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= psy16913
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 99.0 bits (245), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 49/79 (62%), Positives = 58/79 (73%), Gaps = 14/79 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF+PFGNV+S+KVFID+ TN SKCFG FVS+DNP SA AIQ+MNGF
Sbjct: 45 MFMPFGNVVSAKVFIDKQTNLSKCFG--------------FVSYDNPVSAQAAIQSMNGF 90
Query: 61 QIGMKRLKVQLKRPKDAAR 79
QIGMKRLKVQLKR K+ ++
Sbjct: 91 QIGMKRLKVQLKRSKNDSK 109
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 89.0 bits (219), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 46/72 (63%), Positives = 52/72 (72%), Gaps = 14/72 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
FLPFGNVIS+KVFID+ T+ SKCFG FVSFDNP SA AI+AMNGFQ
Sbjct: 61 FLPFGNVISAKVFIDKQTSLSKCFG--------------FVSFDNPDSAQVAIKAMNGFQ 106
Query: 62 IGMKRLKVQLKR 73
+G KRLKVQLK+
Sbjct: 107 VGTKRLKVQLKK 118
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + S K+ DR T QS+ +G FV F + +SA AI +NGF
Sbjct: 62 LFERYGPIESVKIVCDRETRQSRGYG--------------FVKFQSGSSAQQAIAGLNGF 107
Query: 61 QIGMKRLKVQL 71
I KRLKV L
Sbjct: 108 NILNKRLKVAL 118
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 16/65 (24%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAM--NGFQ 61
P+G ++S+K +D+ TN KC G +GFV FD+P++A A+ A+ +G Q
Sbjct: 28 PYGKIVSTKAILDKTTN--KCKG------------YGFVDFDSPSAAQKAVTALKASGVQ 73
Query: 62 IGMKR 66
M +
Sbjct: 74 AQMAK 78
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 14/78 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G++ S K+ D+ T QS G +GFV++ +P A AI +NG
Sbjct: 24 LFGSIGDIESCKLVRDKITGQS--LG------------YGFVNYSDPNDADKAINTLNGL 69
Query: 61 QIGMKRLKVQLKRPKDAA 78
++ K +KV RP A+
Sbjct: 70 KLQTKTIKVSYARPSSAS 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G++ S K+ D+ T QS +G FV++ +P A AI +NG
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYG--------------FVNYSDPNDADKAINTLNGL 69
Query: 61 QIGMKRLKVQLKRPKDAA 78
++ K +KV RP A+
Sbjct: 70 KLQTKTIKVSYARPSSAS 87
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 26/80 (32%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G +I+S++ +D+AT S+ G F+ FD A AI+ +NG
Sbjct: 110 LFSQYGRIITSRILLDQATGVSRGVG--------------FIRFDKRIEAEEAIKGLNG- 154
Query: 61 QIGMKRLKVQLKRPKDAARP 80
++P AA P
Sbjct: 155 -----------QKPLGAAEP 163
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G + S K+ D+ T QS +G FV++ +P A AI +NG
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYG--------------FVNYIDPKDAEKAINTLNGL 67
Query: 61 QIGMKRLKVQLKRPKDAA 78
++ K +KV RP A+
Sbjct: 68 RLQTKTIKVSYARPSSAS 85
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ +D+ T S+ G F+ FD A AI+ +NG
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVG--------------FIRFDKRIEAEEAIKGLNG 152
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AIQ M G
Sbjct: 36 FAPFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQW 81
Query: 62 IGMKRLKVQL 71
+G ++++
Sbjct: 82 LGGRQIRTNW 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 16/75 (21%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S+KV ++ K FGFV F +P A A+ MNG
Sbjct: 36 FSPFGTITSAKVMMEGG----------------RSKGFGFVCFSSPEEATKAVTEMNGRI 79
Query: 62 IGMKRLKVQLKRPKD 76
+ K L V L + K+
Sbjct: 80 VATKPLYVALAQRKE 94
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + S ++ +D T +SK +G F++F + A A++ +NGF
Sbjct: 46 IFEPFGRIESIQLMMDSETGRSKGYG--------------FITFSDSECAKKALEQLNGF 91
Query: 61 QIGMKRLKV 69
++ + +KV
Sbjct: 92 ELAGRPMKV 100
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 14/68 (20%)
Query: 4 PFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIG 63
