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= 022827
(291 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 112 bits (279), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 68/182 (37%), Positives = 96/182 (52%), Gaps = 28/182 (15%)
Query: 1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
MA +DMSLDDIIK + G RR + AR
Sbjct: 15 MADKMDMSLDDIIKLNRNQRRVNR-----------------------GGGPRRNRPAIAR 51
Query: 61 PSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIREL 118
A + R + P WQHDLF+ G G+E G KL VSNL GV++ DI+EL
Sbjct: 52 GGRNRPA-PYSRPKPLPDKWQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQEL 108
Query: 119 FSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA 178
F+E G LK+ A+ +D++GR G+A+V + RR+DA A+K+Y V LDG+PM I++V +
Sbjct: 109 FAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
Query: 179 EI 180
++
Sbjct: 169 DL 170
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 107 bits (268), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 49/103 (47%), Positives = 72/103 (69%), Gaps = 2/103 (1%)
Query: 78 WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
WQHDLF+ G G+E G KL VSNL GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17 WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
Query: 138 PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEI 180
G+A+V + RR+DA A+K+Y V LDG+PM I++V + ++
Sbjct: 75 SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 107 bits (268), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 49/103 (47%), Positives = 72/103 (69%), Gaps = 2/103 (1%)
Query: 78 WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
WQHDLF+ G G+E G KL VSNL GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17 WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
Query: 138 PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEI 180
G+A+V + RR+DA A+K+Y V LDG+PM I++V + ++
Sbjct: 75 SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 98.6 bits (244), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 50/105 (47%), Positives = 71/105 (67%), Gaps = 4/105 (3%)
Query: 72 RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
R + P WQHDLF+ E G KL VSNL GV++ DI+ELF+E G LK+ A
Sbjct: 2 RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 59
Query: 130 IHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV 174
+H+D++GR G+A+V + R++DA A+K+YN V LDG+PM I++V
Sbjct: 60 VHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 104
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 49/105 (46%), Positives = 69/105 (65%), Gaps = 4/105 (3%)
Query: 72 RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
R + P WQHDLF+ E G KL VSNL GV++ DI+ELF+E G LK+ A
Sbjct: 3 RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 60
Query: 130 IHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV 174
+H+D++GR G+A+V + R++DA A K+YN V LDG+P I++V
Sbjct: 61 VHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXNIQLV 105
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T LYV+NL +T+D + +F + G + + I DK GRP G A V Y +R +A A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 158 RYNNVLLDG--KPMKIEV 173
NNV+ +G +P+ + +
Sbjct: 74 ALNNVIPEGGSQPLSVRL 91
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T LYV+NL +T+D + +F + G + + I DK GRP G A V Y +R +A A+
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 158 RYNNVLLDG--KPMKIEV 173
NNV+ +G +P+ + +
Sbjct: 150 ALNNVIPEGGSQPLSVRL 167
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T+ ++ LF IG + I D K G G A V + D+ A+K
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 158 RYNNVLLDGKPMKI 171
N + + K +K+
Sbjct: 64 VLNGITVRNKRLKV 77
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T LYV+NL +T+D + +F + G + + I DK GRP G A V Y +R +A A+
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 158 RYNNVLLDG--KPMKIEV 173
NNV+ +G +P+ + +
Sbjct: 161 ALNNVIPEGGSQPLSVRL 178
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
+LYV +LH +T D +R +F G ++ + D + GR G + ++ A AL++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 159 YNNVLLDGKPMKI 171
N L G+PMK+
Sbjct: 88 LNGFELAGRPMKV 100
