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= psy10320
(262 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 37/72 (51%), Positives = 48/72 (66%), Gaps = 3/72 (4%)
Query: 105 RYGPPTR-SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDM 163
RYGPP+R S++R++V L SWQDLKD MR+ G+VCYAD ++ GVVEF DM
Sbjct: 7 RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDM 64
Query: 164 KKALDKLDNAEL 175
A+ KLDN +
Sbjct: 65 TYAVRKLDNTKF 76
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/72 (51%), Positives = 48/72 (66%), Gaps = 3/72 (4%)
Query: 105 RYGPPTR-SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDM 163
RYGPP+R S++R++V L SWQDLKD MR+ G+VCYAD ++ GVVEF DM
Sbjct: 6 RYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDM 63
Query: 164 KKALDKLDNAEL 175
A+ KLDN +
Sbjct: 64 TYAVRKLDNTKF 75
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 65.1 bits (157), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 35/69 (50%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 108 PPTR-SDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKA 166
PPTR SD R++V L SWQDLKD MR+ G+VCYAD K G+VE+ DM+ A
Sbjct: 9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK--DGMGMVEYLRKEDMEYA 66
Query: 167 LDKLDNAEL 175
L KLD+ +
Sbjct: 67 LRKLDDTKF 75
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 63.9 bits (154), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 38/76 (50%), Positives = 50/76 (65%), Gaps = 3/76 (3%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGKS 61
KVY+G L G + +LE+ YG +R V I +N GF FVEFED RDA+DAV L+GK
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 62 LLGERVTVEIAKGIDR 77
+ G RV VE++ G+ R
Sbjct: 62 ICGSRVRVELSTGMPR 77
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 37/77 (48%), Positives = 49/77 (63%), Gaps = 3/77 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGK 60
KVY+G L + +LE+ YG +R V + +N GF FVEFED RDA DAV EL+G+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 61 SLLGERVTVEIAKGIDR 77
+L G RV VE++ G R
Sbjct: 134 TLCGCRVRVELSNGEKR 150
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 60.8 bits (146), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 34/75 (45%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELN 58
++Y+G LP +R +D+E YG IRD+ LKN F FVEFED RDA+DAVY +
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 82
Query: 59 GKSLLGERVTVEIAK 73
G G R+ VE +
Sbjct: 83 GYDYDGYRLRVEFPR 97
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE--GVVEFESSSDMK 164
GP +D R+ V NL + +D++D + G + D R VEFE D +
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAE 75
Query: 165 KALDKLDNAELNGRRIRL 182
A+ D + +G R+R+
Sbjct: 76 DAVYGRDGYDYDGYRLRV 93
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 60.8 bits (146), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 2/63 (3%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
++R++V L SWQDLKD MR+ G+VCYAD ++ GVVEF DM A+ KLDN
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDN 72
Query: 173 AEL 175
+
Sbjct: 73 TKF 75
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 36/77 (46%), Positives = 49/77 (63%), Gaps = 3/77 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGK 60
KVY+G L + +LE+ YG +R V + +N GF FVEFED RDA DAV +L+G+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 61 SLLGERVTVEIAKGIDR 77
+L G RV VE++ G R
Sbjct: 134 TLCGCRVRVELSNGEKR 150
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GGL + E+ LE+ YG+I +V++ GFGFV FE+ DA DA+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 57 LNGKSLLGERVTVEIA 72
+NGKS+ G ++ V+ A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDK 169
+L V LS + Q L+ + G++ K R R G V FE+ D K A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 170 LDNAELNGRRIRL 182
++ ++GR+IR+
Sbjct: 74 MNGKSVDGRQIRV 86
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 7/76 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K++IGGL E+ L+ +G I +V+L GF F+ FE+ DA +A ++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 58 NGKSLLGERVTVEIAK 73
NGKSL G+ + VE AK
Sbjct: 69 NGKSLHGKAIKVEQAK 84
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
