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= 011912
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 165 bits (418), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 79/181 (43%), Positives = 117/181 (64%), Gaps = 16/181 (8%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERV 63
E K+FIGG++WDT ED LR+YF +G V + IMKD ATGR+RGFGF+ F P+ + V
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 64 VMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFK 123
V +H++DG+ ++ K+A+PRD+Q+ +T KIFVGG+ V +F+
Sbjct: 62 VKTQHILDGKVIDPKRAIPRDEQD----------------KTGKIFVGGIGPDVRPKEFE 105
Query: 124 KYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVEVKRAVP 183
++F Q+G I D +M D +T + RGFGF+TYDS +AVD+V F + + +E+KRA P
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165
Query: 184 K 184
+
Sbjct: 166 R 166
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 34/79 (43%), Positives = 58/79 (73%), Gaps = 1/79 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
K+F+GGL TE + ++YF ++G +TD+ +M D T R RGFGF++++ +VD+V+ K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV-K 63
Query: 167 TFHELNGKMVEVKRAVPKE 185
T H L+GK+++ KRA+P++
Sbjct: 64 TQHILDGKVIDPKRAIPRD 82
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 72/195 (36%), Positives = 117/195 (60%), Gaps = 13/195 (6%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERV 63
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A +
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 64 VMQK-HMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTVTESD 121
+ + H +DGR VE K+AV R+D PG T KKIFVGG+ E
Sbjct: 73 MNARPHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTEEHH 121
Query: 122 FKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVEVKRA 181
+ YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG EV++A
Sbjct: 122 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 181
Query: 182 VPKELSPGPSRNQLG 196
+ K+ S +Q G
Sbjct: 182 LSKQEMASASSSQRG 196
Score = 87.8 bits (216), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 11 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 71 AAMNARPHKVDGRVVEPKRAVSREDSQRP 99
>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 = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 75/199 (37%), Positives = 118/199 (59%), Gaps = 21/199 (10%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA-----DPA 58
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A D A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 59 VAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ R H +DGR VE K+AV R+D PG T KKIFVGG+
Sbjct: 72 MNAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDT 116
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
E + YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG E
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 176
Query: 178 VKRAVPKELSPGPSRNQLG 196
V++A+ K+ S +Q G
Sbjct: 177 VRKALSKQEMASASSSQRG 195
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRP 98
>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 = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 75/199 (37%), Positives = 118/199 (59%), Gaps = 21/199 (10%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA-----DPA 58
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A D A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 59 VAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ R H +DGR VE K+AV R+D PG T KKIFVGG+
Sbjct: 71 MNAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDT 115
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
E + YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG E
Sbjct: 116 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 175
Query: 178 VKRAVPKELSPGPSRNQLG 196
V++A+ K+ S +Q G
Sbjct: 176 VRKALSKQEMASASSSQRG 194
Score = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 9 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 69 AAMNARPHKVDGRVVEPKRAVSREDSQRP 97
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 139 bits (351), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 72/188 (38%), Positives = 114/188 (60%), Gaps = 21/188 (11%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA-----DPA 58
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A D A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 59 VAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ R H +DGR VE K+AV R+D PG T KKIFVGG+
Sbjct: 72 MNAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDT 116
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
E + YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG E
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 176
Query: 178 VKRAVPKE 185
V++A+ K+
Sbjct: 177 VRKALSKQ 184
Score = 86.7 bits (213), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRP 98
>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 = 139 bits (350), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 72/188 (38%), Positives = 114/188 (60%), Gaps = 21/188 (11%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA-----DPA 58
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A D A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 59 VAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ R H +DGR VE K+AV R+D PG T KKIFVGG+
Sbjct: 65 MNAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDT 109
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
E + YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG E
Sbjct: 110 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 169
Query: 178 VKRAVPKE 185
V++A+ K+
Sbjct: 170 VRKALSKQ 177
Score = 86.7 bits (213), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 63 AAMNARPHKVDGRVVEPKRAVSREDSQRP 91
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 139 bits (350), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 72/188 (38%), Positives = 114/188 (60%), Gaps = 21/188 (11%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA-----DPA 58
+L KLFIGG+S++T ++ LR +F+ +G + + V+M+D T R+RGFGF+ +A D A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 59 VAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ R H +DGR VE K+AV R+D PG T KKIFVGG+
Sbjct: 70 MNAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDT 114
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
E + YF+Q+G I + +M D + + RGF F+T+D ++VDK++++ +H +NG E
Sbjct: 115 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 174
Query: 178 VKRAVPKE 185
V++A+ K+
Sbjct: 175 VRKALSKQ 182
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 40/89 (44%), Positives = 61/89 (68%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
P + +K+F+GGL+ T+ + +F+Q+G +TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 8 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 162 KVLLKTFHELNGKMVEVKRAVPKELSPGP 190
+ H+++G++VE KRAV +E S P
Sbjct: 68 AAMNARPHKVDGRVVEPKRAVSREDSQRP 96
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 97.4 bits (241), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 44/86 (51%), Positives = 65/86 (75%), Gaps = 1/86 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
KIFVGG+ E++ ++YF +FG++T+VV++YD QRPRGFGFIT++ E++VD+ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 167 TFHELNGKMVEVKRAVPKE-LSPGPS 191
FH++ GK VEVKRA P++ S GPS
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSGPS 97
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 38/82 (46%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADP-AVAERVVM 65
K+F+GGI + E LR+YF+ FG V E V++ D R RGFGFI F D +V + V M
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 66 QKHMIDGRTVEAKKAVPRDDQN 87
H I G+ VE K+A PRD ++
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKS 93
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 92.8 bits (229), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 38/81 (46%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 4 ELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADP-AVAER 62
E+GKLF+GG+ W T ++ LR YF +GEV++ VIMKD+ T ++RGFGF+ F DP V
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 63 VVMQKHMIDGRTVEAKKAVPR 83
+ + H +DGR ++ K PR
Sbjct: 75 LASRPHTLDGRNIDPKPCTPR 95
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 49/86 (56%), Gaps = 1/86 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
K+FVGGL + T+ + YF Q+G + D V+M D T + RGFGF+ + V VL
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 167 TFHELNGKMVEVKRAVPKELSP-GPS 191
H L+G+ ++ K P+ + P GPS
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSGPS 103
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 90.5 bits (223), Expect = 2e-18, Method: Composition-based stats.
Identities = 40/74 (54%), Positives = 53/74 (71%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
IFVGGL+ T D K YF+QFG + D ++M+D T R RGFGF+T++SE+ V+KV
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 168 FHELNGKMVEVKRA 181
FHE+N KMVE K+A
Sbjct: 62 FHEINNKMVECKKA 75
Score = 66.2 bits (160), Expect = 3e-11, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 49/74 (66%), Gaps = 1/74 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV-MQ 66
+F+GG+S +T + ++ YF+ FG+V +A++M D+ T R RGFGF+ F + E+V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 67 KHMIDGRTVEAKKA 80
H I+ + VE KKA
Sbjct: 62 FHEINNKMVECKKA 75
>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 = 90.5 bits (223), Expect = 2e-18, Method: Composition-based stats.
Identities = 43/80 (53%), Positives = 58/80 (72%), Gaps = 1/80 (1%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
E + GK F+GG+SWDT++ L+DYF FGEV++ I D TGR+RGFGFI+F D A E
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 62 RVVMQK-HMIDGRTVEAKKA 80
+V+ QK H +DGR ++ KKA
Sbjct: 68 KVLDQKEHRLDGRVIDPKKA 87
Score = 68.6 bits (166), Expect = 7e-12, Method: Composition-based stats.
Identities = 34/86 (39%), Positives = 51/86 (59%)
Query: 96 IHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD 155
I+ S K FVGGL+ ++ D K YF +FG + D + D NT R RGFGFI +
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 156 SEEAVDKVLLKTFHELNGKMVEVKRA 181
+V+KVL + H L+G++++ K+A
Sbjct: 62 DAASVEKVLDQKEHRLDGRVIDPKKA 87
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 84.7 bits (208), Expect = 9e-17, Method: Composition-based stats.
Identities = 39/81 (48%), Positives = 57/81 (70%), Gaps = 1/81 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+FIGG+SW T ++ LR+YF FGEV E ++M+D T R+RGFGF+ F D A ++V+ Q
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 67 -KHMIDGRTVEAKKAVPRDDQ 86
+H +D +T++ K A PR Q
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQ 107
Score = 76.6 bits (187), Expect = 2e-14, Method: Composition-based stats.
Identities = 35/82 (42%), Positives = 54/82 (65%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
K+F+GGL+ T+ ++YF QFG + + +VM D T+R RGFGF+T+ + VDKVL +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 167 TFHELNGKMVEVKRAVPKELSP 188
+ HEL+ K ++ K A P+ P
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQP 108
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 83.2 bits (204), Expect = 3e-16, Method: Composition-based stats.
