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= 023820
(276 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 95.1 bits (235), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 47/71 (66%), Positives = 57/71 (80%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
+YVGNLP DIR +++ED+FYKYG I IDLK P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 69 DFDGHRLRVEL 79
D+DG+RLRVE
Sbjct: 85 DYDGYRLRVEF 95
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 39/74 (52%), Positives = 58/74 (78%), Gaps = 4/74 (5%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 169
++V+GLP S SWQDLKDHMR AGDVC++ V+RDG TG+V++ +DM +A++KLD+++
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTK 75
Query: 170 FRN-AFSRAYVRVR 182
FR+ AY+RV+
Sbjct: 76 FRSHEGETAYIRVK 89
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 39/74 (52%), Positives = 58/74 (78%), Gaps = 4/74 (5%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 169
++V+GLP S SWQDLKDHMR AGDVC++ V+RDG TG+V++ +DM +A++KLD+++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTK 74
Query: 170 FRN-AFSRAYVRVR 182
FR+ AY+RV+
Sbjct: 75 FRSHEGETAYIRVK 88
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 39/74 (52%), Positives = 58/74 (78%), Gaps = 4/74 (5%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 169
++V+GLP S SWQDLKDHMR AGDVC++ V+RDG TG+V++ +DM +A++KLD+++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTK 74
Query: 170 FRN-AFSRAYVRVR 182
FR+ AY+RV+
Sbjct: 75 FRSHEGETAYIRVK 88
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/82 (51%), Positives = 59/82 (71%), Gaps = 6/82 (7%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 169
+LV+GLP S SWQDLKDHMR AGDVC++ V +DG G+V+Y +DM++A++KLDD++
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG---MGMVEYLRKEDMEYALRKLDDTK 74
Query: 170 FRN-AFSRAYVRVREYDHRRDG 190
FR+ +Y+RV Y R G
Sbjct: 75 FRSHEGETSYIRV--YPERSSG 94
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/72 (51%), Positives = 47/72 (65%), Gaps = 2/72 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
+YVGNL + E+E F YGP+ + I PPG+AFVEFE+ RDAEDA+RG DG
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 69 DFDGHRLRVELA 80
G R+RVEL+
Sbjct: 61 VICGSRVRVELS 72
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
+YVGNL + + E+E F YGP+ + + PPG+AFVEFE+ RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 69 DFDGHRLRVELA 80
G R+RVEL+
Sbjct: 134 TLCGCRVRVELS 145
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
+YVGNL + + E+E F YGP+ + + PPG+AFVEFE+ RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 69 DFDGHRLRVELA 80
G R+RVEL+
Sbjct: 134 TLCGCRVRVELS 145
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
+AS L+VGN+ +E+ F +YGP+ D+ YAFV E A DA +AIR
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-----VKDYAFVHMERAEDAVEAIR 62
Query: 64 GRDGYDFDGHRLRVELA 80
G D +F G R+ V+L+
Sbjct: 63 GLDNTEFQGKRMHVQLS 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
R+ R+++VGN+P + E +++D+F + GP+ L + +P GY F E+++ A
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 61 AIRGRDGYDFDGHRLRVELA 80
A+R +G +F G LRV+ A
Sbjct: 66 AMRNLNGREFSGRALRVDNA 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L+VG L D E+ +E +F KYG I+ + + + R G+ FV FE DA+DA+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 66 DGYDFDGHRLRVELA 80
+G DG ++RV+ A
Sbjct: 75 NGKSVDGRQIRVDQA 89
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
SR +Y+G++P D E ++ DL GP+ ++ + P R GYAF+EF + + A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 63 RGRDGYDFDGHRLRV 77
R +GY L+
Sbjct: 62 RNLNGYQLGSRFLKC 76
>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 = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
SR +Y+G++P D E ++ DL GP+ ++ + P R GYAF+EF + + A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 63 RGRDGYDFDGHRLRV 77
R +GY L+
Sbjct: 63 RNLNGYQLGSRFLKC 77
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 51.2 bits (121), Expect = 6e-07, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
SR +Y+G++P D E ++ DL GP+ ++ + P R GYAF+EF + + A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 63 RGRDGYDFDGHRLR 76
R +GY L+
Sbjct: 64 RNLNGYQLGSRFLK 77
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 41/77 (53%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
+ +R LY+ NLP I E+ D+F KYGPI I + P G A+V +E+ DA++
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 61 AIRGRDGYDFDGHRLRV 77
A+ G++ L V
Sbjct: 63 AVDHLSGFNVSNRYLVV 79
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
R L V +P + E ++ LF +YGPI + + + GY FV+F+ A+ AI
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 64 GRDGYDFDGHRLRVELA 80
G +G++ RL+V LA
Sbjct: 103 GLNGFNILNKRLKVALA 119
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L++GNLP + E+E+ LF +YG + D+ Y FV E+ AEDAIR Y
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 69 DFDGHRLRVE 78
G + VE
Sbjct: 66 KLHGVNINVE 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
ER++ ++F KYGPIA + + + R G+AFV FE DA++A +G + DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 VELA 80
V+ +
Sbjct: 89 VDFS 92
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRG 64
R LYVGNL I E ++ F GPIA+I + I + YAFVE+ ++ DA A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 65 RDGYDFDGHRLRVELA 80
+G + + +++ A
Sbjct: 61 LNGKQIENNIVKINWA 76
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPP-GYAFVEFEEARDA 58
SS + L+VG+L ++ + + + F + H+ + GY FV F DA
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
++A+ G D +G LR+ A
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWA 164
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
ER++ ++F KYGPIA + + + R G+AFV FE DA++A +G + DG R+R
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
Query: 77 VELA 80
V+ +
Sbjct: 120 VDFS 123
>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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
+ +R LY+ NLP I E+ D+F KYGPI I + P G A+V +E+ DA++
Sbjct: 13 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 61 AIRGRDGYDFDGHRLRV 77
A G++ L V
Sbjct: 73 ACDHLSGFNVCNRYLVV 89
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 38/69 (55%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
