R G SKG F+ Y +++ L
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 96 NGVKVL 101
+G + +
Sbjct: 77 HGSQTM 82
>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 = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYG-EIVNLNLVRDKITGKSKGFCFICYED-QRSTVLSVD 93
+ + LP +E D+ +G + + L+R+K +G+S+GF F+ + Q +T
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 94 NLNGVKVLSRTIRVDHVNDYKP 115
N + + +L + + + H +D KP
Sbjct: 64 NQHSLNILGQKVSM-HYSDPKP 84
>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 = 34.7 bits (78), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS--TV 89
D+ I+VG + Y + ++ F G + + ++ DK +G KGF +I + D+ S T
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 90 LSVD 93
L++D
Sbjct: 64 LALD 67
>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 = 34.7 bits (78), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS--TV 89
D+ I+VG + Y + ++ F G + + ++ DK +G KGF +I + D+ S T
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 90 LSVD 93
L++D
Sbjct: 65 LALD 68
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 34.7 bits (78), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGE-IVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
+A +++G L + E + F+ GE ++++ ++R+++TG G+CF+ + D +
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 92 VDNLNG 97
+ +NG
Sbjct: 69 LHKING 74
>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 = 34.3 bits (77), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 39/73 (53%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L ++ + + F + ++ +++ D TG S+G+ F+ + Q ++D++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96 NGVKVLSRTIRVD 108
G + R +R++
Sbjct: 64 QGQDLNGRPLRIN 76
>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 = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 21/28 (75%)
Query: 53 IFSQYGEIVNLNLVRDKITGKSKGFCFI 80
+FS+ G++VN+ D+ TGK+KGF F+
Sbjct: 32 LFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
S I + LP D++EG+VI + +G++ NL +++ GK++ F + E+ +T+++
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK----GKNQAFIEMNTEEAANTMVN 70
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.9 bits (76), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 54 FSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
FS +G I + ++ + G+SKGF F+C+ +V +NG V ++ + V
Sbjct: 36 FSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
>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 = 33.9 bits (76), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 21/28 (75%)
Query: 53 IFSQYGEIVNLNLVRDKITGKSKGFCFI 80
+FS+ G++VN+ D+ TGK+KGF F+
Sbjct: 32 LFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.9 bits (76), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 39/73 (53%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L ++ + + F + ++ +++ D TG S+G+ F+ + Q ++D++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96 NGVKVLSRTIRVD 108
G + R +R++
Sbjct: 150 QGQDLNGRPLRIN 162
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 12/107 (11%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLN---------LVRDK 69
SSGS D+ D++ I+V GL ++ D+ F Q G +V +N + DK
Sbjct: 2 SSGSSGD-PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCG-VVKMNKRTGQPMIHIYLDK 59
Query: 70 ITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPP 116
TGK KG + YED + +V+ +G ++V + KPP
Sbjct: 60 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV-SLARKKPP 105
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 33.5 bits (75), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
S I + LP D++EG+VI + +G++ NL +++ GK++ F + E+ +T+++
Sbjct: 31 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK----GKNQAFIEMNTEEAANTMVN 85
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 33.5 bits (75), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 7/102 (6%)
Query: 6 NVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNL 65
N + +L E+ELS + + A + V LP L++ + +G + L
Sbjct: 75 NAFHQSRLRERELSVQLQPT-------DALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127
Query: 66 VRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
V + TG+SKG+ F Y + S + +L G + RT+ V
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 33.5 bits (75), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 7/102 (6%)
Query: 6 NVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNL 65
N + +L E+ELS + + A + V LP L++ + +G + L
Sbjct: 75 NAFHQSRLRERELSVQLQPT-------DALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127
Query: 66 VRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
V + TG+SKG+ F Y + S + +L G + RT+ V
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>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 = 33.1 bits (74), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 7/102 (6%)
Query: 6 NVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNL 65
N + +L E+ELS + + A + V LP L++ + +G + L
Sbjct: 73 NAFHQSRLRERELSVQLQPT-------DALLCVANLPPSLTQQQFEELVRPFGSLERCFL 125
Query: 66 VRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
V + TG+SKG+ F Y + S + +L G + RT+ V
Sbjct: 126 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IF+ L + + FS +G I++ +V D+ SKG+ F+ +E Q + +++ +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 96 NGVKVLSRTIRVDHVNDYK 114