Identities = 36/75 (48%), Positives = 54/75 (72%), Gaps = 1/75 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+FIGG+SW T ++ LR+YF FGEV E ++M+D T R+RGFGF+ F D A ++V+ Q
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 67 -KHMIDGRTVEAKKA 80
+H +D +T++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 74.3 bits (181), Expect = 1e-13, Method: Composition-based stats.
Identities = 33/75 (44%), Positives = 51/75 (68%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
K+F+GGL+ T+ ++YF QFG + + +VM D T+R RGFGF+T+ + VDKVL +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 167 TFHELNGKMVEVKRA 181
+ HEL+ K ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 39/87 (44%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+K+F+GGL+ TE + Y++Q+G +TD VVM D ++R RGFGF+T+ S VD +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 166 KTFHELNGKMVEVKRAVPKELS-PGPS 191
H ++G++VE KRAV +E S GPS
Sbjct: 88 ARPHSIDGRVVEPKRAVAREESGSGPS 114
Score = 82.4 bits (202), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 37/80 (46%), Positives = 59/80 (73%), Gaps = 1/80 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPA-VAERVVM 65
KLFIGG+S++T E+ LR+Y++ +G++ + V+M+D A+ R+RGFGF+ F+ A V +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 66 QKHMIDGRTVEAKKAVPRDD 85
+ H IDGR VE K+AV R++
Sbjct: 89 RPHSIDGRVVEPKRAVAREE 108
>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 = 78.6 bits (192), Expect = 8e-15, Method: Composition-based stats.
Identities = 33/74 (44%), Positives = 53/74 (71%), Gaps = 1/74 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+FIGG+SWDT + L+DYF FGEV++ + D TGR+RGFGF++F + ++V+ QK
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 68 -HMIDGRTVEAKKA 80
H ++G+ ++ K+A
Sbjct: 62 EHKLNGKVIDPKRA 75
Score = 73.9 bits (180), Expect = 2e-13, Method: Composition-based stats.
Identities = 33/74 (44%), Positives = 49/74 (66%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+F+GGL+ T+ D K YF +FG + D + D T R RGFGF+ + E+VDKV+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 168 FHELNGKMVEVKRA 181
H+LNGK+++ KRA
Sbjct: 62 EHKLNGKVIDPKRA 75
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 35/82 (42%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 1 MEMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA--DPA 58
M + GKLF+GG+S+DTNE L F +G++ E V++KDR T R+RGFGF+ F D A
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 59 VAERVVMQKHMIDGRTVEAKKA 80
+ M +DGR + +A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89
Score = 61.6 bits (148), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS-EEAVDKVLL 165
K+FVGGL+ E ++ F ++G I++VVV+ D TQR RGFGF+T+++ ++A D ++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 166 KTFHELNGKMVEVKRA 181
++G+ + V +A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/68 (47%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+F+GG+ + T + LR YF+ FG++ EAV++ DR TG++RG+GF+ AD A AER
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 67 KH-MIDGR 73
+ +IDGR
Sbjct: 79 PNPIIDGR 86
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
KIFVGGL T++ +KYF+ FG I + VV+ D T + RG+GF+T A ++
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 167 TFHELNGKMVEVKRAV----PKELSPG 189
++G+ V A P+ L G
Sbjct: 79 PNPIIDGRKANVNLAYLGAKPRSLQTG 105
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 68.9 bits (167), Expect = 5e-12, Method: Composition-based stats.
Identities = 32/80 (40%), Positives = 47/80 (58%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L + G+ W T E L++YF FGEVL + KD TG ++GFGF+ F + +V+ Q+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 68 HMIDGRTVEAKKAVPRDDQN 87
HMIDGR + K + Q+
Sbjct: 78 HMIDGRWCDCKLPNSKQSQD 97
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 34/99 (34%), Positives = 47/99 (47%), Gaps = 6/99 (6%)
Query: 98 GSPGPAR----TKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT 153
GS G R T + V GL TE D K+YF FG + V V D T +GFGF+
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 154 YDSEEAVDKVLLKTFHELNGKMVEVKRAVPKE-LSPGPS 191
+ E KV+ + H ++G+ + K K+ GPS
Sbjct: 64 FTEYETQVKVMSQR-HMIDGRWCDCKLPNSKQSQDSGPS 101
>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 = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 76/159 (47%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + ++ R F + GE+ +++D+ TG++ G+GF+ + DP AE+ + +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 66 QKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKY 125
+ +T++ A P S R ++V GL T+T+ + ++
Sbjct: 65 NGLRLQTKTIKVSYARP----------------SSASIRDANLYVSGLPKTMTQKELEQL 108
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 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 = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 47/188 (25%), Positives = 88/188 (46%), Gaps = 22/188 (11%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ ++++G I ++ ED +R F FG + + D T + +GF F+ + P A+ +
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 65 MQKH--MIDGRTVEAKK------AVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLAS 115
Q + M+ GR ++ + A P DQ + AR +I+V +
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE------------ARAFNRIYVASVHQ 135
Query: 116 TVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAVDKVLLKTFHELNGK 174
+++ D K F+ FG I + D T + +G+GFI Y+ ++ + D V +L G+
Sbjct: 136 DLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195
Query: 175 MVEVKRAV 182
+ V +AV
Sbjct: 196 YLRVGKAV 203
>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 = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 42/159 (26%), Positives = 76/159 (47%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D LR F + GEV A +++D+ G + G+GF+ + AER + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 QKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKY 125
+ +T++ A P + I++ N +++ GL T+T+ D +
Sbjct: 65 NGLRLQSKTIKVSYARP-SSEVIKDAN---------------LYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F +FG I + V+ D T RG FI +D +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 42/159 (26%), Positives = 76/159 (47%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D LR F + GEV A +++D+ G + G+GF+ + AER + +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66 QKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKY 125
+ +T++ A P + I++ N +++ GL T+T+ D +
Sbjct: 65 NGLRLQSKTIKVSYARP-SSEVIKDAN---------------LYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F +FG I + V+ D T RG FI +D +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 77/159 (48%), Gaps = 22/159 (13%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D + F + G++ +++D+ TG++ G+GF+ ++DP A++ + +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 66 QKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKY 125
+ +T++ A P S R ++V GL T+++ + ++
Sbjct: 67 NGLKLQTKTIKVSYARP----------------SSASIRDANLYVSGLPKTMSQKEMEQL 110
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+ V L +T+ +FK F G I ++ D T + G+GF+ Y DK +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI--- 63
Query: 168 FHELNGKMVEVK 179
+ LNG ++ K
Sbjct: 64 -NTLNGLKLQTK 74
>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 = 65.9 bits (159), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 47/188 (25%), Positives = 88/188 (46%), Gaps = 22/188 (11%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ ++++G I ++ ED +R F FG + + D T + +GF F+ + P A+ +
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 65 MQKH--MIDGRTVEAKK------AVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLAS 115
Q + M+ GR ++ + A P DQ + AR +I+V +
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE------------ARAFNRIYVASVHQ 120
Query: 116 TVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAVDKVLLKTFHELNGK 174
+++ D K F+ FG I + D T + +G+GFI Y+ ++ + D V +L G+
Sbjct: 121 DLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 180
Query: 175 MVEVKRAV 182
+ V +AV
Sbjct: 181 YLRVGKAV 188
>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 = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 46/186 (24%), Positives = 83/186 (44%), Gaps = 22/186 (11%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
++++G I ++ ED +R F FG + D T + +GF F+ + P A+ + Q
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 67 KHMID--------GRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPART-KKIFVGGLASTV 117
+ + GR +A P DQ + AR +I+V + +
Sbjct: 74 XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEE------------ARAFNRIYVASVHQDL 121
Query: 118 TESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAVDKVLLKTFHELNGKMV 176
++ D K F+ FG I + D T + +G+GFI Y+ ++ + D V +L G+ +
Sbjct: 122 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Query: 177 EVKRAV 182
V +AV
Sbjct: 182 RVGKAV 187
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 63.9 bits (154), Expect = 2e-10, Method: Composition-based stats.