+ +R LY+ NLP I E+ D+F KYGPI I + P G A+V +E+ DA++
Sbjct: 7 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 66
Query: 61 AIRGRDGYD 69
A G++
Sbjct: 67 ACDHLSGFN 75
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
ER++ ++F KYGPIA + + + R G+AFV FE DA++A +G + DG R+R
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Query: 77 VELA 80
V+ +
Sbjct: 86 VDFS 89
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
ER++ ++F KYGPIA + + + R G+AFV FE DA++A +G + DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 V 77
V
Sbjct: 89 V 89
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 63/159 (39%), Gaps = 26/159 (16%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L V LP ++ + E+ LF G + L K+ GY FV + A+DAE AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQDLK 125
+G ++V A L ++GLP + + +D++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDAN------------------LYISGLPRTMTQKDVE 106
Query: 126 DHMRRAGDVCFSQVFRDGSGTTGI---VDYTNYDDMKHA 161
D R G + S+V D TTG+ V + +D A
Sbjct: 107 DMFSRFGRIINSRVLVD--QTTGLSRGVAFIRFDKRSEA 143
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 8/69 (11%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRGR 65
LY+ LP + +++VED+F ++G I + + + G AF+ F++ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI--- 147
Query: 66 DGYDFDGHR 74
F+GH+
Sbjct: 148 --TSFNGHK 154
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 63/159 (39%), Gaps = 26/159 (16%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L V LP ++ + E+ LF G + L K+ GY FV + A+DAE AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQDLK 125
+G ++V A L ++GLP + + +D++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDAN------------------LYISGLPRTMTQKDVE 106
Query: 126 DHMRRAGDVCFSQVFRDGSGTTGI---VDYTNYDDMKHA 161
D R G + S+V D TTG+ V + +D A
Sbjct: 107 DMFSRFGRIINSRVLVD--QTTGLSRGVAFIRFDKRSEA 143
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 8/69 (11%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRGR 65
LY+ LP + +++VED+F ++G I + + + G AF+ F++ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI--- 147
Query: 66 DGYDFDGHR 74
F+GH+
Sbjct: 148 --TSFNGHK 154
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
TL V NL + +F KYG + + + P P G+AFV F + RDA+DA
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 65 RDGYDFDGHRLRVELA 80
DG + DG LRV++A
Sbjct: 75 MDGAELDGRELRVQVA 90
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
+ R LYVG L ++ ++ + F +G I D++IP + G+AFVEFE A D
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 117
Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
A AI + + G +RV LA
Sbjct: 118 AAAAIDNMNESELFGRTIRVNLA 140
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRG 64
+++G L ++ + + ++F YG I ID+ + P GYA+VEFE +AE A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 65 RDGYDFDGHRL 75
DG DG +
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
S R LYVG L ++ ++ + F +G I D++IP + G+AFVEFE A D
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 59
Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
A AI + + G +RV LA
Sbjct: 60 AAAAIDNMNESELFGRTIRVNLA 82
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
A +TL+V + D E ++ F YGPI I + K +P GYAF+E+E RD A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 62 IRGRDGYDFDGHRLRVEL 79
+ DG DG R+ V++
Sbjct: 161 YKHADGKKIDGRRVLVDV 178
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L+V P D++E E+ ++F +GP+ + + G+AFVEFEEA A AI G
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-----GFAFVEFEEAESAAKAIEEVHGK 88
Query: 69 DFDGHRLRV 77
F L V
Sbjct: 89 SFANQPLEV 97
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
+RA +YV ++ D+ + +++ +F +G I L P + GY F+E+E+A+ ++
Sbjct: 107 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 166
Query: 60 DAIRGRDGYDFDGHRLRV 77
DA+ + +D G LRV
Sbjct: 167 DAVSSMNLFDLGGQYLRV 184
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
+YVG++ ++ E + F +GPI ID+ + + G+AFVE+E A+ A+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 66 DGYDFDGHRLRV 77
+ G ++V
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 45.4 bits (106), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L+V P D++E E+ ++F +GP+ + + G+AFVEFEEA A AI G
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGK 61
Query: 69 DFDGHRLRV 77
F L V
Sbjct: 62 SFANQPLEV 70
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
+ S TLYVGNL E ++ +LF K G I I + K+ G+ FVE+ DAE+
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 61 AIRGRDGYDFDGHRLRVE 78
A+R +G D +R +
Sbjct: 97 AMRYINGTRLDDRIIRTD 114
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
+ R LYVG L ++ ++ + F +G I D++IP + G+AFVEFE A D
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 61
Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
A AI + + G +RV LA
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
+ +R L + NLP I E+ D+F KYGPI I + P G A+V +E+ DA++
Sbjct: 13 LPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 61 AIRGRDGYDFDGHRLRV 77
A G++ L V
Sbjct: 73 ACDHLSGFNVCNRYLVV 89
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEA 55
M +L V NL + +F KYG + D+ IP G+AFV F +
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDK 122
Query: 56 RDAEDAIRGRDGYDFDGHRLRVELA 80
RDAEDA+ DG DG LRV++A
Sbjct: 123 RDAEDAMDAMDGAVLDGRELRVQMA 147
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
+RA +YV ++ D+ + +++ +F +G I L P + GY F+E+E+A+ ++
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181
Query: 60 DAIRGRDGYDFDGHRLRV 77
DA+ + +D G LRV
Sbjct: 182 DAVSSMNLFDLGGQYLRV 199
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
+YVG++ ++ E + F +GPI ID+ + + G+AFVE+E A+ A+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 66 DGYDFDGHRLRV 77
+ G ++V
Sbjct: 91 NSVMLGGRNIKV 102
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
+RA +YV ++ D+ + +++ +F +G I L P + GY F+E+E+A+ ++
Sbjct: 106 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
Query: 60 DAIRGRDGYDFDGHRLRV 77
DA+ + +D G LRV
Sbjct: 166 DAVSSXNLFDLGGQYLRV 183
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
+YVG++ ++ E + F +GPI ID + + G+AFVE+E A+ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 66 DGYDFDGHRLRV 77
+ G ++V
Sbjct: 75 NSVXLGGRNIKV 86