>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 = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
LYV NL T + I ELFS+ G++K+ + DK G V Y R+DA A++ N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 161 NVLLDGKPMKIE 172
LD + ++ +
Sbjct: 81 GTRLDDRIIRTD 92
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%)
Query: 97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+G+ ++V+NL V ++E+FS G + R I DK+G+ G V + + +A A+
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 157 KRYNNVLLDGKPMKIEV 173
+N LL +PM +++
Sbjct: 74 SMFNGQLLFDRPMHVKM 90
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 82 EGLNGQDLMGQPISVD 97
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 83 EGLNGQDLMGQPISVD 98
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 69 EGLNGQDLMGQPISVD 84
>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 = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
G L+V+ +H T +DI + F+E GE+K ++ D + G G V Y +A AA+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
+ N L G+P+ ++
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 56/120 (46%), Gaps = 12/120 (10%)
Query: 54 GPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTND 113
G SN R + + S+ R RN +D L +E G L+V+++H D
Sbjct: 39 GSDSNTREAIH----SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQED 87
Query: 114 DIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
+I+E F + GE+K ++ D + G G A V Y A AA + N + G+ ++++
Sbjct: 88 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T D++R LFS IGE++ + DK G G V Y DA A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 158 RYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGV 191
N + L K +K+ ++E+ A + ++G+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGL 96
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
LY+S L +T D+ ++FS G + + D+ G G A + + +RS+A A+ +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 160 N 160
N
Sbjct: 151 N 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T D++R LFS IGE++ + DK G G V Y DA A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 158 RYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGV 191
N + L K +K+ ++E+ A + ++G+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGL 96
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
LY+S L +T D+ ++FS G + + D+ G G A + + +RS+A A+ +
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 160 N 160
N
Sbjct: 151 N 151
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
G L V NL P V+N+ + + FS+ G +++ + D GR +G V +A + A AL+
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Query: 158 RYNN--VLLDGKPMKIEV 173
R + LL P + V
Sbjct: 156 RCGDGAFLLTTTPRPVIV 173
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 50/105 (47%), Gaps = 8/105 (7%)
Query: 69 SFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY 128
S+ R RN +D L +E G L+V+++H D+I+E F + GE+K
Sbjct: 4 SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 56
Query: 129 AIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
++ D + G G A V Y A AA + N + G+ ++++
Sbjct: 57 HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
LY+ NL P VT D+ LF+ E K I F GR G A + + + A+ AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 160 NNVLLDGKPMKIEV 173
N L GK + IE
Sbjct: 88 NGYKLYGKILVIEF 101
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRY 159
LYV +LH +T D +R +F G++ + D + GR G + ++ A AL++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 160 NNVLLDGKPMKI 171
N L G+PM++
Sbjct: 68 NGFELAGRPMRV 79
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR-PSGSAEVVYARRSDAFAALKRY 159
LYV NL T + I ELFS+ G++K+ + DK + G V Y R+DA A++
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 160 NNVLLDGKPMKIE 172
N LD + ++ +
Sbjct: 102 NGTRLDDRIIRTD 114
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 117 ELFSEIGELKRYAIH----FDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK 170
E F + G++ + I+ + + PS SA V Y R DA A++ NNV++DG+ +K
Sbjct: 37 EYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK 94
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAAL 156
GT L V+ L T D++R LFS IGE++ + DK G G V Y DA A+
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 157 KRYNNVLLDGKPMKI 171