Identities = 30/77 (38%), Positives = 45/77 (58%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
KKIFVGGL+ E ++YF FG + + + D+ T + RGF FIT+ EE V K++
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 166 KTFHELNGKMVEVKRAV 182
K +H + E+K A+
Sbjct: 62 KKYHNVGLSKCEIKVAM 78
Score = 55.8 bits (133), Expect = 5e-08, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 40/62 (64%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+F+GG+S DT E+++R+YF FGEV + D T + RGF FI F + ++++ +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Query: 67 KH 68
K+
Sbjct: 63 KY 64
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 39/59 (66%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
L++G + ++ ED LR F+ FG++ V+MKD TGR++G+GFI F+D A R + Q
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
G + + ++VG L +TE + F+ FG I ++V+M D +T R +G+GFIT+ E
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 161 DKVLLKTFHELNG 173
+ L +LNG
Sbjct: 61 RRAL----EQLNG 69
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 59.7 bits (143), Expect = 4e-09, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 42/74 (56%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
IFVGGL+ E ++YF FG + + + D+ T + RGF FIT+ EE V K++ K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 168 FHELNGKMVEVKRA 181
+H + E+K A
Sbjct: 62 YHNVGLSKCEIKVA 75
Score = 53.9 bits (128), Expect = 2e-07, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 39/61 (63%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+GG+S DT E+++R+YF FGEV + D T + RGF FI F + ++++ +K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 68 H 68
+
Sbjct: 62 Y 62
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 48/77 (62%), Gaps = 3/77 (3%)
Query: 6 GKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV- 64
GKLFIGG++ +TNE L+ F G + E +++KDR T ++RGF FI F +PA A+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66
Query: 65 -MQKHMIDGRTVEAKKA 80
M + G+ ++ ++A
Sbjct: 67 DMNGKSLHGKAIKVEQA 83
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 8/79 (10%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY----DSEEAVDK 162
K+F+GGL E K F + G I++V+++ D T + RGF FIT+ D++ A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 163 VLLKTFHELNGKMVEVKRA 181
+ K+ H GK ++V++A
Sbjct: 68 MNGKSLH---GKAIKVEQA 83
>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 = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 79/174 (45%), Gaps = 22/174 (12%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ L++G + D E L + F G +L + +D T R+ G+ ++ F PA AER +
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 65 --MQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDF 122
M +I G+ V + ++ + S+ S IF+ L ++
Sbjct: 75 DTMNFDVIKGKPVRI----------MWSQRDPSLRKSG----VGNIFIKNLDKSIDNKAL 120
Query: 123 KKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMV 176
F FG I V+ D N +G+GF+ ++++EA ++ + K +NG ++
Sbjct: 121 YDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEK----MNGMLL 168
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
+L++G + ++ ED LR F+ FG + +M D TGR++G+GFI F+D A++ + Q
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 67 KH--MIDGRTVEAKKAVPRDD 85
+ + GR ++ R D
Sbjct: 88 LNGFELAGRPMKVGHVTERTD 108
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 93 NSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFI 152
N+ GS GP R ++VG L +TE + F+ FG I + +M D T R +G+GFI
Sbjct: 17 NNLQKGSAGPMR---LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73
Query: 153 TYDSEEAVDKVLLKTFHELNG 173
T+ E K L +LNG
Sbjct: 74 TFSDSECAKKAL----EQLNG 90
>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 = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 79/174 (45%), Gaps = 22/174 (12%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ L++G + D E L + F G +L + +D T R+ G+ ++ F PA AER +
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 65 --MQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDF 122
M +I G+ V + ++ + S+ S IF+ L ++
Sbjct: 70 DTMNFDVIKGKPVRI----------MWSQRDPSLRKSG----VGNIFIKNLDKSIDNKAL 115
Query: 123 KKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMV 176
F FG I V+ D N +G+GF+ ++++EA ++ + K +NG ++
Sbjct: 116 YDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEK----MNGMLL 163
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 38/159 (23%), Positives = 68/159 (42%), Gaps = 18/159 (11%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L + + D + L F+A G + IM+D TG + G+ F+ F ++R +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI--- 62
Query: 68 HMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTK--KIFVGGLASTVTESDFKKY 125
+++G TV +N+ + PG K ++V L T+T+
Sbjct: 63 KVLNGITV-------------RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 109
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL 164
F ++G I ++ D T RPRG F+ Y+ E + +
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 35/97 (36%), Positives = 53/97 (54%), Gaps = 3/97 (3%)
Query: 98 GSPGPARTKKI-FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD- 155
GS G A TK++ +VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 156 SEEAVDKVLLKTFHELNGKMVEVKRAVPKELSP-GPS 191
+E+A + EL G+ + V A P + GPS
Sbjct: 64 AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPS 100
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L++GG++ + ++ L F FG++ + I D T + RGF F+ F A+ A A M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 66 QKHMIDGRTVEAKKAVP 82
+ + GRT+ A P
Sbjct: 75 NESELFGRTIRVNLAKP 91
>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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 66/159 (41%), Gaps = 18/159 (11%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L + + D + L F+A G + I +D TG + G+ F+ F ++R +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI--- 73
Query: 68 HMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTK--KIFVGGLASTVTESDFKKY 125
+++G TV K+ + PG K ++V L T+T+
Sbjct: 74 KVLNGITVRNKRL-------------KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 120
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL 164
F ++G I ++ D T RPRG F+ Y+ E + +
Sbjct: 121 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 48/81 (59%), Gaps = 2/81 (2%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+ I+VG L + T K+ F QFG + +V ++YD T++P+GFGF+ EE+V + +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 166 KTFH-ELNGKMVEVKRAVPKE 185
K + + G+ + V A PK+
Sbjct: 61 KLDNTDFMGRTIRVTEANPKK 81
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV-MQ 66
+++G + + +++++ F FG+V ++ DR T + +GFGF+ + +V+E + +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 67 KHMIDGRTVEAKKAVPR 83
GRT+ +A P+
Sbjct: 64 NTDFMGRTIRVTEANPK 80
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+G + D ED LR++F +G+V++ I K R F F+ FAD +A+ + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGED 62
Query: 68 HMIDGRTVEAKKAVPRDDQN 87
+I G +V A P+ + N
Sbjct: 63 LIIKGISVHISNAEPKHNSN 82
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRP-RGFGFITYDSEEA 159
G + + +FVG +TE + +++F Q+G + DV + +P R F F+T+ +++
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI------PKPFRAFAFVTF-ADDQ 53
Query: 160 VDKVLLKTFHELNGKMVEVKRAVPKELS-PGPS 191
+ + L + G V + A PK S GPS
Sbjct: 54 IAQSLCGEDLIIKGISVHISNAEPKHNSNSGPS 86
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 79/171 (46%), Gaps = 14/171 (8%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATG--RARGFGFIVFADPAV 59
+++ K+F+G + +E LR+ F+ +G V E +++DR+ +++G F+ F
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 60 AERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTE 119
A H + K +P IQ + S + +K+F+G ++ TE
Sbjct: 72 ALEAQNALHNM--------KVLPGMHHPIQMKPADSEKNN--AVEDRKLFIGMISKKCTE 121
Query: 120 SDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHE 170
+D + F FG I + ++ + RG F+T+ + A+ + +K H+
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTF-TTRAMAQTAIKAMHQ 170
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 39/166 (23%), Positives = 76/166 (45%), Gaps = 14/166 (8%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATG--RARGFGFIVFADPAVAERVV 64
K+F+G + +E LR+ F+ +G V E +++DR+ +++G F+ F A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 65 MQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKK 124
H + K +P IQ + S + +K+F+G ++ TE+D +
Sbjct: 65 NALHNM--------KVLPGMHHPIQMKPADSEKNN--AVEDRKLFIGMISKKCTENDIRV 114
Query: 125 YFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHE 170
F FG I + ++ + RG F+T+ + A+ + +K H+
Sbjct: 115 MFSSFGQIEECRILRGPDG-LSRGCAFVTFTT-RAMAQTAIKAMHQ 158
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 56/106 (52%), Gaps = 15/106 (14%)
Query: 83 RDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHN 142
R +++ NR N P P +F GL+ TE D ++ F ++G I DV ++YD
Sbjct: 32 RGSRHVGNRAN------PDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQ 83
Query: 143 TQRPRGFGFITY----DSEEAVDKVLLKTFHELNGKMVEVKRAVPK 184
++R RGF F+ + D++EA ++ EL+G+ + V ++ K
Sbjct: 84 SRRSRGFAFVYFENVDDAKEAKERA---NGMELDGRRIRVDFSITK 126
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L + G+S T E LR+ F +G + + I+ D+ + R+RGF F+ F D A +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 66 QKHMIDGRTVEAKKAVPR 83
+DGR + ++ +
Sbjct: 109 NGMELDGRRIRVDFSITK 126
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 9/92 (9%)
Query: 97 HGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY-- 154
+P P +F GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ +
Sbjct: 9 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 155 --DSEEAVDKVLLKTFHELNGKMVEVKRAVPK 184
D++EA ++ EL+G+ + V ++ K
Sbjct: 67 VDDAKEAKERA---NGMELDGRRIRVDFSITK 95