NG+ + R + V K
Sbjct: 159 NGMLLNDRKVFVGRFKSRK 177
>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 = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S IF+ L + + FS +G I++ +V D+ SKG+ F+ +E Q + ++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAI 62
Query: 93 DNLNGVKVLSRTIRVDHVNDYK 114
+ +NG+ + R + V K
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRK 84
>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 = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IF+ L + + FS +G I++ +V D+ SKG+ F+ +E Q + +++ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 96 NGVKVLSRTIRVDHVNDYK 114
NG+ + R + V K
Sbjct: 164 NGMLLNDRKVFVGRFKSRK 182
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 53 IFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKV-LSRTIRVDHVN 111
IFS++G+I N + GK+KG+ F+ Y V +V N +G K+ T RV+
Sbjct: 41 IFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFT 98
Query: 112 DY 113
D+
Sbjct: 99 DF 100
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 28 DQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
Q +D +++ LP + E ++ + +G++++ ++RD +G S+G F E
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 78
Query: 88 TVLSVDNLNG 97
+ + NG
Sbjct: 79 CEAVIGHFNG 88
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVN--------LNLVRDKITGKSKGFCFICYE 83
D+ IFV GL +++ V F Q G I +NL D+ TGK KG + ++
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 84 DQRSTVLSVDNLNGVKVLSRTIRV 107
D S ++D +G + I+V
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPIKV 89
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L SE DV+ +F +G I ++R G SKG F+ + ++ L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 96 NGVKVL 101
+G + +
Sbjct: 77 HGSQTM 82
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IF+ L + + FS +G I++ +V D+ SKG+ F+ +E Q + +++ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 96 NGVKVLSRTIRVDHVNDYK 114
NG+ + R + V K
Sbjct: 72 NGMLLNDRKVFVGRFKSRK 90
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV P D+ E ++ IF +G + + ++ GF F+ +E+ S +++ +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 96 NGVKVLSRTIRV 107
+G ++ + V
Sbjct: 86 HGKSFANQPLEV 97
>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 = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVN--------LNLVRDKITGKSKGFCFICYE 83
D+ IFV GL +++ V F Q G I +NL D+ TGK KG + ++
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 84 DQRSTVLSVDNLNGVKVLSRTIRV 107
D S ++D +G + I+V
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKV 95
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L + ++ ++ F YG + ++ + R+ GF F+ +ED R +V +L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 96 NGVKVLSRTIRVDHVNDYK 114
+G + +RV+ N K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 9/56 (16%)
Query: 34 AWIFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+ +F+G LP ++S+ D+ IFS YG I+ +N+ F FI +++ +S
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 58
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 9/54 (16%)
Query: 36 IFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+F+G LP ++S+ D+ IFS YG I+ +N+ F FI +++ +S
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 70
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/66 (19%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGK-SKGFCFICYEDQRSTVLSVDN 94
+ +G L ++++ ++ IFS YG+I +++ +++ SKG+ ++ +E+ ++ +
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 95 LNGVKV 100
++G ++
Sbjct: 67 MDGGQI 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L + ++ ++ F YG + ++ + R+ GF F+ +ED R +V L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 96 NGVKVLSRTIRVDHVNDYK 114
+G + +RV+ N K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV P D+ E ++ IF +G + + ++ GF F+ +E+ S +++ +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEEV 58
Query: 96 NGVKVLSRTIRV 107
+G ++ + V
Sbjct: 59 HGKSFANQPLEV 70
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 31.2 bits (69), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVG + + ++ +F + G ++ ++V+D + F+ E + ++ L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 96 NGVKVLSRTIRVD 108
NG +V + I V+
Sbjct: 64 NGKEVKGKRINVE 76
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.2 bits (69), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 9/54 (16%)
Query: 36 IFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+F+G LP ++S+ D+ IFS YG I+ +N+ F FI +++ +S
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 50
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 53 IFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKV-LSRTIRVD 108
IFS++G+I N + GK+KG+ F+ Y V +V N +G K+ T RV+
Sbjct: 27 IFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 81
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.8 bits (68), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV L ++E + FS++G++ + ++D + F+ +ED+ + V ++D +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 96 NG 97
NG
Sbjct: 70 NG 71
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.8 bits (68), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 9/54 (16%)