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAE 59
+ R LYVG L ++ ++ + F +G I D++IP + G+AFVEFE A DA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAA 58
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
AI + + G +RV LA
Sbjct: 59 AAIDNMNESELFGRTIRVNLA 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 44.7 bits (104), Expect = 5e-05, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
R +YVGNL +V++LF ++G + ++ L + +P G+ FVE +E +E AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIA 60
Query: 64 GRDGYDFDGHRLRVELA 80
D DF G +RV A
Sbjct: 61 KLDNTDFMGRTIRVTEA 77
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP--GYAFVEFEEARDAEDA 61
+ S TLYVGNL E ++ +LF K G I I + + G+ FVE+ DAE+A
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENA 75
Query: 62 IRGRDGYDFDGHRLRVE 78
+R +G D +R +
Sbjct: 76 MRYINGTRLDDRIIRTD 92
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRGR 65
L++G L + E+ ++ +F K+GPI+ + L I R G+AF+ FE DA++A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 66 DGYDFDGHRLRVELA 80
+G G ++VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L+VGNLP DI E E+ LF KYG + + + G+ F+ E AE A D
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 69 DFDGHRLRVELA 80
G +LRV A
Sbjct: 75 PLRGKQLRVRFA 86
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDA 61
R LYVG L ++ ++ + F +G I D++IP + G+AFVEFE A DA A
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 62 IRGRDGYDFDGHRLRVELA 80
I + + G +RV LA
Sbjct: 71 IDNMNESELFGRTIRVNLA 89
>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 = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 40/165 (24%), Positives = 67/165 (40%), Gaps = 25/165 (15%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L V LP ++ + E LF G I L KI + GY FV + + +DAE AI
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 66 DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQDLK 125
+G ++V A L V+GLP + + ++L+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDAN------------------LYVSGLPKTMTQKELE 106
Query: 126 DHMRRAGDVCFSQVFRDG-SGTTGIVDYTNYD---DMKHAIKKLD 166
+ G + S++ D +G + V + +D + + AIK L+
Sbjct: 107 QLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
LYV LP + ++E+E LF +YG I + ++ G F+ F++ +AE+AI+G
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 66 DGYDFDG 72
+G G
Sbjct: 151 NGQKPSG 157
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 43/165 (26%), Positives = 62/165 (37%), Gaps = 30/165 (18%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L+VGNLP DI E E+ LF KYG + + + G+ F+ E AE A D
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 81
Query: 69 DFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQDLKDHM 128
G +LRV A L V LP S + L++
Sbjct: 82 PLRGKQLRVRFACHSAS------------------------LTVRNLPQYVSNELLEEAF 117
Query: 129 RRAGDVCFSQVFRDGSGT---TGIVDYTNYDDMKHAIKKLDDSEF 170
G V + V D G GIV+++ + A+ + + F
Sbjct: 118 SVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSF 162
>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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 2 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA 83
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
LYV NLP I + +++ +F KYG I ++ K+ RP G AFV + + +A++AI
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 66 DGYDFDG--HRLRVELA 80
+ +G L V LA
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDA 61
++ L V LP D+ +RE+ LF GPI + + GYAFV+F D++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 62 IRGRDGYDFDGHRLRVELA 80
I+ +G RL+V A
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA 84
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 9 LYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
+++GNL +++ +VE +F KYG +A + GYAFV++ R A A+ G +G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLGENG 84
Query: 68 YDFDGHRLRVELA 80
G L + +A
Sbjct: 85 RVLAGQTLDINMA 97
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 1 MSSRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
M+SR +++GNL +++ +VE +F KYG I + G+AFV++ R+A
Sbjct: 14 MNSR----VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNAR 64
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
A+ G DG G L + LA
Sbjct: 65 AAVAGEDGRMIAGQVLDINLA 85
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 39/166 (23%), Positives = 67/166 (40%), Gaps = 25/166 (15%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
L V LP ++ + E + LF G I L KI + GY FV + + DA+ AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 65 RDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQDL 124
+G ++V A L V+GLP + S +++
Sbjct: 66 LNGLKLQTKTIKVSYARPSSASIRDAN------------------LYVSGLPKTMSQKEM 107
Query: 125 KDHMRRAGDVCFSQVFRD-GSGTTGIVDYTNYD---DMKHAIKKLD 166
+ + G + S++ D +G + V + +D + + AIK L+
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRG 64
LYV LP + ++E+E LF +YG I + + G F+ F++ +AE+AI+G
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 65 RDG 67
+G
Sbjct: 152 LNG 154
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
A +TL+V + D E ++ F YGPI I + K +P GYAF+E+E RD A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 62 IRGRDGYDFDGHRLRVEL 79
+ DG DG R+ V++
Sbjct: 161 YKHADGKKIDGRRVLVDV 178
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG------YAFVEFEEAR 56
S S L++ NL E ++ +F K G I + G + FVE+++
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 57 DAEDAIRGRDGYDFDGHRLRVELA 80
A+ A++ G+ DGH+L V ++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS 85
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
LYV NLP I + +++ +F KYG I ++ K+ RP G AFV + + +A++AI
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 65 RDGYDFDG--HRLRVELA 80
+ +G L V LA
Sbjct: 162 LNNVIPEGGSQPLSVRLA 179
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 4 RASRT-LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAE 59
RAS T L V LP D +RE+ LF GPI + + GYAFV+F D++
Sbjct: 11 RASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQ 70
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
AI+ +G RL+V A
Sbjct: 71 RAIKVLNGITVRNKRLKVSYA 91
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 1 MSSRASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEAR 56
M R + T+Y+ N+ I++ E++ LF ++G + I + G AFV F+E