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L + G+S T E LR+ F +G + + I+ D+ + R+RGF F+ F D A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 66 QKHMIDGRTVEAKKAVPR 83
+DGR + ++ +
Sbjct: 78 NGMELDGRRIRVDFSITK 95
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 9/86 (10%)
Query: 97 HGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY-- 154
+P P +F GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ +
Sbjct: 9 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 155 --DSEEAVDKVLLKTFHELNGKMVEV 178
D++EA ++ EL+G+ + V
Sbjct: 67 VDDAKEAKERA---NGMELDGRRIRV 89
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L + G+S T E LR+ F +G + + I+ D+ + R+RGF F+ F D A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 66 QKHMIDGRTV 75
+DGR +
Sbjct: 78 NGMELDGRRI 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
LF+ G+S DT E+ L++ F + A I+ DR TG ++GFGF+ F + A A + M
Sbjct: 18 LFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 66 QKHMIDGRTVEAKKAVPR 83
+ IDG V A P+
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 98 GSPGP-ART---KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT 153
GS GP AR+ K +FV GL+ TE K+ FD G + +V D T +GFGF+
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVT-DRETGSSKGFGFVD 60
Query: 154 YDSEEAVDKVLLKTFH--ELNGKMVEVKRAVPK 184
++SEE K + E++G V + A PK
Sbjct: 61 FNSEEDA-KAAKEAMEDGEIDGNKVTLDWAKPK 92
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 77/167 (46%), Gaps = 16/167 (9%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATG--RARGFGFIVFADPAVAERVV 64
K F+G + +E LR+ F+ +G V E +++DR+ +++G F+ F
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF---------Y 55
Query: 65 MQKHMIDGR-TVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFK 123
+K ++ + + K +P IQ + S + +K+F+G ++ TE+D +
Sbjct: 56 TRKAALEAQNALHNXKVLPGXHHPIQXKPADSEKNN--AVEDRKLFIGXISKKCTENDIR 113
Query: 124 KYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKTFHE 170
F FG I + ++ + RG F+T+ + A + +K H+
Sbjct: 114 VXFSSFGQIEECRILRGPDG-LSRGCAFVTFTT-RAXAQTAIKAXHQ 158
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 9/92 (9%)
Query: 97 HGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY-- 154
+P P +F GL+ TE D ++ F ++G I DV ++YD ++R RGF F+ +
Sbjct: 6 RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 155 --DSEEAVDKVLLKTFHELNGKMVEVKRAVPK 184
D++EA ++ EL+G+ + V ++ K
Sbjct: 64 VDDAKEAKERA---NGMELDGRRIRVDFSITK 92
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L + G+S T E LR+ F +G + + I+ D+ + R+RGF F+ F D A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 66 QKHMIDGRTV 75
+DGR +
Sbjct: 75 NGMELDGRRI 84
>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 = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 50/95 (52%), Gaps = 8/95 (8%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+GGI +E +R +F +G V E I+ DR TG ++G+GF+ F + +++V +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68 HMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGP 102
G+ ++ A I+ +N S+ H P P
Sbjct: 71 INFHGKKLKLGPA-------IRKQNLSTYHVQPRP 98
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+FVGG+ + E++ + +F ++G + +V ++ D T +G+GF+++ ++ V K++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 FHELNGKMVEVKRAVPKE 185
+ +GK +++ A+ K+
Sbjct: 71 IN-FHGKKLKLGPAIRKQ 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 103 ARTKKI-FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAV 160
A TK++ +VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++ +E+A
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 161 DKVLLKTFHELNGKMVEVKRA 181
+ EL G+ + V A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L++GG++ + ++ L F FG++ + I D T + RGF F+ F A+ A A M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 66 QKHMIDGRTVEAKKA 80
+ + GRT+ A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT-YDSEEAVDKVLLK 166
+FVG L+ +T D K F FG I+D V+ D T + +G+GF++ Y+ +A + ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 167 TFHELNGKMVEVKRAVPKELSP-GPS 191
L G+ + A K +P GPS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+G +S + + ++ F FG++ +A ++KD ATG+++G+GF+ F + AE ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV-- 75
Query: 68 HM 69
HM
Sbjct: 76 HM 77
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 103 ARTKKI-FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAV 160
A TK++ +VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++ +E+A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 161 DKVLLKTFHELNGKMVEVKRA 181
+ EL G+ + V A
Sbjct: 64 AAIDNMNESELFGRTIRVNLA 84
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L++GG++ + ++ L F FG++ + I D T + RGF F+ F A+ A A M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 66 QKHMIDGRTVEAKKA 80
+ + GRT+ A
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 71/161 (44%), Gaps = 27/161 (16%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
+LF+G + D E+ + F+ +GE E I +D RGFGFI +AE +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE---IA 74
Query: 67 KHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYF 126
K +DG ++++ R + HG+ + V L+ V+ ++ F
Sbjct: 75 KAELDGTILKSRPL----------RIRFATHGA-------ALTVKNLSPVVSNELLEQAF 117
Query: 127 DQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
QFG + VV+ D + R G GF+ + ++ K L +
Sbjct: 118 SQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 20/97 (20%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
++FVG L + +TE DFK+ F+++G ++V + D RGFGFI +S + + K
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE--IAK 75
Query: 167 TFHELNGKMVEVKRAVPKELSPGPSRNQLGTHNYGLS 203
EL+G +++ + P R + TH L+
Sbjct: 76 A--ELDGTILKSR----------PLRIRFATHGAALT 100
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEA 159
G + ++VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++ +E+A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 160 VDKVLLKTFHELNGKMVEVKRA 181
+ EL G+ + V A
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L++GG++ + ++ L F FG++ + I D T + RGF F+ F A+ A A M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 66 QKHMIDGRTVEAKKA 80
+ + GRT+ A
Sbjct: 68 NESELFGRTIRVNLA 82
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+G +S + + ++ F FG + +A ++KD ATG+++G+GF+ F + AE + Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 68 --HMIDGRTVEAKKAV 81
+ GR + A
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT----YDSEEAVDKV 163
+FVG L+ +T D K F FG I+D V+ D T + +G+GF++ +D+E A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 164 LLKTFHELNGKMVEVKRAVPKELSP 188
L G+ + A K +P
Sbjct: 78 ---GGQWLGGRQIRTNWATRKPPAP 99
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+ +FVG + TE K F + G + ++YD T +P+G+GF Y +E L
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA----L 64
Query: 166 KTFHELNGK 174
LNG+
Sbjct: 65 SAMRNLNGR 73
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVA 60
L +F+G I ++ E++L+D F G V+ ++ DR TG+ +G+GF + D A
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ L + +++ T+ D LR F+ +G V + I +DR T +RGF F+ F D AE +
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 65 --MQKHMIDGRTVEAKKA 80
M ++DGR + + A
Sbjct: 107 DAMDGAVLDGRELRVQMA 124
>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 = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD-SEEAVDKVLLK 166
++VGGLA V + F FG ITD+ + D+ T++ RGF F+ ++ +E+A +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 167 TFHELNGKMVEVKRA 181
EL G+ + V A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF--ADPAVAERVVM 65
L++GG++ + ++ L F FG++ + I D T + RGF F+ F A+ A A M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 66 QKHMIDGRTVEAKKA 80
+ + GRT+ A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 49/93 (52%), Gaps = 3/93 (3%)
Query: 99 SPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEE 158
+P P + + V + +TV E ++ F+++G I V ++ D T++ RG+GF+ + S
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 159 AVDKVL--LKTFHELNGKMVEVKRAVPKELSPG 189
+ + + L F+ LN K ++V A PG
Sbjct: 96 SAQQAIAGLNGFNILN-KRLKVALAASGHQRPG 127
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L L + I +E +LR F+ +G + I+ DR T ++RG+GF+ F + A++ +
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEA-VIMKDRATGRARGFGFIVFA--DPAVAERVV 64
+FIG + + +E L D F AFG +L+ IM+D TG ++G+ FI FA D + A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 65 MQKHMIDGRTVEAKKAVPRDDQ 86
M + R + A +D +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDV-VVMYDHNTQRPRGFGFITYDSEEA 159
G + + IF+G L + E F FG+I +M D +T +G+ FI + S +A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 160 VDKVLLKTFHELNGKMV 176
D + +NG+ +
Sbjct: 61 SDAAI----EAMNGQYL 73
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 1 MEME-LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAV 59
M++E + L + +++ T+ D LR F+ +G V + I +DR T +RGF F+ F D
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 60 AERVV--MQKHMIDGRTVEAKKA 80
AE + M ++DGR + + A
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMA 147
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 45.4 bits (106), Expect = 7e-05, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+F+G + D + L+ +F +GEV++ I K R F F+ FAD VA+ + +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE 67
Query: 67 KHMIDGRTVEAKKAVPRDDQ 86
+I G +V A P+ ++
Sbjct: 68 DLIIKGISVHISNAEPKHNK 87
Score = 35.0 bits (79), Expect = 0.098, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRP-RGFGFITYDSEEAVDKVLL 165
K+FVG +T + +++F Q+G + DV + +P R F F+T+ +++ V + L
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFI------PKPFRAFAFVTF-ADDKVAQSLC 65
Query: 166 KTFHELNGKMVEVKRAVPK 184
+ G V + A PK
Sbjct: 66 GEDLIIKGISVHISNAEPK 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L++ + +++RLR F FG + A +M + GR++GFGF+ F+ P A + V +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE- 74