PFG + ++V D AT +SK +G FVSF N A AIQ M G +G
Sbjct: 29 PFGRISDARVVKDMATGKSKGYG--------------FVSFFNKWDAENAIQQMGGQWLG 74
Query: 64 MKRLKVQL 71
++++
Sbjct: 75 GRQIRTNW 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + ++V D AT +SK +G FVSF N A AI M G
Sbjct: 36 FAPFGKISDARVVKDMATGKSKGYG--------------FVSFYNKLDAENAIVHMGGQW 81
Query: 62 IGMKRLKVQL--KRPKDAARP 80
+G ++++ ++P + P
Sbjct: 82 LGGRQIRTNWATRKPPAPSGP 102
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 14/59 (23%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNG 59
+F +G +I+S++ +D+AT S+ G F+ FD A AI+ +NG
Sbjct: 21 LFSQYGRIITSRILLDQATGVSRGVG--------------FIRFDKRIEAEEAIKGLNG 65
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV-QLKRP 74
+ F F++F+NPA A A + MNG + K +KV Q K+P
Sbjct: 48 RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKP 86
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S + D V++ K F FV ++ P +A A++ MN
Sbjct: 34 FAPFGPIKSIDMSWD--------------SVTMKHKGFAFVEYEVPEAAQLALEQMNSVM 79
Query: 62 IGMKRLKV 69
+G + +KV
Sbjct: 80 LGGRNIKV 87
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +GF+ ++ S+ A+ +MN F +G + L+V
Sbjct: 151 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>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 = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V S+K+ D KV+ + +GFV++ A AI +NG
Sbjct: 39 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVTAKDAERAINTLNGL 84
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 85 RLQSKTIKVSYARP 98
>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 = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S + D V++ K F FV ++ P +A A++ MN
Sbjct: 49 FAPFGPIKSIDMSWD--------------SVTMKHKGFAFVEYEVPEAAQLALEQMNSVM 94
Query: 62 IGMKRLKV 69
+G + +KV
Sbjct: 95 LGGRNIKV 102
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 36 QKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K +GF+ ++ S+ A+ +MN F +G + L+V
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>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 = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V S+K+ D KV+ + +GFV++ A AI +NG
Sbjct: 24 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVTAKDAERAINTLNGL 69
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 70 RLQSKTIKVSYARP 83
>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 = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V S+K+ D KV+ + +GFV++ A AI +NG
Sbjct: 22 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVTAKDAERAINTLNGL 67
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 68 RLQSKTIKVSYARP 81
Score = 32.3 bits (72), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 14/61 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF FG +I+S+V +D+ T S+ F+ FD + A AI + NG
Sbjct: 108 MFSRFGRIINSRVLVDQTTGLSRGVA--------------FIRFDKRSEAEEAITSFNGH 153
Query: 61 Q 61
+
Sbjct: 154 K 154
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G + V DR T +S+ FG FV+F+N A A+ AMNG
Sbjct: 32 VFSKYGQISEVVVVKDRETQRSRGFG--------------FVTFENIDDAKDAMMAMNGK 77
Query: 61 QIGMKRLKV 69
+ ++++V
Sbjct: 78 SVDGRQIRV 86
>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 = 33.1 bits (74), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F + + AI+ +NG + KRLKV RP
Sbjct: 58 YAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARP 93
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V S+K+ D KV+ + +GFV++ A AI +NG
Sbjct: 22 LFSSIGEVESAKLIRD--------------KVAGHSLGYGFVNYVTAKDAERAINTLNGL 67
Query: 61 QIGMKRLKVQLKRP 74
++ K +KV RP
Sbjct: 68 RLQSKTIKVSYARP 81
Score = 32.3 bits (72), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 14/61 (22%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