Sbjct: 1 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG 60
Query: 57 DAEDAIRGRDGYDFDGHRLRVELA 80
+ +A+R G+ F G +R++ A
Sbjct: 61 SSTNALRQLQGFPFYGKPMRIQYA 84
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
+L V NL + +F KYG + D+ IP G+AFV F + RDAEDA+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 63 RGRDGYDFDGHRLRVELA 80
DG DG LRV++A
Sbjct: 107 DAMDGAVLDGRELRVQMA 124
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
LYV NLP I + +++ +F KYG I ++ K+ RP G AFV + + +A++AI
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 65 RDGYDFDG--HRLRVELA 80
+ +G L V LA
Sbjct: 75 LNNVIPEGGSQPLSVRLA 92
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRG 64
RTLYVGNL D+ E + LF + GP + P Y FVEF E RDA A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAA 74
Query: 65 RDGYDFDGHRLRVELA 80
+G G ++V A
Sbjct: 75 MNGRKILGKEVKVNWA 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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYDFDGHRLRVELA 80
+G D G + V+
Sbjct: 70 NGQDLMGQPISVDWC 84
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F R++ A
Sbjct: 65 TNALRSXQGFPFYDKPXRIQYA 86
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F R++ A
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYA 87
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 3 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F R++ A
Sbjct: 63 TNALRSXQGFPFYDKPXRIQYA 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 = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYDFDGHRLRVE 78
+G D G + V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYDFDGHRLRVE 78
+G D G + V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 66 DGYDFDGHRLRVE 78
+G D G + V+
Sbjct: 72 NGQDLMGQPISVD 84
>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 = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 1 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA 82
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
SS + ++VGN+ +E+ LF + G + D+ YAFV E+ DA+ A
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAA 59
Query: 62 IRGRDGYDFDGHRLRVELA 80
I +G + G R+ VEL+
Sbjct: 60 IAQLNGKEVKGKRINVELS 78
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 66 DGYDFDGHRLRVELA 80
+G D G + V+
Sbjct: 85 NGQDLMGQPISVDWC 99
>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 = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGR 65
L+V NL E ++E LF YGP++ + I +P G+AFV F A A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 66 DGYDFDGHRLRV 77
DG F G L V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGR 65
LYVG+L +I E + +F +G I I L + R GY F+ F ++ A+ A+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 66 DGYDFDGHRLRV 77
+G++ G ++V
Sbjct: 89 NGFELAGRPMKV 100
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
L+V + + E ++ D F +YG I +I L + R GY VE+E ++A+ A+ G
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 66 DGYDFDGHRLRVELA 80
+G D G + V+
Sbjct: 86 NGQDLMGQPISVDWC 100
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
T+YVG L + E + +LF + GP+ + + ++ + GY FVEF DA+ AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 65 RDGYDFDGHRLRVELA 80
D G +RV A
Sbjct: 77 MDMIKLYGKPIRVNKA 92
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAE 59
S S LYVG+L +I E + +F +G I +I L R GY F+ F ++ A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 60 DAIRGRDGYDFDGHRLRV 77
A+ +G++ G +RV
Sbjct: 62 RALEQLNGFELAGRPMRV 79
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
++ L++G LP + + +V++L +GP+ +L GYAF E+ + + A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 62 IRGRDGYDFDGHRLRVELA 80
I G +G +L V+ A
Sbjct: 173 IAGLNGMQLGDKKLLVQRA 191
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 19/85 (22%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-------------YAFVEF 52
+R LYVGN+P I E + D F A + L + PG +AF+EF
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFN-----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 58
Query: 53 EEARDAEDAIRGRDGYDFDGHRLRV 77
+ A+ DG F G L++
Sbjct: 59 RSVDETTQAM-AFDGIIFQGQSLKI 82
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDA 61
S+TL + NL E ++++F K +K+P + GYAF+EF DA++A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEK-----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 62 IRGRDGYDFDGHRLRVEL 79
+ + + +G +R+EL
Sbjct: 70 LNSCNKREIEGRAIRLEL 87
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
+ L++G LP + + +V++L +GP+ +L GYAF E+ + + A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 62 IRGRDGYDFDGHRLRVELA 80
I G +G +L V+ A
Sbjct: 153 IAGLNGMQLGDKKLLVQRA 171
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---------PGYAFVEFEEA 55
++R LYVGN+P I E + D F + + + P P +AF+EF
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 56 RDAEDAIRGRDGYDFDGHRLRV 77
+ A+ DG F G L++
Sbjct: 62 DETTQAM-AFDGIIFQGQSLKI 82
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
+LYVG+L D+ E + + F GPI I + I R GYA+V F++ DAE A+
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 69
Query: 65 RDGYDFD 71
D +FD
Sbjct: 70 -DTMNFD 75
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGRD 66
+++ NL I + + D F +G I + GY FV FE AE AI +
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 67 GYDFDGHRLRV 77
G + ++ V
Sbjct: 160 GMLLNDRKVFV 170
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3 SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
+R + T+Y+ NL I++ E++ +F ++G I I + + G AFV F+E A
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
+ L++G LP + + +V++L +GP+ +L GYAF E+ + + A
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 62 IRGRDGYDFDGHRLRVELA 80
I G +G +L V+ A
Sbjct: 155 IAGLNGMQLGDKKLLVQRA 173
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 19/86 (22%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-------------YAFVE 51
++R LYVGN+P I E + D F A + L + PG +AF+E
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFN-----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59
Query: 52 FEEARDAEDAIRGRDGYDFDGHRLRV 77
F + A+ DG F G L++
Sbjct: 60 FRSVDETTQAM-AFDGIIFQGQSLKI 84
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDGSGTTGIVDYTNYDDMKHAIKKLDD 167
+ + LP SWQDLKD R + FS V RD G TG +++ + + + A+++L++