Query: 68 HMIDGRTVEAK 78
++GR V K
Sbjct: 75 --MNGRIVATK 83
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
++V L + + +K F FG IT VM + R +GFGF+ + S E K +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAV--- 72
Query: 168 FHELNGKMVEVK 179
E+NG++V K
Sbjct: 73 -TEMNGRIVATK 83
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 43/178 (24%), Positives = 76/178 (42%), Gaps = 20/178 (11%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L++G + ED L+ YFQ G + IM D+ + + F+ + A + +Q
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDA-NIALQT 60
Query: 68 HMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFD 127
++G+ +E NI N + T +FVG L V + + F
Sbjct: 61 --LNGKQIE---------NNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFK 109
Query: 128 QFGIITDVVVMYDHNTQRPRGFGFITY----DSEEAVDKVLLKTFHELNGKMVEVKRA 181
F VM+D T RG+GF+++ D++ A+D + +LNG+ + + A
Sbjct: 110 DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM---QGQDLNGRPLRINWA 164
>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 = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
K +FV + TES ++ F+ +G I + ++Y + +PRG+ FI Y+ E + +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE----RDMH 158
Query: 166 KTFHELNGKMVEVKRAV 182
+ +GK ++ +R +
Sbjct: 159 SAYKHADGKKIDGRRVL 175
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ- 66
LF+ +++DT E +LR F+ +G + ++ + +G+ RG+ FI + ER +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE----HERDMHSA 160
Query: 67 -KHMIDGRTVEAKKAV 81
KH DG+ ++ ++ +
Sbjct: 161 YKH-ADGKKIDGRRVL 175
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+GGI +E +R +F +G V E I+ DR TG ++G+GF+ F + +++V +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 68 HMIDGRTVEAKKAVPRDD 85
G+ ++ A+ + +
Sbjct: 72 INFHGKKLKLGPAIRKQN 89
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+FVGG+ + E++ + +F ++G + +V ++ D T +G+GF+++ ++ V K++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 168 FHELNGKMVEVKRAVPKE 185
+ +GK +++ A+ K+
Sbjct: 72 IN-FHGKKLKLGPAIRKQ 88
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD 56
KLFIG I + +E L+ F+ FG++ E ++KDR TG +G F+ + +
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 98 GSPGPARTK-----KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFI 152
GS G + K K+F+G + + E D K F++FG I ++ V+ D T +G F+
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 153 TYDSEEAVDK 162
TY E+ K
Sbjct: 61 TYCERESALK 70
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 49/85 (57%), Gaps = 9/85 (10%)
Query: 98 GSPGPART-KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
GS G +T ++VGGL T+TE+D + +F QFG I + V+ QR + FI + +
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-----QRQQ-CAFIQFAT 57
Query: 157 EEAVDKVLLKTFHEL--NGKMVEVK 179
+A + K+F++L NG+ + VK
Sbjct: 58 RQAAEVAAEKSFNKLIVNGRRLNVK 82
Score = 29.3 bits (64), Expect = 5.0, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--- 64
L++GG+ E LR++F FGE+ +++ + FI FA AE
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAEKS 68
Query: 65 MQKHMIDGRTVEAK 78
K +++GR + K
Sbjct: 69 FNKLIVNGRRLNVK 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 12/80 (15%)
Query: 98 GSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSE 157
GS G A+ K +FV LA+TVTE +K F QFG + V + D + FI +D
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDER 55
Query: 158 EAVDKVLLKTFHELNGKMVE 177
+ +K E+NGK +E
Sbjct: 56 DGA----VKAMEEMNGKDLE 71
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 9/83 (10%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV-- 64
KLFIGG+ N+D++++ +FG + ++KD ATG ++G+ F + D V ++ +
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 65 ---MQ----KHMIDGRTVEAKKA 80
MQ K ++ +V AK A
Sbjct: 176 LNGMQLGDKKLLVQRASVGAKNA 198
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 42/194 (21%), Positives = 81/194 (41%), Gaps = 27/194 (13%)
Query: 7 KLFIGGISWDTNEDRLRDYF----------QAFGE-VLEAVIMKDRATGRARGFGFIVF- 54
+L++G I + E+ + D+F QA G VL I +D+ F F+ F
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFR 59
Query: 55 ADPAVAERVVMQKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPG------PARTKKI 108
+ + + + G++++ ++ P D Q + + + PG P K+
Sbjct: 60 SVDETTQAMAFDGIIFQGQSLKIRR--PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKL 117
Query: 109 FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL-KT 167
F+GGL + + + K+ FG + ++ D T +G+ F Y D+ +
Sbjct: 118 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177
Query: 168 FHELNGKMVEVKRA 181
+L K + V+RA
Sbjct: 178 GMQLGDKKLLVQRA 191
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+GGI +E +R +F +G V E I+ DR TG ++G+GF+ F + +++V +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68 HMIDGRTVEAKKAVPR 83
G+ ++ A+ +
Sbjct: 71 INFHGKKLKLGPAIRK 86
Score = 35.8 bits (81), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+FVGG+ + E++ + +F ++G + +V ++ D T +G+GF+++ ++ V K++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 FHELNGKMVEVKRAVPKE 185
+ +GK +++ A+ K+
Sbjct: 71 IN-FHGKKLKLGPAIRKQ 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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
KLFIGG+ N+D++++ +FG + ++KD ATG ++G+ F + D V ++ +
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 79/184 (42%), Gaps = 27/184 (14%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
+L++G I + E+ + D+F A + R G + G +P +A ++
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNA----------QMRLGGLTQAPG-----NPVLAVQINQD 52
Query: 67 KHM--IDGRTV-EAKKAVPRDD-----QNIQNRNNSSIHGSPGPARTKKIFVGGLASTVT 118
K+ ++ R+V E +A+ D Q+++ R PG K+F+GGL + +
Sbjct: 53 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPG---AHKLFIGGLPNYLN 109
Query: 119 ESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL-KTFHELNGKMVE 177
+ K+ FG + ++ D T +G+ F Y D+ + +L K +
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 178 VKRA 181
V+RA
Sbjct: 170 VQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
KLFIGG+ N+D++++ +FG + ++KD ATG ++G+ F + D V ++ +
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Score = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 79/184 (42%), Gaps = 27/184 (14%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
+L++G I + E+ + D+F A + R G + G +P +A ++
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNA----------QMRLGGLTQAPG-----NPVLAVQINQD 50
Query: 67 KHM--IDGRTV-EAKKAVPRDD-----QNIQNRNNSSIHGSPGPARTKKIFVGGLASTVT 118
K+ ++ R+V E +A+ D Q+++ R PG K+F+GGL + +
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPG---AHKLFIGGLPNYLN 107
Query: 119 ESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL-KTFHELNGKMVE 177
+ K+ FG + ++ D T +G+ F Y D+ + +L K +
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 178 VKRA 181
V+RA
Sbjct: 168 VQRA 171
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 66/159 (41%), Gaps = 27/159 (16%)
Query: 6 GKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVM 65
+LF+G + D E+ +R F+ +G+ E I KD +GFGFI +AE +
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE---I 73
Query: 66 QKHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKY 125
K +D + K Q R + H + + V L V+ ++
Sbjct: 74 AKVELDNMPLRGK----------QLRVRFACHSA-------SLTVRNLPQYVSNELLEEA 116
Query: 126 FDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL 164
F FG + VV+ D + RP G G + + + A K L
Sbjct: 117 FSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
LF+G ++ + +++ LR+ F+ F L +M D TG +RG+GF+ F A+ + M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 66 QKHMIDGRTVEAKKA 80
Q ++GR + A
Sbjct: 64 QGQDLNGRPLRINWA 78
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 7/85 (8%)
Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY----DSEEAV 160
T +FVG L V + + F F VM+D T RG+GF+++ D++ A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 161 DKVLLKTFHELNGKMVEVKRAVPKE 185
D + +LNG+ + + A E
Sbjct: 61 DSM---QGQDLNGRPLRINWAAKLE 82
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D LR F + GEV A +++D+ G + G+GF+ + AER + +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 66 QKHMIDGRTVEAKKAVP 82
+ +T++ A P
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
++FV L+ T +E D +K F +G ++++ D T++P+GF F+T+ E +K
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA----VK 65
Query: 167 TFHELNGKMVE 177
+ E++G++ +
Sbjct: 66 AYAEVDGQVFQ 76
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
+LF+ +S+ ++E+ L F A+G + E D T + +GF F+ F P E V
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP---EHAVKA 66
Query: 67 KHMIDGRTVEAK 78
+DG+ + +
Sbjct: 67 YAEVDGQVFQGR 78
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D LR F + GEV A +++D+ G + G+GF+ + AER + +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 66 QKHMIDGRTVEAKKAVP 82
+ +T++ A P
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%)
Query: 10 IGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+ +S DT E L++ F+ FG + + KD+ TG+++GF FI F A R +
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 98 GSPGPAR----TKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT 153
GS GP R I V L+ E+D ++ F FG I+ + + D T + +GF FI+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 154 YDSEEAVDKVL 164
+ E + +
Sbjct: 64 FHRREDAARAI 74
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
KLFIGG+ N+D++++ +FG + ++KD ATG ++G+ F + D V ++ +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLK 166
K+F+GGL + + + K+ FG + ++ D T +G+ F Y D+ +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 167 TFHELNGKMVEVKRAVPKELSPG 189
LNG + K+ + + S G
Sbjct: 63 ----LNGMQLGDKKLLVQRASVG 81
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
K +FV + TES ++ F+ +G I + ++Y + +PRG+ FI Y+ E + +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE----RDMH 158