MF FG +I+S+V +D+ T S+ F+ FD + A AI + NG
Sbjct: 108 MFSRFGRIINSRVLVDQTTGLSRGVA--------------FIRFDKRSEAEEAITSFNGH 153
Query: 61 Q 61
+
Sbjct: 154 K 154
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F + + AI+ +NG + KRLKV RP
Sbjct: 47 YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP 74
+ FV F + + AI+ +NG + KRLKV RP
Sbjct: 47 YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 14/73 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ A AI MN +
Sbjct: 33 FIPFGDITDIQIPLDYETEK--------------HRGFAFVEFELAEDAAAAIDNMNESE 78
Query: 62 IGMKRLKVQLKRP 74
+ + ++V L +P
Sbjct: 79 LFGRTIRVNLAKP 91
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 18/82 (21%)
Query: 1 MFLPFGNVISSKVFI--DRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMN 58
+F PFG++ S++++ D+ T QSK F F+SF A AI ++
Sbjct: 35 LFRPFGSI--SRIYLAKDKTTGQSKGFA--------------FISFHRREDAARAIAGVS 78
Query: 59 GFQIGMKRLKVQLKRPKDAARP 80
GF L V+ +P + P
Sbjct: 79 GFGYDHLILNVEWAKPSTNSGP 100
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.3 bits (72), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 16/66 (24%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FGN++S KV D K +GFV F+ +A AI+ MNG
Sbjct: 32 FSAFGNILSCKVVCDEN----------------GSKGYGFVHFETQEAAERAIEKMNGML 75
Query: 62 IGMKRL 67
+ +++
Sbjct: 76 LNDRKV 81
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.0 bits (71), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 39 FGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
F FV F++P A A+ +G+ RL+V+ R
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
>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 = 32.0 bits (71), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 16/68 (23%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FGN++S KV D K +GFV F+ +A AI+ MNG
Sbjct: 26 FSAFGNILSCKVVCDEN----------------GSKGYGFVHFETQEAAERAIEKMNGML 69
Query: 62 IGMKRLKV 69
+ +++ V
Sbjct: 70 LNDRKVFV 77
>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 = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 16/68 (23%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FGN++S KV D K +GFV F+ +A AI+ MNG
Sbjct: 119 FSAFGNILSCKVVCDEN----------------GSKGYGFVHFETQEAAERAIEKMNGML 162
Query: 62 IGMKRLKV 69
+ +++ V
Sbjct: 163 LNDRKVFV 170
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 16/68 (23%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F FGN++S KV D K +GFV F+ +A AI+ MNG
Sbjct: 124 FSAFGNILSCKVVCDEN----------------GSKGYGFVHFETQEAAERAIEKMNGML 167
Query: 62 IGMKRLKV 69
+ +++ V
Sbjct: 168 LNDRKVFV 175
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F PFG + + + D T +SK +G F++F + A A++ +NGF
Sbjct: 25 IFEPFGKIDNIVLMKDSDTGRSKGYG--------------FITFSDSECARRALEQLNGF 70
Query: 61 QIGMKRLKV 69
++ + ++V
Sbjct: 71 ELAGRPMRV 79
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 14/71 (19%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
F + +++ DR T SK FG FV F++ A A +AM +I
Sbjct: 36 FDGSVRARIVTDRETGSSKGFG--------------FVDFNSEEDAKAAKEAMEDGEIDG 81
Query: 65 KRLKVQLKRPK 75
++ + +PK
Sbjct: 82 NKVTLDWAKPK 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 14/73 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V + DR T +S+ F FV F + A A+ AM+G
Sbjct: 90 VFEKYGRVGDVYIPRDRYTKESRGFA--------------FVRFHDKRDAEDAMDAMDGA 135
Query: 61 QIGMKRLKVQLKR 73
+ + L+VQ+ R
Sbjct: 136 VLDGRELRVQMAR 148
>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 = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 14/73 (19%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F +G V + DR T +S+ F FV F + A A+ AM+G
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFA--------------FVRFHDKRDAEDAMDAMDGA 112