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNN 89
Query: 168 SEFRNA 173
EFR +
Sbjct: 90 IEFRGS 95
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
T+YV NLP + ++ +F KYG + + + K + G AF+ F + A++ R
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 65 RDGYDFDGHRLRVELA 80
+ G ++ +A
Sbjct: 78 INNKQLFGRVIKASIA 93
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
LYV LP + ++E+E LF +YG I + + G F+ F++ +AE+AI+G
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 66 DG 67
+G
Sbjct: 64 NG 65
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
L+VGNLP DI E + + LF +YG + + + R G+ F+ E AE A DG
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGT 81
Query: 69 DFDGHRLRVELA 80
LR+ A
Sbjct: 82 ILKSRPLRIRFA 93
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
L V LP + + E+ LF G + L K+ GY FV + A+DAE AI
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 65 RDGYDFDGHRLRVELA 80
+G ++V A
Sbjct: 81 LNGLRLQSKTIKVSYA 96
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
+LYVG+L D+ E + + F GPI I + I R GYA+V F++ DAE A+
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 74
Query: 65 RDGYDFD 71
D +FD
Sbjct: 75 -DTMNFD 80
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGRD 66
+++ NL I + + D F +G I + GY FV FE AE AI +
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 67 GYDFDGHRLRV 77
G + ++ V
Sbjct: 165 GMLLNDRKVFV 175
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
+ L++G LP + + +V++L +GP+ +L GYAF E+ + + AI
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 63 RGRDGYDFDGHRLRVELA 80
G +G +L V+ A
Sbjct: 61 AGLNGMQLGDKKLLVQRA 78
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
RA+RTL NL +I E E++++F I + + G A++EF+ DAE +
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLE 71
Query: 64 GRDGYDFDGHRLRV 77
+ G + DG + +
Sbjct: 72 EKQGAEIDGRSVSL 85
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDA 61
++ L V LP D+ +RE+ LF GPI + + GYAFV+F D++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 62 IRGRDGYDFDGHRLRVELA 80
I+ +G RL+V A
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-RPPGYAFVEFEEARDAEDA 61
S + ++V NLP D + ++D F + G + + D+K+ + G V+FE AE A
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 64
Query: 62 IRGRDGYDFDGHRLRVEL 79
R +G G + V +
Sbjct: 65 CRMMNGMKLSGREIDVRI 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
L+V ++ + +E E+++ F YG I +I L + R GYA VE+E + A A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 66 DGYDFDGHRLRVELA 80
+G + G ++V+
Sbjct: 89 NGAEIMGQTIQVDWC 103
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 11/86 (12%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYG----------PIAHIDL-KIPPRPPGYAFVEFEE 54
+ +YV L + ++ D F + G P+ HI L K +P G A V +E+
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 55 ARDAEDAIRGRDGYDFDGHRLRVELA 80
A+ A+ DG DF G +L+V LA
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
RA+RTL NL +I E E++++F I + + G A++EF+ DAE +
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLE 154
Query: 64 GRDGYDFDGHRLRV 77
+ G + DG + +
Sbjct: 155 EKQGAEIDGRSVSL 168
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRD 66
L++ LP + E+E++ +G + + L +P G A+VE+E A A+ D
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 67 GYDFDGHRLRVELA 80
G + ++V ++
Sbjct: 80 GMTIKENIIKVAIS 93
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
L+V ++ + +E E+++ F YG I +I L + R GYA VE+E + A A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 66 DGYDFDGHRLRVELA 80
+G + G ++V+
Sbjct: 135 NGAEIMGQTIQVDWC 149
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
R++YVGN+ +++E F G I I + K P GYA++EF E R++ DA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAV 95
Query: 64 GRDGYDFDGHRLRV 77
D F G ++V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPI-------AHIDLKIPPRPPGYAFVEFEEARDAE 59
R ++VG LP DI E E+ F ++GP+ A PP+ GYAF+ F+E +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPK--GYAFLLFQEESSVQ 66
Query: 60 ---DAIRGRDG 67
DA DG
Sbjct: 67 ALIDACLEEDG 77
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAI 62
A RT++VGNL +RE + +LF + GP+ + + +P + FV F+ AI
Sbjct: 15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI 74
Query: 63 RGRDGYDFDGHRLRV 77
+G G + V
Sbjct: 75 ALLNGIRLYGRPINV 89
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
SS + T+Y G + + ++ + F +G I +++++ P GY+FV F A A
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQI--MEIRVFPEK-GYSFVRFSTHESAAHA 77
Query: 62 IRGRDGYDFDGHRLRV 77
I +G +GH ++
Sbjct: 78 IVSVNGTTIEGHVVKC 93
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGR 65
+ L+V N+P R+ ++ +F ++G I +++ R G+ FV FE + DA+ A
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 66 DGYDFDGHRLRVELA 80
G +G ++ V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGR 65
+ L+V N+P R+ ++ +F ++G I +++ R G+ FV FE + DA+ A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 66 DGYDFDGHRLRVELA 80
G +G ++ V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 8/62 (12%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL-----KIPPRPPGYAFVEF---EEARDAED 60
++VG +P E+++ +LF +YG + I++ + PP+ G FV F + A +A++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 61 AI 62
A+
Sbjct: 66 AL 67
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 36.6 bits (83), Expect = 0.016, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-RPPGYAFVEFEEARDAEDA 61
S S ++V NLP D + ++D F + G + + D+K+ + G V+FE AE A
Sbjct: 2 SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 61
Query: 62 IRGRDGYDFDGHRLRVEL 79
R +G G + V +
Sbjct: 62 CRMMNGMKLSGREIDVRI 79
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 115 LPSSASWQDLKDHMRRAG-DVCFSQV-FRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRN 172
LP SWQDLKD R + FS V RD G TG +++ + + + A+++L++ EFR
Sbjct: 14 LPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNNIEFRG 72
Query: 173 A 173
+
Sbjct: 73 S 73
>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 = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L V LP ++ + E+ LF G + L K+ GY FV + A+DAE AI
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 66 DGYDFDGHRLRVELA 80
+G ++V A
Sbjct: 67 NGLRLQSKTIKVSYA 81