Query: 166 KTFHELNGKMVEVKRAV 182
+ +GK ++ +R +
Sbjct: 159 SAYKHADGKKIDGRRVL 175
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 29/47 (61%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ +++DT E +LR F+ +G + ++ + +G+ RG+ FI +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 5/68 (7%)
Query: 17 TNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE---RVVMQKHMIDGR 73
TN D R F +G+V++ IMKD+ T +++G FI+F D A+ R + K + GR
Sbjct: 29 TNNDLYR-IFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF-GR 86
Query: 74 TVEAKKAV 81
++A A+
Sbjct: 87 VIKASIAI 94
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD 56
+++G I +D E+++ D G V+ +M D TGR++G+ FI F D
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 55
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 27/55 (49%)
Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEA 159
++ +++G + TE G + ++ +M+D T R +G+ FI + E+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 58
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEA-VIMKDRATGRARGFGFIVFADPAVAERVVM 65
+L + I + + LR F FG++L+ +I +R + +GFGF+ F + A A+R
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRARE 73
Query: 66 QKH--MIDGRTVEAKKAVPR 83
+ H +++GR +E A R
Sbjct: 74 KLHGTVVEGRKIEVNNATAR 93
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 4/88 (4%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
K++ V + + D ++ F QFG I DV +++ N + +GFGF+T+++ D+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 73
Query: 166 KTFHE-LNGKMVEVKRAVPKELS-PGPS 191
K + G+ +EV A + ++ GPS
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSGPS 101
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD 56
+++G I +D E+++ D G V+ +M D TGR++G+ FI F D
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 54
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEA 159
GP+R +++G + TE G + ++ +M+D T R +G+ FI + E+
Sbjct: 1 GPSRV--VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 57
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEA-VIMKDRATGRARGFGFIVFADPAVAERVVM 65
+L + I + + LR F FG++L+ +I +R + +GFGF+ F + A A+R
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADRARE 87
Query: 66 QKH--MIDGRTVEAKKAVPR 83
+ H +++GR +E A R
Sbjct: 88 KLHGTVVEGRKIEVNNATAR 107
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 103 ARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
++ K++ V + + D ++ F QFG I DV +++ N + +GFGF+T+++ D+
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADR 84
Query: 163 VLLKTFHELNGKMVE 177
K L+G +VE
Sbjct: 85 AREK----LHGTVVE 95
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
++V GL T+++ + ++ F Q+G I ++ D T RG GFI +D +EEA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L++ G+ ++ + F +G ++ + I+ D+ATG +RG GFI F AE +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 1 MEMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADP-AV 59
ME + +++G + + + L +F G V I+ D+ +G +GF +I F+D +V
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 60 AERVVMQKHMIDGRTVEAKKAVPR 83
+ + + + GR + K +P+
Sbjct: 61 RTSLALDESLFRGRQI---KVIPK 81
Score = 37.0 bits (84), Expect = 0.024, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 103 ARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
A + I+VG + T + + +F G + V ++ D + P+GF +I + +E+V
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 62
Query: 163 VLLKTFHELNGKMVEVKRAVPKELS-PG 189
L G+ ++V +PK + PG
Sbjct: 63 SLALDESLFRGRQIKV---IPKRTNRPG 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD 56
+++G I +D E+++ D G V+ +M D TGR++G+ FI F D
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 53
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEA 159
P+R +++G + TE G + ++ +M+D T R +G+ FI + E+
Sbjct: 1 PSRV--VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 56
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
KLF+G I +E L+ F+ FG + E ++KDR TG +G F+ +
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
K+FVG + + E D K F++FG I ++ V+ D T +G F+TY + ++ K
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALK 72
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV--M 65
L + + + +D + F + G++ +++D+ TG++ G+GF+ ++DP A++ + +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 66 QKHMIDGRTVEAKKAVP 82
+ +T++ A P
Sbjct: 67 NGLKLQTKTIKVSYARP 83
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+ V L +T+ +FK F G I ++ D T + G+GF+ Y DK +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI--- 63
Query: 168 FHELNGKMVEVK 179
+ LNG ++ K
Sbjct: 64 -NTLNGLKLQTK 74
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 29/121 (23%), Positives = 54/121 (44%), Gaps = 13/121 (10%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
GP + IF+ L ++ F FG I V+ D N +G+GF+ ++++EA
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAA 58
Query: 161 DKVLLKTFHELNGKMVEVKRAVPKELSPGPSRN-QLGTHNYGLSRVSSFLNGYTQSYNPS 219
++ + K +NG ++ ++ R +LG +R F N Y +++ P
Sbjct: 59 ERAIEK----MNGMLLNDRKVFVGRFKSRKEREAELG------ARAKEFTNVYIKNFGPG 108
Query: 220 S 220
S
Sbjct: 109 S 109
Score = 34.3 bits (77), Expect = 0.16, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 6 GKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV- 64
G +FI + + L D F AFG +L ++ D ++G+GF+ F AER +
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63
Query: 65 -MQKHMIDGRTV 75
M +++ R V
Sbjct: 64 KMNGMLLNDRKV 75
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+ + +D L+D F G VL A I + G+++G G + F P VAER
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC--- 62
Query: 68 HMIDGRTVEAKKAVPRDDQN 87
M++G + ++ R D+N
Sbjct: 63 RMMNGMKLSGREIDVRIDRN 82
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+++GG+ +E L + F G V+ + KDR TG+ +G+GF+ F A+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 68 HMID--GRTVEAKKA 80
MI G+ + KA
Sbjct: 78 DMIKLYGKPIRVNKA 92
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVD-KVLLK 166
++VGGL V+E + F Q G + + + D T + +G+GF+ + SEE D + +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 167 TFHELNGKMVEVKRA 181
+L GK + V +A
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY-DSEEAVDKVLLK 166
+ V L + ++ F+++G + DV + + +T+ PRGF F+ + D +A D
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 167 TFHELNGK--MVEVKRAVPKELSPGPS 191
EL+G+ V+V R ++LS GPS
Sbjct: 76 DGAELDGRELRVQVARYGRRDLS-GPS 101
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 10/88 (11%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSE--EAVDKVL 164
++FVG L +TE + +K F+++G +V + D +GFGFI ++ + KV
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 165 LKTFHELNGKMVEVKRAV-PKELSPGPS 191
L L GK + V+ A L+ GPS
Sbjct: 71 LDNM-PLRGKQLRVRFACHSASLTSGPS 97
Score = 37.4 bits (85), Expect = 0.019, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
+LF+G + D E+ +R F+ +G+ E I KD +GFGFI +AE
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 65
>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 = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFG--FITYDSEEA 159
K+FVG + T +E D ++ F+Q+G + ++ V+ D + P+ G F+T+ + +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATG--RARGFGFIVF 54
K+F+G + +E LR+ F+ +G V E +++DR+ +++G F+ F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF 54
>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 = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL 164
++V L T+T+ F ++G I ++ D T RPRG F+ Y+ E + +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Score = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 30/57 (52%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L++ + +D+L F +G +++ I++D+ TGR RG F+ + A+ +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>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 = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+F+G +S + + F FG + +A ++KD ATG+++G+GF+ F + AE + Q
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 68 --HMIDGRTVEAKKAV 81
+ GR + A
Sbjct: 69 GGQWLGGRQIRTNWAT 84
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT----YDSEEAVDKV 163
+FVG L+ +T + F FG I+D V+ D T + +G+GF++ +D+E A+ ++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
>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 = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADP-AVA 60
E + +++G + + + L +F G V I+ D+ +G +GF +I F+D +V
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 61 ERVVMQKHMIDGRTVEAKKAVPR 83
+ + + + GR + K +P+
Sbjct: 63 TSLALDESLFRGRQI---KVIPK 82
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 103 ARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
A + I+VG + T + + +F G + V ++ D + P+GF +I + +E+V
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 163 VLLKTFHELNGKMVEVKRAVPKELS-PG 189
L G+ ++V +PK + PG
Sbjct: 64 SLALDESLFRGRQIKV---IPKRTNRPG 88
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATG---RARGFGFIVFADPAVAERVV 64
LFI +++ T E+ L+ F G + I K + + GFGF+ + P A++ +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 65 --MQKHMIDGRTVEAK 78
+Q H +DG +E +
Sbjct: 68 KQLQGHTVDGHKLEVR 83
Score = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 4/83 (4%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQ---RPRGFGFITYDSE 157
G + + +F+ L + TE K F + G I + N GFGF+ Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 158 EAVDKVLLK-TFHELNGKMVEVK 179
E K L + H ++G +EV+
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVR 83
>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 = 0.019, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD-PAVA 60
E++ +++G + + + L +F + G + I+ D+ +G +G+ +I FA+ +V
Sbjct: 33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92
Query: 61 ERVVMQKHMIDGRTVEAKKAVPR 83
V M + + GRT+ K +P+
Sbjct: 93 AAVAMDETVFRGRTI---KVLPK 112
Score = 35.0 bits (79), Expect = 0.089, Method: Composition-based stats.