N + L K +K+
Sbjct: 79 NTLNGLRLQSKTIKV 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
L V NL V+N+ + E FS G+++R + D GRPSG V ++ + A AL R +
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Query: 161 --NVLLDGKPMKIEV 173
+ LL P + V
Sbjct: 159 EGSFLLTTFPRPVTV 173
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 5/95 (5%)
Query: 86 SLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVV 145
+ R G ++L+V NL P +T +++R+LF + G+ IH DK G +
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----GFGFIR 64
Query: 146 YARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEI 180
R+ A A +N+ L GK +++ +A +
Sbjct: 65 LETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL 99
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALK 157
+ +YVSNL +TN+D+ +FS+ G++ + I DK+ R S G A +++ + A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 158 RYNNVLLDGKPMKIEV 173
NN L G+ +K +
Sbjct: 77 AINNKQLFGRVIKASI 92
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
LYV NL +T D +++ F G + I DKN + A V Y + DA AL+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT-- 60
Query: 161 NVLLDGKPMKIEVVGTNAEIPLQ 183
L+GK ++ +V N Q
Sbjct: 61 ---LNGKQIENNIVKINWAFQSQ 80
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
++V N+ T + ++++FSE+G + + + +D+ G+P G Y + A +A++
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 160 NNVLLDGKPMKIE 172
N G+ ++++
Sbjct: 71 NGREFSGRALRVD 83
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
LYV +LHP VT + E FS G + + D R S G A V + + +DA AL
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 160 NNVLLDGKPMKI 171
N ++ GKP++I
Sbjct: 73 NFDVIKGKPVRI 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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
LYV +LHP VT + E FS G + + D R S G A V + + +DA AL
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 160 NNVLLDGKPMKI 171
N ++ GKP++I
Sbjct: 78 NFDVIKGKPVRI 89
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 53/101 (52%), Gaps = 8/101 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS+ G++ I ++ + G A V++ S A AL
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKR 197
+ KPM+I+ T+++I A++ T V RKR
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDII--AKMKGTFVERDRKR 107
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK--------RYAIHFDK-NGRPSGSAEVVYARR 149
+ +YV L+ VT DD+ + F + G +K I+ DK G+P G A V Y
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 150 SDAFAALKRYNNVLLDGKPMKIEVV 174
A AA++ ++ G +K+ +
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T D++R LFS IGE++ + DK G G V Y DA A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 158 RYNNVLLDGKPMKI 171
N + L K +K+
Sbjct: 65 TLNGLRLQSKTIKV 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 = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
++L+V NL P +T +++R+LF + G+ IH DK G + R+ A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVE 70
Query: 159 YNNVLLDGKPMKIEVVGTNAEI 180
+N+ L GK +++ +A +
Sbjct: 71 LDNMPLRGKQLRVRFACHSASL 92
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
L V L T D+RE+FS+ G + +I +D+ R S G A V + DA A +R
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 160 NNVLLDGKPMKIE 172
N + LDG+ ++++
Sbjct: 109 NGMELDGRRIRVD 121
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
L V L T D+RE+FS+ G + +I +D+ R S G A V + DA A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 160 NNVLLDGKPMKIE 172
N + LDG+ ++++
Sbjct: 78 NGMELDGRRIRVD 90
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
TKL+V N+ P TN ++R F E G + I D A V R DA A++
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY-------AFVHMERAEDAVEAIRG 63
Query: 159 YNNVLLDGKPMKIEV 173
+N GK M +++
Sbjct: 64 LDNTEFQGKRMHVQL 78
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
L V L T D+RE+FS+ G + +I +D+ R S G A V + DA A +R
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 160 NNVLLDGKPMKIE 172
N + LDG+ ++++
Sbjct: 75 NGMELDGRRIRVD 87
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 34/76 (44%)
Query: 96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAA 155
E ++V NL V + + ELF + G L + I D+ G+P V + A
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYA 73