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 8/62 (12%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL-----KIPPRPPGYAFVEF---EEARDAED 60
++VG +P E+++ +LF +YG + I++ + PP+ G FV F + A +A++
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 61 AI 62
A+
Sbjct: 78 AL 79
>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 = 35.8 bits (81), Expect = 0.028, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
+++G L D +++++D F K+G + LK+ P R G+ FV F+E+ + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 66 D 66
+
Sbjct: 62 E 62
>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 = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAH---IDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
++VG+L +I +++ F +G I+ + + GY FV F DAE+AI+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 66 DGYDFDGHRLRVELA 80
G G ++R A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
R +RTL NLP + + E++++F I + + G A++EF+ DAE
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSK--DGKSKGIAYIEFKTEADAEKTFE 148
Query: 64 GRDGYDFDGHRLRV 77
+ G + DG + +
Sbjct: 149 EKQGTEIDGRSISL 162
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
L V LP ++ + E + LF G I L KI + GY FV + + DA+ AI
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 66 DGYDFDGHRLRVELA 80
+G ++V A
Sbjct: 67 NGLKLQTKTIKVSYA 81
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.0 bits (79), Expect = 0.041, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
S S ++VG GD+ E E+ + F +YG + +D+ IP +AFV F + + A+
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDV--MDVFIPKPFRAFAFVTFADDQIAQ 56
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
++VG +P + E E+ + F K+G + + + RP G+ F+ FE+ + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 66 DGYDFDGHRLRVELA 80
+D G ++ V+ A
Sbjct: 72 HFHDIMGKKVEVKRA 86
>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 = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 8/61 (13%)
Query: 10 YVGNLPGDIREREVEDLFYKYGPIAHIDL-----KIPPRPPGYAFVEF---EEARDAEDA 61
+VG +P E+++ +LF +YG + I++ + PP+ G FV F + A +A++A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 62 I 62
+
Sbjct: 67 L 67
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
+ LYV NL E +E F P A +K + YAFV F DA +A++ +
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKALN 72
Query: 67 GYDFDGHRLRVELA 80
G DG + V LA
Sbjct: 73 GKVLDGSPIEVTLA 86
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
+ L+V NL + E +E F ++G + + + YAF+ F+E A A+ +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK-----KLKDYAFIHFDERDGAVKAMEEMN 66
Query: 67 GYDFDGHRLRVELA 80
G D +G + + A
Sbjct: 67 GKDLEGENIEIVFA 80
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-----PPRPPGYAFVEFEEARDAEDAIR 63
++VG+L +I +++ F +G I+ D ++ + GY FV F DAE+AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKIS--DARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 64 GRDGYDFDGHRLRVELA 80
G G ++R A
Sbjct: 76 HMGGQWLGGRQIRTNWA 92
>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 = 34.7 bits (78), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 156
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 157 IQKYHTVNGHNCEVRKA 173
>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 = 34.3 bits (77), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 163
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 164 IQKYHTVNGHNCEVRKA 180
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
L V NL + + ++++LF ++G + A +D R G A V FE DA A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 67 GYDFDGHRLRVEL 79
G DG + ++L
Sbjct: 98 GVPLDGRPMDIQL 110
>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 = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 162
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 163 IQKYHTVNGHNCEVRKA 179
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
L V NL + + ++++LF ++G + A +D R G A V FE DA A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 67 GYDFDGHRLRVEL 79
G DG + ++L
Sbjct: 98 GVPLDGRPMDIQL 110
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 163
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 164 IQKYHTVNGHNCEVRKA 180
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.3 bits (77), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 164
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 165 IQKYHTVNGHNCEVRKA 181
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
+ ++VG + D E + D F +YG I I++ + G+AFV F++ D+ D I
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 161
Query: 64 GRDGYDFDGHRLRVELA 80
+ + +GH V A
Sbjct: 162 IQKYHTVNGHNCEVRKA 178
>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 = 33.9 bits (76), Expect = 0.094, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 8/62 (12%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL-----KIPPRPPGYAFVEF---EEARDAED 60
++VG +P E+++ +LF +YG + I++ + PP+ G FV F + A +A++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 61 AI 62
A+
Sbjct: 66 AL 67
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
L V NL + + ++++LF ++G + A + R G A V FE DA A++ +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 67 GYDFDGHRLRVEL 79
G DG + ++L
Sbjct: 91 GVPLDGRPMNIQL 103
>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 = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 9/69 (13%)
Query: 10 YVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGRD 66
+VG L D +++++D F K+G + +K P R G+ F+ F++A E + ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 67 GYDFDGHRL 75
HRL
Sbjct: 75 ------HRL 77
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
++VG + D+R +E E+ F ++G I L K + G+ FV ++ A DA D +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQN 148
Query: 66 DGYDFDGHRLRVELA 80
DF ++ ++ A
Sbjct: 149 KFIDFKDRKIEIKRA 163
Score = 32.0 bits (71), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAED 60
+ S +++G L D E + + F KYG + + + P R G+ F+ FE+ ++
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 61 AIR 63
++
Sbjct: 61 VVK 63
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-YAFVEFEEARDAEDAIRGR 65
R+++V P + ++ + F +GP+A + + + G +A VE + A +A+ +
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD---KDKGVFAIVEMGDV-GAREAVLSQ 64
Query: 66 DGYDFDGHRLRV 77
+ GHRLRV