+ T++++ P V+E +L + +G +++V + NGF FVEFE+ A A+ E++GK
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGK 88
Query: 61 SLLGERVTVEIAK 73
S + + V +K
Sbjct: 89 SFANQPLEVVYSK 101
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 42/70 (60%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
T++++ P V+E +L + +G +++V + NGF FVEFE+ A A+ E++GKS
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFA 64
Query: 64 GERVTVEIAK 73
+ + V +K
Sbjct: 65 NQPLEVVYSK 74
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 60/144 (41%), Gaps = 31/144 (21%)
Query: 39 FGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGW 98
FG+V+FE D + A+ EL G + G + +E KG D +ER R
Sbjct: 50 FGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGKDSKKERDAR-------------- 94
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFE 158
L+ +NL +V+ +LK+ E+ + + +EF+
Sbjct: 95 ----------------TLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFK 138
Query: 159 SSSDMKKALDKLDNAELNGRRIRL 182
+ +D +K ++ E++GR I L
Sbjct: 139 TEADAEKTFEEKQGTEIDGRSISL 162
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 4 TKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ + +
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN 70
Query: 63 LGERVTVEIAKGIDRSQ 79
G+++ +E++ R Q
Sbjct: 71 FGKKLILEVSSSNARPQ 87
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 9/78 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
K+++GG+P+ E +L ++ K +G + +V++ GFGF+ FED + D AV
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 56 ELNGKSLLGERVTVEIAK 73
++ ++G++V V+ A+
Sbjct: 70 NMHFHDIMGKKVEVKRAE 87
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
K++IG LP E+++ + YG++ + + +GFV ED A+DA+ L+ L
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 64 GERVTVEIAK 73
G + VE +K
Sbjct: 69 GVNINVEASK 78
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 79/184 (42%), Gaps = 32/184 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV---ILKNG----FGFVEFEDYRDADDAVYELN 58
+Y+G L + E L+++ + G I ++ I KN + FVE+ DA+ A+ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 59 GKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIV 118
GK + V + A +SQ+ DD + D + V
Sbjct: 63 GKQIENNIVKINWAF---QSQQSSS-------------------DDTFNLFV-GDLNVNV 99
Query: 119 ENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGR 178
++ + R +++D ++ G V + R G V F S D + A+D + +LNGR
Sbjct: 100 DDETLRNAFKDFPSYLS--GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157
Query: 179 RIRL 182
+R+
Sbjct: 158 PLRI 161
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/194 (20%), Positives = 81/194 (41%), Gaps = 34/194 (17%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDA 53
+ ++VY+G + Y + E + + +G I+ + + GF FVE+E A A
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 54 VYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD 113
+ ++N L G + V GR P G D+ R+
Sbjct: 87 LEQMNSVMLGGRNIKV------------GR---------PSNIGQAQPIIDQLAEEARAF 125
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALD 168
+R+ V ++ +S D+K G++ A + +H+ G +E+E + + A+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 169 KLDNAELNGRRIRL 182
++ +L G+ +R+
Sbjct: 186 SMNLFDLGGQYLRV 199
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K++I GLP+ + +LE+ K +G ++D+ L G +VE+E+ A AV ++
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 58 NGKSLLGERVTVEIA 72
+G ++ + V I+
Sbjct: 79 DGMTIKENIIKVAIS 93
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 61/144 (42%), Gaps = 31/144 (21%)
Query: 39 FGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGW 98
FG+V+FE D + A+ EL G + G + +E KG D + R R
Sbjct: 56 FGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR-------------- 100
Query: 99 GHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFE 158
L+ +NLS ++ +LK+ E+ + + +EF+
Sbjct: 101 ----------------TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFK 144
Query: 159 SSSDMKKALDKLDNAELNGRRIRL 182
S +D +K L++ AE++GR + L
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSL 168
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 107 GPPTRSDHRLIVENLSSRVSWQDLKDFMRQV---GEVCYADAHK-RHRNEGVVEFESSSD 162