Query: 156 LKRYNNVLLDGKPMKI 171
+ N + L G+P+ +
Sbjct: 74 IALLNGIRLYGRPINV 89
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
L V L T D+RE+FS+ G + +I +D+ R S G A V + DA A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 160 NNVLLDGKPMKI 171
N + LDG+ +++
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 91 GISGIEVGTKLYVSNLHPGVTNDDIRELFSE 121
G SG KLY+ NL P VT DD+R+LF +
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGD 31
>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 = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAF 153
+ + ++YV +++ + D IR+ F+ G +K + +D + G A V Y A
Sbjct: 10 LAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 69
Query: 154 AALKRYNNVLLDGKPMKI 171
AL++ N+V+L G+ +K+
Sbjct: 70 LALEQMNSVMLGGRNIKV 87
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
++YV+++H +++DDI+ +F G++K + D G+ G + Y + + A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 159 YNNVLLDGKPMKI 171
N L G+ +++
Sbjct: 172 MNLFDLGGQYLRV 184
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
KL+V L+ + DD+R LF G ++ I +G G A V Y+ ++A AA+
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 53/101 (52%), Gaps = 8/101 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS+ G++ I ++ + G A V++ S A AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKR 197
+ KPM+I+ T+++I A++ T V RKR
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDI--IAKMKGTFVERDRKR 108
>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 = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAF 153
+ + +++YV +++ + D IR+ F+ G +K + +D + G A V Y A
Sbjct: 25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84
Query: 154 AALKRYNNVLLDGKPMKI 171
AL++ N+V+L G+ +K+
Sbjct: 85 LALEQMNSVMLGGRNIKV 102
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
++YV+++H +++DDI+ +F G++K + D G+ G + Y + + A+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 159 YNNVLLDGKPMKI 171
N L G+ +++
Sbjct: 187 MNLFDLGGQYLRV 199
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
KL++ + T +DIR +FS G+++ I +G G A V + R+ A A+K
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 45/84 (53%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS+ G++ I ++ + G A V++ S A AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
KL++ + T +DIR +FS G+++ I +G G A V + R+ A A+K
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDI 89
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 66
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDI 90
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 34.7 bits (78), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T D+ + LF IG+++ + DK G+ G V Y+ +DA A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 158 RYNNVLLDGKPMKI 171
N + L K +K+
Sbjct: 65 TLNGLKLQTKTIKV 78
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
LYVS L ++ ++ +LFS+ G + I D+ G G + + +R +A A+K
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 160 N 160
N
Sbjct: 153 N 153
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 34.7 bits (78), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 34.7 bits (78), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 65 RSMQGFPFYDKPMRIQYAKTDSDI 88
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 34.7 bits (78), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 34.7 bits (78), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTDSDI 87
>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 = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
KL++ + T +DIR FS G+++ I +G G A V + R+ A A+K
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++NL+ + D++++ +FS G++ I ++ + G A V++ S A AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
+ KPM+I+ T+++I
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
+L+VSN+ + D+R++F + G++ I F++ G G V + +DA A ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKL 89
Query: 160 NNVLLDGKPMKIEVVGTNAEI 180
+ +++G+ KIEV A +
Sbjct: 90 HGTVVEGR--KIEVNNATARV 108
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
+L+VSN+ + D+R++F + G++ I F++ G G V + +DA A ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKL 75