Sbjct: 65 SQHSLGGHRLRV 76
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 32.7 bits (73), Expect = 0.22, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAED 60
S S + V NLP D +EV DL Y DLK R AFV A++
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDY------DLKYCYVDRNKRTAFVTLLNGEQAQN 55
Query: 61 AIRGRDGYDFDGHRLRVEL 79
AI+ Y F G L V+L
Sbjct: 56 AIQMFHQYSFRGKDLIVQL 74
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
+R++YVGN+ E+E F+ G + + + K P G+A++EF + ++
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 63 RGRDGYDFDGHRLRV 77
D F G +++V
Sbjct: 65 -ALDESLFRGRQIKV 78
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 32.3 bits (72), Expect = 0.27, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 19/86 (22%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-------------YAFVE 51
++R LYVGN+P I E + D F A + L + PG +AF+E
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFN-----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59
Query: 52 FEEARDAEDAIRGRDGYDFDGHRLRV 77
F + A+ DG F G L++
Sbjct: 60 FRSVDETTQAM-AFDGIIFQGQSLKI 84
>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 = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
+R++YVGN+ E+E F+ G + + + K P G+A++EF + ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 63 RGRDGYDFDGHRLRV 77
D F G +++V
Sbjct: 66 -ALDESLFRGRQIKV 79
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
T Y+GN+P E ++ LF +G I +D K P G F++++ A I
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFI--LDFKHYPE-KGCCFIKYDTHEQAAVCIVALAN 85
Query: 68 YDFDGHRLRV 77
+ F G LR
Sbjct: 86 FPFQGRNLRT 95
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
L V NL + + ++++LF ++G + A +D R G A V FE DA A++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 67 GYDFDGHRLRVEL 79
G DG + ++L
Sbjct: 151 GVPLDGRPMDIQL 163
>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 = 31.6 bits (70), Expect = 0.46, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
GY FV F DA++A+ G D +G LR+ A
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPP------GYAFVEFEE 54
S S +++GNL +I E+ + D F +G I L+ P R P GYAF+ F
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFAS 57
Query: 55 ARDAEDAIRGRDG 67
++ AI +G
Sbjct: 58 FDASDAAIEAMNG 70
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP------GYAFVEFEEARD 57
+ + + V N+P +RE+ +LF +G + + ++P + G+ FV+F +D
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTV--RLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 58 AEDA 61
A+ A
Sbjct: 71 AKKA 74
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 31.2 bits (69), Expect = 0.60, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 19/85 (22%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-------------YAFVEF 52
+R LYVGN+P I E + D F A + L + PG +AF+EF
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFN-----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 55
Query: 53 EEARDAEDAIRGRDGYDFDGHRLRV 77
+ A+ DG F G L++
Sbjct: 56 RSVDETTQAM-AFDGIIFQGQSLKI 79
>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 = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIR 63
S +++ NL I + + D F +G I + GY FV FE AE AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 63
Query: 64 GRDG 67
+G
Sbjct: 64 KMNG 67
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-GYAFVEFEEARDAEDAIRGRDG 67
+YVGNLP D R V DL + + L++ + P AF+ + ++ A+ A+ G
Sbjct: 22 VYVGNLPRDAR---VSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQG 78
Query: 68 YDFDGHRLRVELA 80
LRV LA
Sbjct: 79 LRLGTDTLRVALA 91
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGRD 66
+++ NL I + + D F +G I + GY FV FE AE AI +
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 67 G 67
G
Sbjct: 73 G 73
>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 = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
L V NL + + ++++LF ++G + A + R G A V FE DA A + +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 67 GYDFDGHRLRVEL 79
G DG ++L
Sbjct: 92 GVPLDGRPXNIQL 104
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 6 SRTLYVGNLPGDIREREVEDLFYKY----GPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
++ LY+ NL + ER++ LF ++ GP + + R G AF+ F A A
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAWQA 83
Query: 62 IRGRDGYDFDGHRLRVELA 80
+ +GY G L +E
Sbjct: 84 LHLVNGYKLYGKILVIEFG 102
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
R +RT++ L IR R++ED F G + + + + R G A+VEF E +
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 61 AI 62
AI
Sbjct: 83 AI 84
>pdb|2DIU|A Chain A, Solution Structure Of The Rrm Domain Of Kiaa0430 Protein
Length = 96
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 167
L V LP++ + + + +RR D C +V +G + I+ + N D + A K++++
Sbjct: 12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-TGCSAILRFINQDSAERAQKRMEN 68
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 56/167 (33%), Gaps = 34/167 (20%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
R R + + LPGD+ +EV DL Y + + G AFV AE AI
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAIN 75
Query: 64 GRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQD 123
L V+L L V LP S + Q
Sbjct: 76 AFHQSRLRERELSVQLQPTDA------------------------LLCVANLPPSLTQQQ 111
Query: 124 LKDHMRRAGDV--CFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKL 165
++ +R G + CF V+ + +G + G +Y D A L
Sbjct: 112 FEELVRPFGSLERCFL-VYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
G+A +E+E A AE+A + DG G LRV
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 56/167 (33%), Gaps = 34/167 (20%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
R R + + LPGD+ +EV DL Y + + G AFV AE AI
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAIN 75
Query: 64 GRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQD 123
L V+L L V LP S + Q
Sbjct: 76 AFHQSRLRERELSVQLQPTDA------------------------LLCVANLPPSLTQQQ 111
Query: 124 LKDHMRRAGDV--CFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKL 165
++ +R G + CF V+ + +G + G +Y D A L
Sbjct: 112 FEELVRPFGSLERCFL-VYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
G+A +E+E A AE+A + DG G LRV
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