G + + L + NL+ S +LK + ++ ++ D +R G V+FES+ D
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66
Query: 163 MKKALDKLDNAELNGRRIRL 182
++KAL+ L ++ G I+L
Sbjct: 67 LEKALE-LTGLKVFGNEIKL 85
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ + +
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMN 82
Query: 63 LGERVTVEIA 72
G+++ +E++
Sbjct: 83 FGKKLILEVS 92
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ + +
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN 82
Query: 63 LGERVTVEIA 72
G+++ +E++
Sbjct: 83 FGKKLILEVS 92
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 2 VGTKVYIGGLPYG-VRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
+ ++V+IG L V++ D+E YGR+ + G+ FV++ + R A AV NG+
Sbjct: 26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 61 SLLGERVTVEIA 72
L G+ + + +A
Sbjct: 86 VLAGQTLDINMA 97
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-----GFGFVEFEDYRDADDAVYELN 58
++++ +P+ R+ DL + +G+I DV I+ N GFGFV FE+ DAD A +L+
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90
Query: 59 GKSLLGERVTVEIAKG 74
G + G ++ V A
Sbjct: 91 GTVVEGRKIEVNNATA 106
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE---GVVEFESSSDMKKALDKLD 171
RL V N+ R DL+ Q G++ + R G V FE+S+D +A +KL
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 90
Query: 172 NAELNGRRIRL 182
+ GR+I +
Sbjct: 91 GTVVEGRKIEV 101
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVG-EVCYADAHKRHRN-EGVVEFESSSDMKKALDKLD 171
+R+ ++NL SWQDLKD R+ E ++ + R + G +EF S + +AL++L+
Sbjct: 29 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88
Query: 172 NAELNGRRIRLIED 185
N E G I + D
Sbjct: 89 NIEFRGSVITVERD 102
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-----GFGFVEFEDYRDADDAVYELN 58
++++ +P+ R+ DL + +G+I DV I+ N GFGFV FE+ DAD A +L+
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 59 GKSLLGERVTVEIAKG 74
G + G ++ V A
Sbjct: 77 GTVVEGRKIEVNNATA 92
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE---GVVEFESSSDMKKALDKLD 171
RL V N+ R DL+ Q G++ + R G V FE+S+D +A +KL
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 172 NAELNGRRIRL 182
+ GR+I +
Sbjct: 77 GTVVEGRKIEV 87
>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 = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 39/194 (20%), Positives = 79/194 (40%), Gaps = 34/194 (17%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDA 53
+ +VY+G + Y + E + + +G I+ + + GF FVE+E A A
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 71
Query: 54 VYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD 113
+ ++N L G + V GR P G D+ R+
Sbjct: 72 LEQMNSVMLGGRNIKV------------GR---------PSNIGQAQPIIDQLAEEARAF 110
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALD 168
+R+ V ++ +S D+K G++ + +H+ G +E+E + + A+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 169 KLDNAELNGRRIRL 182
++ +L G+ +R+
Sbjct: 171 SMNLFDLGGQYLRV 184
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
K+++G + ++L + GR+ + + + FV E DA A+ +LNGK + G
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKG 70
Query: 65 ERVTVEIA-KGIDRS 78
+R+ VE++ KG +S
Sbjct: 71 KRINVELSTKGQKKS 85
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + ++++E+ YGRI + + G GF+ F+ +A++A+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ LG E +TV+ A
Sbjct: 153 NGQKPLGAAEPITVKFA 169
Score = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + + + G I RD I G+GFV + D DAD A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGLPY-GVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++++IG LP V + DL + YG I + +KN FGF++F++ + DA+ + +
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN 62
Query: 63 LGERVTVEIA 72
G+++ +E++
Sbjct: 63 FGKKLILEVS 72
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
T + + L Y L + + YGR+ DV + GF FV F D RDA+DA+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 56 ELNGKSLLGERVTVEIAK 73
++G L G + V++A+
Sbjct: 108 AMDGAVLDGRELRVQMAR 125
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALD 168
L V+NL+ R S L+ + G V D + K R V F D + A+D
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 169 KLDNAELNGRRIRL 182