Query: 160 NNVLLDGKPMKIEVVGTNAEI 180
+ +++G+ KIEV A +
Sbjct: 76 HGTVVEGR--KIEVNNATARV 94
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAF 153
+ + ++YV +++ + D IR+ F+ G +K +D + G A V Y A
Sbjct: 9 LAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQ 68
Query: 154 AALKRYNNVLLDGKPMKI 171
AL++ N+V L G+ +K+
Sbjct: 69 LALEQXNSVXLGGRNIKV 86
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
++YV+++H +++DDI+ +F G++K + D G+ G + Y + + A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 159 YNNVLLDGKPMKI 171
N L G+ +++
Sbjct: 171 XNLFDLGGQYLRV 183
>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 = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
L+V+ ++ T +R F G +KR + ++ ++G+P G A + Y D +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 160 NNVLLDGKPMKIEV 173
+ +DG+ + ++V
Sbjct: 165 DGKKIDGRRVLVDV 178
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
KL++S L T +++ E+ G +K + ++ G+P G A V Y S A A+ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 160 NNVLLDGKPMKIEV 173
+ + + +K+ +
Sbjct: 79 DGMTIKENIIKVAI 92
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T D+ + LF IG+++ + DK G+ G V Y+ +DA A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 158 RYNNVLLDGKPMKI 171
N + L K +K+
Sbjct: 65 TLNGLKLQTKTIKV 78
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR----PSGSAEVVYARRSDAFAAL 156
L++ NL+ T + ++ +FS++G +K I KN G V Y + A AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 157 KRYNNVLLDGKPMKIEV 173
K+ +DG +++ +
Sbjct: 68 KQLQGHTVDGHKLEVRI 84
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 21/90 (23%)
Query: 89 AAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR------YA-IHFDKNGRPSGS 141
++G SG+ L+V NL VT + + + FS+ G+L+R YA IHFD+
Sbjct: 2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDE------- 54
Query: 142 AEVVYARRSDAFAALKRYNNVLLDGKPMKI 171
R A A++ N L+G+ ++I
Sbjct: 55 -------RDGAVKAMEEMNGKDLEGENIEI 77
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
+Y++N++ + ++++ LFS+ G + I K + G A V++ + AL
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHV--VDIVALKTMKMRGQAFVIFKELGSSTNAL 66
Query: 157 KRYNNVLLDGKPMKIEVVGTNAEIPLQAR 185
++ GKPM+I+ T+++I + R
Sbjct: 67 RQLQGFPFYGKPMRIQYAKTDSDIISKMR 95
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
L NL VT D+++E+F + E++ + K+G+ G A + + +DA +
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEIRLVS----KDGKSKGIAYIEFKTEADAEKTFEEKQ 151
Query: 161 NVLLDGKPMKIEVVG 175
+DG+ + + G
Sbjct: 152 GTEIDGRSISLYYTG 166
>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 = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
L+V+ ++ T +R F G +KR + ++ ++G+P G A + Y D +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 160 NNVLLDGKPMKIEV 173
+ +DG+ + ++V
Sbjct: 165 DGKKIDGRRVLVDV 178
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 89 AAGISGIEV----GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAE 143
++G SG+ + KL+V + G+ D++ LF E G + + D+ G G A
Sbjct: 2 SSGSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAF 61
Query: 144 VVYARRSDAFAA 155
+ Y R A A
Sbjct: 62 LTYCARDSALKA 73
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
KL+V L T++D+R++F G + + +G G A V + ++A AA+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 12/76 (15%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELK-------RYAIHFDKNGRPSGSAEVVYARRSD 151
TK+++ L VT D I E+FS G++K R H K G A V + +
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSK-----GYAYVEFENPDE 59
Query: 152 AFAALKRYNNVLLDGK 167
A ALK + +DG+
Sbjct: 60 AEKALKHMDGGQIDGQ 75
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 35/71 (49%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
+YV NL T++ ++ELFS+ G++ + +D+ + V + A+ + +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 161 NVLLDGKPMKI 171
N G+ +++
Sbjct: 64 NTDFMGRTIRV 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
+ V+NL D++ELF G + R + DK G+ G A + + RR DA A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 160 NNVLLDGKPMKIE 172
+ D + +E
Sbjct: 78 SGFGYDHLILNVE 90
>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 = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