Query: 61 QIGMKRLKVQLKR 73
+ + L+VQ+ R
Sbjct: 113 VLDGRELRVQMAR 125
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFG + S ID + + V+ K F FV ++ P +A A++ N
Sbjct: 33 FAPFGPIKS----IDXSWD----------SVTXKHKGFAFVEYEVPEAAQLALEQXNSVX 78
Query: 62 IGMKRLKV 69
+G + +KV
Sbjct: 79 LGGRNIKV 86
>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 = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 14/63 (22%)
Query: 6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK 65
G VI+ K+ D T +SK + F+ F + S+ +A++ +NG+Q+G +
Sbjct: 29 GPVINLKMMFDPQTGRSKGYA--------------FIEFRDLESSASAVRNLNGYQLGSR 74
Query: 66 RLK 68
LK
Sbjct: 75 FLK 77
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 14/63 (22%)
Query: 6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK 65
G VI+ K+ D T +SK + F+ F + S+ +A++ +NG+Q+G +
Sbjct: 27 GPVINLKMMFDPQTGRSKGYA--------------FIEFRDLESSASAVRNLNGYQLGSR 72
Query: 66 RLK 68
LK
Sbjct: 73 FLK 75
>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 = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 14/63 (22%)
Query: 6 GNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMK 65
G VI+ K+ D T +SK + F+ F + S+ +A++ +NG+Q+G +
Sbjct: 28 GPVINLKMMFDPQTGRSKGYA--------------FIEFRDLESSASAVRNLNGYQLGSR 73
Query: 66 RLK 68
LK
Sbjct: 74 FLK 76
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQI 62
K + +V F+NP A A++ M+G QI
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQI 72
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQK-CFGFVSFDNPASAHTAIQ 55
LP NV +F + F + +N K FGF+ FDNP S AI+
Sbjct: 30 LPLKNVSKEDLF--------RIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 14/72 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ A AI MN +
Sbjct: 26 FIPFGDITDIQIPLDYETEK--------------HRGFAFVEFELAEDAAAAIDNMNESE 71
Query: 62 IGMKRLKVQLKR 73
+ + ++V L +
Sbjct: 72 LFGRTIRVNLAK 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ A AI MN +
Sbjct: 84 FIPFGDITDIQIPLDYETEK--------------HRGFAFVEFELAEDAAAAIDNMNESE 129
Query: 62 IGMKRLKVQL 71
+ + ++V L
Sbjct: 130 LFGRTIRVNL 139
>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 = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 14/72 (19%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ A AI MN +
Sbjct: 28 FIPFGDITDIQIPLDYETEK--------------HRGFAFVEFELAEDAAAAIDNMNESE 73
Query: 62 IGMKRLKVQLKR 73
+ + ++V L +
Sbjct: 74 LFGRTIRVNLAK 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 29.3 bits (64), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL 71
K + FV + A A AI +NG ++ KR+ V+L
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL 77
>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 = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F+PFG++ ++ +D T + + F FV F+ A AI MN +
Sbjct: 23 FIPFGDITDIQIPLDYETEK--------------HRGFAFVEFELAEDAAAAIDNMNESE 68
Query: 62 IGMKRLKVQL 71
+ + ++V L
Sbjct: 69 LFGRTIRVNL 78
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKR 73
+ F FV F + A A AM+G ++ + L+VQ+ R
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQK-CFGFVSFDNPASAHTAIQ 55
LP NV +F + F + +N K FGF+ FDNP S AI+
Sbjct: 30 LPLKNVSKEDLF--------RIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQK-CFGFVSFDNPASAHTAIQ 55
LP NV +F + F + +N K FGF+ FDNP S AI+
Sbjct: 18 LPLKNVSKEDLF--------RIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 3 LPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQK-CFGFVSFDNPASAHTAIQ 55
LP NV +F + F + +N K FGF+ FDNP S AI+
Sbjct: 10 LPLKNVSKEDLF--------RIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 55
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQI 62
K FGFV F +P S AI +NG ++