Query: 36 IFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+F+G LP ++S+ D+ IFS YG I+ +N+ F FI +++ +S
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 70
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S+ +FVG D++E ++ FSQYG+++++ + + + F F+ + D +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIA---- 55
Query: 93 DNLNGVKVLSRTIRVDHVNDYKP 115
+L G ++ + I V H+++ +P
Sbjct: 56 QSLCGEDLIIKGISV-HISNAEP 77
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 13/73 (17%), Positives = 39/73 (53%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ L ++E D++ +F+++ E + +TG+ +G FI + ++ ++ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 96 NGVKVLSRTIRVD 108
NG K+ + + ++
Sbjct: 88 NGYKLYGKILVIE 100
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.0 bits (66), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICY---EDQRSTVLSV 92
+FV GL D +E + + V +V D+ TG SKGF F+ + ED ++ ++
Sbjct: 18 LFVKGLSEDTTE---ETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 93 DN--LNGVKV 100
++ ++G KV
Sbjct: 75 EDGEIDGNKV 84
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 11/85 (12%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG D++ ++ F QYGE+V++ I + F F+ + D + +L
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDKVA----QSL 64
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNK 120
G ++ + I V H+++ + PK NK
Sbjct: 65 CGEDLIIKGISV-HISNAE-PKHNK 87
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S+ IFV LP+D + + F++ G ++ ++ + GKSKG + +E +
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 62
Query: 93 DNLNGVKVLSRTI--RVDH 109
+NG+K+ R I R+D
Sbjct: 63 RMMNGMKLSGREIDVRIDR 81
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKI-TGKSKGFCFICY 82
I V +P+ ++ ++ +FS +GE+ + L + TG +GF F+ +
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/71 (18%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++ GG+ L++ + FS +G+I+ + + + KG+ F+ + S ++ ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 96 NGVKVLSRTIR 106
NG + ++
Sbjct: 82 NGTTIEGHVVK 92
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
+D+ + LPY +++ ++ +F EI LV GKSKG +I ++ +
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEI---RLVSK--DGKSKGIAYIEFKTEADAEK 145
Query: 91 SVDNLNGVKVLSRTIRVDHVNDYK 114
+ + G ++ R+I + + + K
Sbjct: 146 TFEEKQGTEIDGRSISLYYTGEPK 169
>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 = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 54 FSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
FS +G I++L++ + F+ YE S +V LNG +V S ++V+
Sbjct: 58 FSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN 106
>pdb|2DNR|A Chain A, Solution Structure Of Rna Binding Domain In Synaptojanin 1
Length = 91
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 9/54 (16%)
Query: 54 FSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
F+ +GE++ + V DK+ ++ + + S+ L+V +LNG ++L+RTI +
Sbjct: 36 FASFGEVILIRFVEDKM--------WVTFL-EGSSALNVLSLNGKELLNRTITI 80
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 54 FSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
FS +G I++L++ + F+ YE S +V LNG +V S ++V+
Sbjct: 34 FSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN 82
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Hypothetical Protein Flj201171
Length = 123
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 10/49 (20%)
Query: 40 GLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
GLP+ + +V+ F Q+ ITG +G F+ Y D R T
Sbjct: 30 GLPFTATAEEVVAFFGQH----------CPITGGKEGILFVTYPDGRPT 68
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFV LP+D + + F++ G ++ ++ + GKSKG + +E + +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68
Query: 96 NGVKVLSRTI--RVDH 109
NG+K+ R I R+D
Sbjct: 69 NGMKLSGREIDVRIDR 84
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST--VLSVD 93
+F+ L +D E + + Q+G++ + +V T SKG F + Q + L+
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 94 NL----NGVKVLSRTIRVD 108
+L G+K+ R ++VD
Sbjct: 78 SLEAEGGGLKLDGRQLKVD 96
>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 = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 34 AWIFVGGLPYDLSEGDVICIFSQYG--EIVNLNLVRDKITGKSKGFCFICYEDQRST--- 88
A ++VG + ++ +I + G ++V L ++ G+SKG+ + + S
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 89 --VLSVDNLNGVKV 100
+L LNG KV
Sbjct: 116 LELLPGKVLNGEKV 129
>pdb|2QP2|A Chain A, Structure Of A Macpf/perforin-like Protein
Length = 511
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 26/56 (46%)
Query: 76 GFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKLRT 131
G C D+R S DN V +L +T++V + D D KYT+ + + +
Sbjct: 59 GSCMNSLFDERKINASEDNFKKVTILGKTLKVPYYIDCYSVGDLKYTNASGESIES 114
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
0.313 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,105,117
Number of Sequences: 62578
Number of extensions: 203403
Number of successful extensions: 555
Number of sequences better than 100.0: 170
Number of HSP's better than 100.0 without gapping: 125
Number of HSP's successfully gapped in prelim test: 45
Number of HSP's that attempted gapping in prelim test: 386
Number of HSP's gapped (non-prelim): 193
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)