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 4/87 (4%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+ ++VG + T D + +F G I + ++ D + P+G+ +I + +VD +
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 166 KTFHELNGKMVEVKRAVPKELS-PGPS 191
G+ ++V +PK + PG S
Sbjct: 97 MDETVFRGRTIKV---LPKRTNMPGIS 120
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 12/72 (16%)
Query: 103 ARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDK 162
A+ K +FV LA+TVTE +K F +FG + V + D + F+ ++ A
Sbjct: 13 AKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAA-- 62
Query: 163 VLLKTFHELNGK 174
+K E+NGK
Sbjct: 63 --VKAMDEMNGK 72
>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 = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
LFI + + + L F FG V+ A + D+ T ++ FGF+ + +P A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+F+ L + D + F FG + V D T + FGF++YD+ + +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI--- 84
Query: 168 FHELNGKMVEVKR 180
+NG + +KR
Sbjct: 85 -QSMNGFQIGMKR 96
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
KLFIG + + E +R F+ +G+VLE I+K+ +GF+ D AE +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 67 KH 68
H
Sbjct: 62 LH 63
Score = 35.8 bits (81), Expect = 0.060, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 10/96 (10%)
Query: 98 GSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSE 157
GS G + K+F+G L TE + + F+Q+G + + ++ + +GF+ + +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDK 52
Query: 158 EAVDKVLLKTFH-ELNGKMVEVKRAVPK-ELSPGPS 191
A + + H +L+G + V+ + K + S GPS
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPS 88
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 36.6 bits (83), Expect = 0.030, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQR-----PRGFGFITYDSEEAV 160
+K+FVGGL + E + F +FG +VV + H + P+G+ F+ + E +V
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFG---PLVVDWPHKAESKSYFPPKGYAFLLFQEESSV 65
Query: 161 DKVLLKTFHELNGKM 175
+ L+ E +GK+
Sbjct: 66 -QALIDACLEEDGKL 79
Score = 29.3 bits (64), Expect = 5.0, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRA----RGFGFIVFADPAVAER 62
K+F+GG+ D +ED + F+ FG ++ V +A ++ +G+ F++F + + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV--VDWPHKAESKSYFPPKGYAFLLFQEESSVQA 67
Query: 63 VV 64
++
Sbjct: 68 LI 69
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.6 bits (83), Expect = 0.031, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
++F+ + +D L+D F G VL A I + G+++G G + F P VAER
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC-- 65
Query: 67 KHMIDGRTVEAKKAVPRDDQN 87
M++G + ++ R D+N
Sbjct: 66 -RMMNGMKLSGREIDVRIDRN 85
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFG--EVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L+IG ++W T ++ L + + G ++LE ++RA G+++GF + A +++++
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 36.2 bits (82), Expect = 0.039, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 31/64 (48%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
G + + +++ GL T+ D K +G I + D T + +G+GF+ +DS A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 161 DKVL 164
K +
Sbjct: 61 QKAV 64
Score = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L+I G+ T + L Q +G+++ + D+ T + +G+GF+ F P+ A++ V
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 36.2 bits (82), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
E + L+I + +E L + + FG+V+ I++D ++G +RG GF E
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCE 80
Query: 62 RVV 64
V+
Sbjct: 81 AVI 83
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 36.2 bits (82), Expect = 0.045, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
KLF+G ++ +ED +R F+AFG + E I++ G ++G F+ ++ A A+ +
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 67 KH 68
H
Sbjct: 76 LH 77
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 102 PARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMY--DHNTQRPRGFGFITYDS 156
P +K+FVG L +E D ++ F+ FG I + ++ D N+ +G F+ Y S
Sbjct: 12 PPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS---KGCAFVKYSS 65
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFG--EVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L+IG ++W T ++ L + + G ++LE ++RA G+++GF + A +++++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 35.8 bits (81), Expect = 0.059, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAV-IMKDRATGRARGFGFIVFADPAVAERVVMQ 66
L++G + +E+ + F GE + +V I+++R TG G+ F+ FAD A AE+ +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL-- 69
Query: 67 KHMIDGRTVEAKKAVPR 83
H I+G+ + R
Sbjct: 70 -HKINGKPLPGATPAKR 85
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.4 bits (80), Expect = 0.068, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 8/94 (8%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
K +F+ L+ E + QFG + V V+ +T+ +G F + ++EA K L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 166 KTFHE-------LNGKMVEVKRAVPK-ELSPGPS 191
E L+G+ ++V AV + E + GPS
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
+FI +S+D+ E+ L + Q FG++ ++ T ++G F F A++ +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 68 HM--------IDGRTVEAKKAVPRDD 85
+ +DGR ++ AV RD+
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLAVTRDE 103
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.4 bits (80), Expect = 0.073, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
+G +FI + + L D F AFG +L ++ D ++G+GF+ F AER +
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAI 68
Query: 65 --MQKHMIDGRTV 75
M +++ R V
Sbjct: 69 EKMNGMLLNDRKV 81
Score = 32.0 bits (71), Expect = 0.72, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
IF+ L ++ F FG I V+ D N + G+GF+ ++++EA ++ + K
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK- 70
Query: 168 FHELNGKMVEVKR 180
+NG ++ ++
Sbjct: 71 ---MNGMLLNDRK 80
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRA-TGRARGFGFIVFADPAVAER 62
K+ + I + N+ +R+ F FGE+ + K TG RGFGF+ F A++
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 35.0 bits (79), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 9/95 (9%)
Query: 5 LGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L +F+ G + +L +YF AFG V V+ KD+ F + D E V+
Sbjct: 8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVL 62
Query: 65 MQ-KHMIDGRTVEAKKAVPRDDQNIQNRNNSSIHG 98
Q +H + G + + PR+ + Q+ + S G
Sbjct: 63 SQSQHSLGGHRLRVR---PREQKEFQSPASKSPKG 94
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+ +FV G V + +YF FG + VV+ D F + A + VL
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLS 63
Query: 166 KTFHELNGKMVEVKRAVPKELSPGPSRNQLG 196
++ H L G + V+ KE S++ G
Sbjct: 64 QSQHSLGGHRLRVRPREQKEFQSPASKSPKG 94
>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 = 35.0 bits (79), Expect = 0.099, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 100 PGPARTKK---IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
PGP R+ + +FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 14 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 73
Score = 31.6 bits (70), Expect = 0.89, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
L + + D + L F+A G + IM+D TG + G+ F+ F ++R +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI--- 62
Query: 68 HMIDGRTVEAKK 79
+++G TV K+
Sbjct: 63 KVLNGITVRNKR 74
>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 = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 100 PGPARTKK---IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
PGP R+ + +FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 58
>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 = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 100 PGPARTKK---IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
PGP R+ + +FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 15 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA--DPAVAERVVM 65
LF+ I + ED +++ F +GE+ + DR TG ++G+ + + A+A + +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 66 QKHMIDGRTVE 76
I G+T++
Sbjct: 89 NGAEIMGQTIQ 99
Score = 32.3 bits (72), Expect = 0.62, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 7/86 (8%)
Query: 91 RNNSSIHGSPGPARTKK---IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPR 147
RN PGP R+ + +FV + E + ++ F +G I ++ + D T +
Sbjct: 9 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68
Query: 148 GFGFITYDSEEAVDKVLLKTFHELNG 173
G+ + Y++ K L LNG
Sbjct: 69 GYALVEYETH----KQALAAKEALNG 90
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
+F+ L T++D F FG + V D T + FGF+++D+ ++ +V +K
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA-QVAIKA 101
Query: 168 FHELNGKMVEVKR 180
+NG V KR
Sbjct: 102 ---MNGFQVGTKR 111
Score = 33.5 bits (75), Expect = 0.29, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
LFI + + + L F FG V+ A + D+ T ++ FGF+ F +P A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 7/89 (7%)
Query: 91 RNNSSIHGSPGPARTKK---IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPR 147
RN PGP R+ + +FV + E + ++ F +G I ++ + D T +
Sbjct: 55 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 148 GFGFITYDSEEAVDKVLLKTFHELNGKMV 176
G+ + Y++ K L LNG +
Sbjct: 115 GYALVEYETH----KQALAAKEALNGAEI 139
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFA--DPAVAERVVM 65
LF+ I + ED +++ F +GE+ + DR TG ++G+ + + A+A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 66 QKHMIDGRTVE 76
I G+T++
Sbjct: 135 NGAEIMGQTIQ 145
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEE-- 158
P R ++G + TE+D F FG I D + H + +G FI YD+ E
Sbjct: 23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILD----FKHYPE--KGCCFIKYDTHEQA 76
Query: 159 AVDKVLLKTF 168
AV V L F
Sbjct: 77 AVCIVALANF 86
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL- 164
K +++ L+ VTE D F +F + + T R RG FIT+ ++E + L
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 165 LKTFHELNGKMVEVKRAV-PKELSPGPS 191