Sbjct: 57 KSFGFVCFKHPESVSYAIALLNGIRL 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 5 FGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQIGM 64
N ++ ++ +++A +Q FG+ R + K + F+ FD A A++ MNG +
Sbjct: 19 LANTVTEEI-LEKAFSQ---FGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEG 72
Query: 65 KRLKVQLKRPKDAAR 79
+ +++ +P D R
Sbjct: 73 ENIEIVFAKPPDQKR 87
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 28.5 bits (62), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K FGFV+F+N A A A + ++G + ++++V
Sbjct: 55 KGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
K FGFV+F+N A A A + ++G + ++++V
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 37 KCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRP--KDAARP 80
+ + FV F N A A++A+NG + ++V L +P KD++ P
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGP 96
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL---KRP 74
S + F FV F+N A A + NG ++ +R++V KRP
Sbjct: 53 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 97
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL---KRP 74
S + F FV F+N A A + NG ++ +R++V KRP
Sbjct: 50 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 94
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 20/72 (27%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFGN+I + +D N C FV+++ SA A+ +NG Q
Sbjct: 34 FSPFGNII--DLSMDPPRN-----------------C-AFVTYEKMESADQAVAELNGTQ 73
Query: 62 IGMKRLKVQLKR 73
+ +LKV + R
Sbjct: 74 VESVQLKVNIAR 85
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQL---KRP 74
S + F FV F+N A A + NG ++ +R++V KRP
Sbjct: 84 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 20/72 (27%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGFQ 61
F PFGN+I + +D N C FV+++ SA A+ +NG Q
Sbjct: 58 FSPFGNIID--LSMDPPRN-----------------C-AFVTYEKMESADQAVAELNGTQ 97
Query: 62 IGMKRLKVQLKR 73
+ +LKV + R
Sbjct: 98 VESVQLKVNIAR 109
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 42 VSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPK 75
VS+++P +A A++ +G +LKV L R K
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 1 MFLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQAMNGF 60
+F G V+S ++ DR T + K +G C + + +A +A++ +NG
Sbjct: 28 IFSEVGPVVSFRLVYDRETGKPKGYGFC--------------EYQDQETALSAMRNLNGR 73
Query: 61 QIGMKRLKV 69
+ + L+V
Sbjct: 74 EFSGRALRV 82
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 33 SVNQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKV 69
S + F FV F+N A A + NG ++ +R++V
Sbjct: 53 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 17/68 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA---MN 58
F +G V K+ D AT +S+ FG F+SF+ P+S ++ ++
Sbjct: 24 FGKYGTVTDLKIMKDPATGRSRGFG--------------FLSFEKPSSVDEVVKTQHILD 69
Query: 59 GFQIGMKR 66
G I KR
Sbjct: 70 GKVIDPKR 77
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 2 FLPFGNVISSKVFIDRATNQSKCFGECNRKVSVNQKCFGFVSFDNPASAHTAIQA 56
F +G V+ + D+ TNQS + FGFV F +P T + +
Sbjct: 37 FSQYGEVVDCVIMKDKTTNQS--------------RGFGFVKFKDPNCVGTVLAS 77
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 35 NQKCFGFVSFDNPASAHTAIQAMNGFQIGMKRLKVQLKRPKDA 77
N K + F++F + ++ AI+AMNG + + + V KD+
Sbjct: 46 NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88
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
0.325 0.136 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,096,446
Number of Sequences: 62578
Number of extensions: 61616
Number of successful extensions: 233
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 59
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 153
Number of HSP's gapped (non-prelim): 75
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)