+D A L+GR +R+
Sbjct: 108 AMDGAVLDGRELRV 121
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + ++++E+ YGRI + + G GF+ F+ +A++A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ LG E +TV+ A
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/172 (23%), Positives = 67/172 (38%), Gaps = 44/172 (25%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNGKS 61
+++++G LP + E ++ K + YG+ +V + GFGF+ E A+ A EL+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 82
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENL 121
L G+++ V A H L V NL
Sbjct: 83 LRGKQLRVRFA--------------------------CHSAS------------LTVRNL 104
Query: 122 SSRVSWQDLKDFMRQVGE----VCYADAHKRHRNEGVVEFESSSDMKKALDK 169
VS + L++ G+ V D R +G+VEF +KALD+
Sbjct: 105 PQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDR 156
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/172 (23%), Positives = 66/172 (38%), Gaps = 44/172 (25%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNGKS 61
++++G LP + E D ++ + YG +V + GFGF+ E A+ A EL+G
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI 82
Query: 62 LLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENL 121
L + + A +G+ L V+NL
Sbjct: 83 LKSRPLRIRFAT------------HGAA--------------------------LTVKNL 104
Query: 122 SSRVSWQDLKDFMRQVGE----VCYADAHKRHRNEGVVEFESSSDMKKALDK 169
S VS + L+ Q G V D R +G VEF + +KAL++
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVG-EVCYADAHKRHRN-EGVVEFESSSDMKKALDKLD 171
+R+ ++NL SWQDLKD R+ E ++ + R + G +EF S + +AL++L+
Sbjct: 7 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 66
Query: 172 NAELNGRRIRLIED 185
N E G I + D
Sbjct: 67 NIEFRGSVITVERD 80
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
T + + L Y L + + YGR+ DV + GF FV F D RDA+DA+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 56 ELNGKSLLGERVTVEIAK 73
++G L G + V++A+
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALD 168
L V+NL+ R S L+ + G V D + K R V F D + A+D
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 169 KLDNAELNGRRIRL 182
+D A L+GR +R+
Sbjct: 131 AMDGAVLDGRELRV 144
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADA---HKRHRNEGVVEFESSSDMKKALDKLD 171
++ V NL +W+ LKD + G V YAD + + + GVV+FES ++A ++
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 172 NAELNGRRI 180
+L+GR I
Sbjct: 70 GMKLSGREI 78
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI--RDVILKNG----FGFVEFEDYRDADDAVYEL 57
++++ LP+ + L+ G + D+ ++NG G V+FE A+ A +
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 58 NGKSLLGERVTVEI 71
NG L G + V I
Sbjct: 69 NGMKLSGREIDVRI 82
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADA---HKRHRNEGVVEFESSSDMKKALDKLDN 172
+ V NL +W+ LKD + G V YAD + + + GVV+FES ++A ++
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 67
Query: 173 AELNGRRI 180
+L+GR I
Sbjct: 68 MKLSGREI 75
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI---RDVI-----LKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + +++LE+ YGRI R ++ + G GF+ F+ +A++A+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ G E +TV+ A
Sbjct: 151 NGQKPSGATEPITVKFA 167
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + + G I RD I G+GFV + D +DA+ A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 11/92 (11%)
Query: 1 MVGTK--VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDA 50
M TK +Y+GGL V ++ L +G I D+ + GF FVEFE DA
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 51 DDAVYELNGKSLLGERVTVEIAKGIDRSQERG 82
A+ +N L G + V +AK + R +E G
Sbjct: 68 AAAIDNMNESELFGRTIRVNLAKPM-RIKESG 98
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++HR VEFE + D A+D ++ +EL GR IR+
Sbjct: 51 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVY 55
+ VY+ LP+ + DL + YG++ V I+K+ G F+ F D A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 56 ELNGKSLLGERVTVEIA 72
+N K L G + IA
Sbjct: 77 AINNKQLFGRVIKASIA 93
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
TK+++GGLPY + L K+ +G+G I + ++ G+GFV D A+ A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 56 ELN 58
+ N
Sbjct: 78 DPN 80
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNGKS 61