K++V + P V + E FS+ G + + DK+ G+ G V Y D+ A+ R
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY----DSADAVDR 144
Query: 159 -YNNVLLDGKPMKIEV 173
N +D K KIE+
Sbjct: 145 VCQNKFIDFKDRKIEI 160
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALK 157
K+++ L+ T D++RE F + G + I D GR G + + + S +K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 158 RYNNVLLDGK 167
+ +LDGK
Sbjct: 64 TQH--ILDGK 71
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.8 bits (68), Expect = 0.95, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA-FAALK 157
T LYV L +T D+R F + GE++ + + A + +A R A AA K
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITV-----VQRQQCAFIQFATRQAAEVAAEK 67
Query: 158 RYNNVLLDGKPMKIE 172
+N ++++G+ + ++
Sbjct: 68 SFNKLIVNGRRLNVK 82
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
L NL +T D+++E+F + E++ + ++G+ G A + + +DA L+
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 161 NVLLDGKPMKIEVVG 175
+DG+ + + G
Sbjct: 75 GAEIDGRSVSLYYTG 89
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
+YV N+ G T +++ F G + R I DK +G P G A + ++ + +L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-L 66
Query: 160 NNVLLDGKPMKI 171
+ L G+ +K+
Sbjct: 67 DESLFRGRQIKV 78
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
LYV NL + + I + F+ I K A+ K R A V ++ R DA A+K N
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNI---KPGAVERVKKIRDY--AFVHFSNREDAVEAMKALN 72
Query: 161 NVLLDGKPMKI 171
+LDG P+++
Sbjct: 73 GKVLDGSPIEV 83
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 1/81 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
KL+V L + ++FS+ G++ + D+ R G V + DA A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 159 YNNVLLDGKPMKIEVVGTNAE 179
N +DG+ ++++ G +++
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSD 94
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
L NL +T D+++E+F + E++ + ++G+ G A + + +DA L+
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQ 157
Query: 161 NVLLDGKPMKIEVVG 175
+DG+ + + G
Sbjct: 158 GAEIDGRSVSLYYTG 172
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
LYVS L +T ++ +LFS+ G + I D+ G G + + +R +A A+K
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 160 N 160
N
Sbjct: 151 N 151
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 7/43 (16%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKR------YA-IHFDKNG 136
L+V NL VT + + + FSE G+L+R YA +HF+ G
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRG 60
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 89 AAGISGIEV--GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVV 145
++G SG++ KL++ + + D++ LF E G++ + D+ G G A +
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 146 YARRSDAFAA 155
Y R A A
Sbjct: 62 YCERESALKA 71
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 34/73 (46%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
KL++ L+ ++ +F + G + + D+ + G A + + +DA A K
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 160 NNVLLDGKPMKIE 172
N L GK +K+E
Sbjct: 69 NGKSLHGKAIKVE 81
>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 = 28.9 bits (63), Expect = 3.2, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
+YV N+ G T +++ F G + R I DK +G P G A + ++ + +L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-L 67
Query: 160 NNVLLDGKPMKIEVVGTN 177
+ L G+ +K+ TN
Sbjct: 68 DESLFRGRQIKVIPKRTN 85
>pdb|4A0S|A Chain A, Structure Of The 2-Octenoyl-Coa Carboxylase Reductase Cinf
In Complex With Nadp And 2-Octenoyl-Coa
pdb|4A0S|B Chain B, Structure Of The 2-Octenoyl-Coa Carboxylase Reductase Cinf
In Complex With Nadp And 2-Octenoyl-Coa
pdb|4A0S|C Chain C, Structure Of The 2-Octenoyl-Coa Carboxylase Reductase Cinf
In Complex With Nadp And 2-Octenoyl-Coa
pdb|4A0S|D Chain D, Structure Of The 2-Octenoyl-Coa Carboxylase Reductase Cinf
In Complex With Nadp And 2-Octenoyl-Coa
pdb|4A10|A Chain A, Apo-Structure Of 2-Octenoyl-Coa Carboxylase Reductase Cinf
From Streptomyces Sp.
pdb|4A10|B Chain B, Apo-Structure Of 2-Octenoyl-Coa Carboxylase Reductase Cinf
From Streptomyces Sp.
pdb|4A10|C Chain C, Apo-Structure Of 2-Octenoyl-Coa Carboxylase Reductase Cinf
From Streptomyces Sp.