>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 = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 56/167 (33%), Gaps = 34/167 (20%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
R R + + LPGD+ +EV DL Y + + G AFV AE AI
Sbjct: 18 RNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAIN 73
Query: 64 GRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYLLVTGLPSSASWQD 123
L V+L L V LP S + Q
Sbjct: 74 AFHQSRLRERELSVQLQPTDA------------------------LLCVANLPPSLTQQQ 109
Query: 124 LKDHMRRAGDV--CFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKL 165
++ +R G + CF V+ + +G + G +Y D A L
Sbjct: 110 FEELVRPFGSLERCFL-VYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
G+A +E+E A AE+A + DG G LRV
Sbjct: 225 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 259
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
++VG D+ E++ F +YG + +D+ IP +AFV F + + A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEV--VDVFIPKPFRAFAFVTFADDKVAQ 62
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI-RGRD 66
TLYVG L I E ++ + FY++G I I + + AF++F + AE A + +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV---QRQQCAFIQFATRQAAEVAAEKSFN 70
Query: 67 GYDFDGHRLRVE 78
+G RL V+
Sbjct: 71 KLIVNGRRLNVK 82
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 43 RPPGYAFVEFEEARDAEDAIRGRDGYDFDG-HRLRVEL 79
+ GY F+E+ A DA++ DGY D H RV L
Sbjct: 59 KTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNL 96
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 37/78 (47%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
S+ S+TL+V L D E +++ F + + G+ FV+F DA+ A
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 63 RGRDGYDFDGHRLRVELA 80
+ + DG+++ ++ A
Sbjct: 72 EAMEDGEIDGNKVTLDWA 89
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYD 156
L+V GLP + QDLK++ G+V QV +D S G V +T Y+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
T++VG + + E E+ F +YG + + + I R GY FV F D + +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 65 RDGYDFDGHRLRV 77
+ +F G +L++
Sbjct: 71 Q--INFHGKKLKL 81
>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 = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
T++VG + + E E+ F +YG + + + I R GY FV F D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 65 RDGYDFDGHRLRV 77
+ +F G +L++
Sbjct: 70 Q--INFHGKKLKL 80
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 110 LLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHA 161
L ++ LP S Q+L++ ++ G V +++ RD SGT+ V + + +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 17 DIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGRDGYDFDGH 73
++RE ++D+ KYG + +++ + PR G A V F R A++ ++ G+
Sbjct: 17 NVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGN 76
Query: 74 RLRVEL 79
+ +L
Sbjct: 77 IIHAQL 82
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 1 MSSRASRTLYVGNL----PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEAR 56
M ++T+Y+ NL + ++ + +F ++G I I + G AFV F+E
Sbjct: 1 MEMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIG 60
Query: 57 DAEDAIRGRDGYDF 70
A +A+R G+ F
Sbjct: 61 SASNALRTMQGFPF 74
>pdb|2D9O|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj10634
Length = 100
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 26 LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
L KYG + ++L + + PG A VEF + AE A++ G
Sbjct: 37 LLQKYGEV--LNLVLSSKKPGTAVVEFATVKAAELAVQNEVG 76
>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 = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRG 64
T++VG + + E E+ F +YG + + + I R GY FV F D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 65 RDGYDFDGHRLRV 77
+ +F G +L++
Sbjct: 70 Q--INFHGKKLKL 80
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
Length = 292
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL 38
+R T+ V NLP + +V F GPI H+D+
Sbjct: 38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV 73
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL 38
R T+ V NLP + +V F GPI H+D+
Sbjct: 2 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV 36
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI 36
M SR L++ LPG++ E EV L +G + +I
Sbjct: 10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI 45
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.9 bits (63), Expect = 3.0, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 23 VEDLFYKYGPIAH-IDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG-HRLRV 77
+ +F K+G I + + + GY F+E+ A DA++ DGY D H RV
Sbjct: 24 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV 80
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 28.9 bits (63), Expect = 3.2, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
S S + + LPGD+ +EV DL Y + + G AFV AE AI
Sbjct: 2 SSGSSGILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAI 57
Query: 63 RGRDGYDFDGHRLR 76
F RLR
Sbjct: 58 N-----TFHQSRLR 66
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 28/70 (40%), Gaps = 9/70 (12%)
Query: 7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
R + + LPGD+ +EV DL Y + + G AFV AE AI
Sbjct: 3 RKILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAINA-- 56
Query: 67 GYDFDGHRLR 76
F RLR
Sbjct: 57 ---FHQSRLR 63
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
T YVGNLP + + ++ D +K I + L K + G+ +VEF+E ++A+
Sbjct: 17 TAYVGNLPFNTVQGDI-DAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 65 RDGYDFDGHRLRVELA 80
DG LRV++A
Sbjct: 75 YDGALLGDRSLRVDIA 90
>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 = 27.3 bits (59), Expect = 8.3, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 43 RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
+ GY FV F DAE+AI+ G G ++R A
Sbjct: 46 KSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.140 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,985,420
Number of Sequences: 62578
Number of extensions: 219749
Number of successful extensions: 635
Number of sequences better than 100.0: 185
Number of HSP's better than 100.0 without gapping: 111
Number of HSP's successfully gapped in prelim test: 74
Number of HSP's that attempted gapping in prelim test: 419
Number of HSP's gapped (non-prelim): 227
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)