L ++L GK++ ++ K+ S GPS
Sbjct: 86 LVNGYKLYGKILVIEFGKNKKQRSSGPS 113
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 19 EDRLRDYFQAFG-EVLEAVIMKDRATGRARGFGFIVFADPAVAER 62
ED +R Q+ G + E +M+++++G++RGF F+ F+ A R
Sbjct: 15 EDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 59
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 16/90 (17%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLLKT 167
++ GG+AS +T+ ++ F FG I ++ V + +G+ F+ + + E+ ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS- 80
Query: 168 FHELNGKMVE---VKRAVPKE---LSPGPS 191
+NG +E VK KE ++ GPS
Sbjct: 81 ---VNGTTIEGHVVKCYWGKESPDMTSGPS 107
Score = 31.6 bits (70), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQK 67
++ GGI+ + +R F FG+++E + + +G+ F+ F+ A ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS- 80
Query: 68 HMIDGRTVE 76
++G T+E
Sbjct: 81 --VNGTTIE 87
>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 = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 12/97 (12%)
Query: 81 VPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYD 140
VPR R + S P + ++V G +T + + F FG I D+
Sbjct: 15 VPRGSHMGPFRRSDSFPERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDL----- 67
Query: 141 HNTQRPRGFGFITYDSEEAVDKVLLKTFHELNGKMVE 177
+ PR F+TY+ E+ D+ + ELNG VE
Sbjct: 68 -SMDPPRNCAFVTYEKMESADQAV----AELNGTQVE 99
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADP 57
+F+G + E+ L + F G + + I KDR G+ + FGF+ F P
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHP 67
>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 = 32.0 bits (71), Expect = 0.72, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.0 bits (71), Expect = 0.84, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 22 LRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFAD 56
L D+F A G+V + I+ DR + R++G ++ F +
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 0.87, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>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 = 31.6 bits (70), Expect = 0.90, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVF 54
LF+ G+ + E+ + D F +GE+ + DR TG +G+ + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 56
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDS 156
+FV G+ TE D F ++G I ++ + D T +G+ + Y++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 101 GPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
P + ++V G +T + + F FG I D+ + PR F+TY+ E+
Sbjct: 11 APRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDL------SMDPPRNCAFVTYEKMESA 62
Query: 161 DKVLLKTFHELNGKMVE 177
D+ + ELNG VE
Sbjct: 63 DQAV----AELNGTQVE 75
>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 = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 5/86 (5%)
Query: 69 MIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQ 128
+++G EA A+ Q+ S+ P A + V L ++T+ F++
Sbjct: 62 LLNGEQAEA--AINAFHQSRLRERELSVQLQPTDA---LLCVANLPPSLTQQQFEELVRP 116
Query: 129 FGIITDVVVMYDHNTQRPRGFGFITY 154
FG + ++Y T + +G+GF Y
Sbjct: 117 FGSLERCFLVYSERTGQSKGYGFAEY 142
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 5/86 (5%)
Query: 69 MIDGRTVEAKKAVPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQ 128
+++G EA A+ Q+ S+ P A + V L ++T+ F++
Sbjct: 64 LLNGEQAEA--AINAFHQSRLRERELSVQLQPTDA---LLCVANLPPSLTQQQFEELVRP 118
Query: 129 FGIITDVVVMYDHNTQRPRGFGFITY 154
FG + ++Y T + +G+GF Y
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEY 144
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITY 154
+ V L ++T+ F++ FG + ++Y T + +G+GF Y
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 144
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGIIT--------DVVVMYDHNTQRPRGFGFITYD 155
I+V GL +VT D +F Q G++ + + D T +P+G ++Y+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 8 LFIGGISWDTNEDRLRDYF-QAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
LF+G ++ D ++ L ++F + + ++ D+ TG ++G+GF+ F D +R + +
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 67 KHMIDG---RTVEAKKAVPR 83
G + V A+P+
Sbjct: 71 CQGAVGLGSKPVRLSVAIPK 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
KLF+G + ++ +R F+ FG + E +++ G ++G F+ F A A+ +
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG-PDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 67 KH 68
H
Sbjct: 73 LH 74
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+K+FVG L T+ D +K F+ FG I + V+ + +G F+ + + A + +
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTS-KGCAFVKFQT-HAEAQAAI 70
Query: 166 KTFH 169
T H
Sbjct: 71 NTLH 74
>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 = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 32/57 (56%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L++G +S+ T E+++ + F G++ + ++ D+ A GF F+ + A AE +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVL 164
T +++VGGL + + + FD+FG I + DH + F +I Y+S +A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTI----DH--VKGDSFAYIQYESLDAAQAAC 70
Query: 165 LK 166
K
Sbjct: 71 AK 72
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
KLF+G ++ +E+ + FQ FG + E +++ G ++G F+ F+ A+ +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 67 KH 68
H
Sbjct: 76 LH 77
Score = 28.9 bits (63), Expect = 7.2, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYDSEEAVDKVLL 165
+K+FVG L +E D + F FG+I + V+ + +G F+ + S +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS-KGCAFVKFSSHTEAQAAI- 73
Query: 166 KTFHELNG 173
H L+G
Sbjct: 74 ---HALHG 78
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 109 FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD 155
F+G L VTE K++F I + N +R +GFG+ ++
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 109 FVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFITYD 155
F+G L VTE K++F I + N +R +GFG+ ++
Sbjct: 23 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.6 bits (65), Expect = 4.4, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRA 42
KL +G IS LR F+ +G V+E I+KD A
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYA 47
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 29.3 bits (64), Expect = 4.4, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
E+ +LF+ D E L + F FG + E I+ GF F+ F + A
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 52
Query: 62 RVVMQKH 68
+ + + H
Sbjct: 53 KAIEEVH 59
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFGFIT-YDSEEAVDKVL 164
+ ++VG L+ VTE + F Q G ++ +H + P + F+ Y+ +A +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALA 73
Query: 165 LKTFHELNGKMVEVKRA-VPKELSPGPS 191
++ GK V+V A P GPS
Sbjct: 74 AMNGRKILGKEVKVNWATTPSSQKSGPS 101
>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 = 4.8, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 7 KLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVVMQ 66
K+F+G +S LR F+ G V+E ++KD + F+ A A+ + Q
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 67 KHMIDGRTVEAKK 79
++G+ V+ K+
Sbjct: 63 ---LNGKEVKGKR 72
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 29.3 bits (64), Expect = 5.2, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 91 RNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHNTQRPRGFG 150
R + H G ++FV V ES+ + F FG + +V ++ GF
Sbjct: 17 RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFA 68
Query: 151 FITYDSEEAVDKVLLKTFHELNGK 174
F+ ++ E+ K + E++GK
Sbjct: 69 FVEFEEAESAAKAI----EEVHGK 88
Score = 28.9 bits (63), Expect = 6.7, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 2 EMELGKLFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAE 61
E+ +LF+ D E L + F FG + E I+ GF F+ F + A
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAA 79
Query: 62 RVVMQKH 68
+ + + H
Sbjct: 80 KAIEEVH 86
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 93 NSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGIITDVVVMYDHN 142
+S G G K+ V L V+++D ++ F +FG + V YD +
Sbjct: 76 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 125
>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 = 28.5 bits (62), Expect = 8.9, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 8 LFIGGISWDTNEDRLRDYFQAFGEVLEAVIMKDRATGRARGFGFIVFADPAVAERVV 64
L++G +S+ T E+++ + F G++ + +IM A GF F+ + A AE +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDI-KKIIMGLDKMKTACGFCFVEYYSRADAENAM 76
>pdb|3UAQ|A Chain A, Crystal Structure Of The N-Lobe Domain Of Lactoferrin
Binding Protein B (Lbpb) Of Moraxella Bovis
pdb|3UAQ|B Chain B, Crystal Structure Of The N-Lobe Domain Of Lactoferrin
Binding Protein B (Lbpb) Of Moraxella Bovis
Length = 341
Score = 28.5 bits (62), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 81 VPRDDQNIQNRNNSSIHGSPGPARTKKIFVGGLASTVTESDFKKYFDQFGII-----TDV 135
VP D+ NI ++ H +P PA TK++ + +SD K F + G I D
Sbjct: 80 VPLDENNI-----TTAHTNPLPALTKELQERYEGGKIYQSDDKYKFVKAGWIFTGLRPDE 134
Query: 136 VVMYDHNTQRP----RGFGFITY 154
+ D +T +P +G G++ Y
Sbjct: 135 TIKTDEDTDQPKQYTKGDGYLYY 157
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 28.5 bits (62), Expect = 9.5, Method: Composition-based stats.
Identities = 25/107 (23%), Positives = 45/107 (42%), Gaps = 13/107 (12%)
Query: 98 GSPGPARTKKIFVGGLASTVTESDFKKYFDQF--GIITDVVVMYDHNTQRPRGFGFITYD 155
GS G + ++F+GG+ + + + G++ +V + + RGF F+ Y+
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60
Query: 156 SEEA---VDKVLLKTFHELNGKMVEVKRAVPK--------ELSPGPS 191
S A + L+ +L G + V A P+ E GPS
Sbjct: 61 SHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPS 107
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
0.315 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,227,571
Number of Sequences: 62578
Number of extensions: 539293
Number of successful extensions: 1106
Number of sequences better than 100.0: 157
Number of HSP's better than 100.0 without gapping: 127
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 284
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)