pdb|4A10|D Chain D, Apo-Structure Of 2-Octenoyl-Coa Carboxylase Reductase Cinf
From Streptomyces Sp
Length = 447
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 90 AGISGIEVGT--KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYA 147
A +S + GT ++ VS+ + DI ++ G L YAI F KNG A V A
Sbjct: 196 AAVSPLCAGTAYRMLVSDRGAQMKQGDIVLIWGASGGLGSYAIQFVKNGGGIPVAVVSSA 255
Query: 148 RRSDAFAAL 156
++ A AL
Sbjct: 256 QKEAAVRAL 264
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
LYVS L ++ ++ +LFS+ G + I D+ G G + + +R +A A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 160 N 160
N
Sbjct: 64 N 64
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 96 EVGTKLYVSNLHPGVTNDDIRELFSEI----GELKR--YAIHFDKNGRPSGSAEVVYARR 149
E ++YV NL V D++ +F E +R + I K GR G A +
Sbjct: 43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102
Query: 150 SDAFAALKRYNNVLLDGKPMKIE 172
A ALK N +L GKPM ++
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQ 125
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 89 AAGISGIEVG--TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR-PSGSAEVV 145
++G SG +V L V NL + D +R +F + G + I + + + P G A V
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 146 YARRSDAFAALKRYNNVLLDGKPMKIEVV 174
+ R DA A + LDG+ ++++V
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
++YV NL P + DI ++F + G ++ + + G P E R DA A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPR--DAEDAVYG 80
Query: 159 YNNVLLDGKPMKIEV 173
+ DG +++E
Sbjct: 81 RDGYDYDGYRLRVEF 95
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
+YV L V+ + ELF + G + + D+ G+ G V + DA A+K
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 160 NNVLLDGKPMKI 171
+ + L GKP+++
Sbjct: 78 DMIKLYGKPIRV 89
>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 = 28.1 bits (61), Expect = 6.2, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL-K 157
K++V L P + IRE F GE++ + D K + G + + + K
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 158 RYNNVLLDGKPMKI 171
+Y+NV L +K+
Sbjct: 63 KYHNVGLSKCEIKV 76
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
KL+V L+ + +D+ LF G + + +G G A V ++ ++A AA+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAI 73
>pdb|1KSI|A Chain A, Crystal Structure Of A Eukaryotic (Pea Seedling)
Copper-Containing Amine Oxidase At 2.2a Resolution
pdb|1KSI|B Chain B, Crystal Structure Of A Eukaryotic (Pea Seedling)
Copper-Containing Amine Oxidase At 2.2a Resolution
Length = 642
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 2/91 (2%)
Query: 94 GIEVGTKLYVS-NLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA 152
G EVG +L + HP +T DD ++ + +++ + +G V ++R D
Sbjct: 513 GNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDT 572
Query: 153 FAALKRYNNVLLDGKPMKIEVVGTNAEIPLQ 183
A + N +++ + VVG + +P Q
Sbjct: 573 LAVWTKQNREIVNKDIVMWHVVGIH-HVPAQ 602
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
+L+V NL + +D+ +LFS G L D +P G A V + A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 159 YNNVLLDGKPMKI 171
+ + G+ + +
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALK 157
T L V+ L +T+ ++ LF IG + I D K G G A V + D+ A+K
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 158 RYNNVLLDGKPMKI 171
N + + K +K+
Sbjct: 64 VLNGITVRNKRLKV 77
>pdb|1W2Z|A Chain A, Psao And Xenon
pdb|1W2Z|B Chain B, Psao And Xenon
pdb|1W2Z|C Chain C, Psao And Xenon
pdb|1W2Z|D Chain D, Psao And Xenon
Length = 649
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 2/91 (2%)
Query: 94 GIEVGTKLYVS-NLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA 152
G EVG +L + HP +T DD ++ + +++ + +G V ++R D
Sbjct: 518 GNEVGYRLIPAIPAHPLLTEDDYPQIRGAFTNYNVWVTAYNRTEKWAGGLYVDHSRGDDT 577
Query: 153 FAALKRYNNVLLDGKPMKIEVVGTNAEIPLQ 183
A + N +++ + VVG + +P Q
Sbjct: 578 LAVWTKQNREIVNKDIVMWHVVGIH-HVPAQ 607
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
0.316 0.132 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,787,474
Number of Sequences: 62578
Number of extensions: 199953
Number of successful extensions: 703
Number of sequences better than 100.0: 107
Number of HSP's better than 100.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 613
Number of HSP's gapped (non-prelim): 122
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)