+++++G LP + E ++ K + YG+ +V + GFGF+ E A+ A EL+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 62 LLGERVTVEIA 72
L G+++ V A
Sbjct: 76 LRGKQLRVRFA 86
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 39/194 (20%), Positives = 76/194 (39%), Gaps = 34/194 (17%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDV--------ILKNGFGFVEFEDYRDADDA 53
+ +VY+G + Y + E + + +G I+ + GF FVE+E A A
Sbjct: 11 IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLA 70
Query: 54 VYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSD 113
+ + N L G + V GR P G D+ R+
Sbjct: 71 LEQXNSVXLGGRNIKV------------GR---------PSNIGQAQPIIDQLAEEARAF 109
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALD 168
+R+ V ++ +S D+K G++ + +H+ G +E+E + + A+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 169 KLDNAELNGRRIRL 182
+ +L G+ +R+
Sbjct: 170 SXNLFDLGGQYLRV 183
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 14/78 (17%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV-- 54
++Y+ + + + D++ + +G+I+ L G+GF+E+E + + DAV
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 55 ---YELNGKSL-LGERVT 68
++L G+ L +G+ VT
Sbjct: 171 XNLFDLGGQYLRVGKAVT 188
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 3/98 (3%)
Query: 1 MVGTKV-YIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNG 59
M KV ++ L V E LEK +G++ V + F+ F++ A A+ E+NG
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNG 67
Query: 60 KSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRG 97
K L GE + + AK D Q+R R A P G
Sbjct: 68 KDLEGENIEIVFAKPPD--QKRKERKAQRQAASGPSSG 103
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYELNG 59
+ L Y L + + YGR+ DV + GF FV F D RDA DA ++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 60 KSLLGERVTVEIAK 73
L G + V++A+
Sbjct: 78 AELDGRELRVQVAR 91
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV----CYADAH-KRHRNEGVVEFESSSDMKKALDKL 170
L V+NL+ R S L+ + G V + H K R V F D + A +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 171 DNAELNGRRIRL 182
D AEL+GR +R+
Sbjct: 76 DGAELDGRELRV 87
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGL-PYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++V+IG L V++ D+E YG+I + GF FV++ + R+A AV +G+ +
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMI 75
Query: 63 LGERVTVEIA 72
G+ + + +A
Sbjct: 76 AGQVLDINLA 85
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+YI GLP + ++D+E +GRI + L G F+ F+ +A++A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 58 NGKSLLG--ERVTVEIAKGID 76
NG G E +TV+ A ++
Sbjct: 151 NGHKPPGSSEPITVKFAANLE 171
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + +L G IRD + + G+GFV + +DA+ A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 83 EGLNGQDLMGQPISVD 98
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 67 EGLNGQDLMGQPISVD 82
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 82 EGLNGQDLMGQPISVD 97
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 69 EGLNGQDLMGQPISVD 84
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNG 59
+ GL ERDL + YG I DV + GF FV FE+ DA +A NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 60 KSLLGERVTVEIA 72
L G R+ V+ +
Sbjct: 80 MELDGRRIRVDFS 92
Score = 35.0 bits (79), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V LS + +DL++ + G + Y +R R V FE+ D K+A ++
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 171 DNAELNGRRIRL 182
+ EL+GRRIR+
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 67 EGLNGQDLMGQPISVD 82
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ G+ E D+ YG I+++ L G+ VE+E Y++A A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 55 YELNGKSLLGERVTVE 70
LNG+ L+G+ ++V+
Sbjct: 67 EGLNGQDLMGQPISVD 82
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 1 MVGTK--VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDA 50
M TK +Y+GGL V ++ L +G I D+ + GF FVEFE DA
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 51 DDAVYELNGKSLLGERVTVEIAK 73
A+ +N L G + V +AK
Sbjct: 63 AAAIDNMNESELFGRTIRVNLAK 85
Score = 34.3 bits (77), Expect = 0.063, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++HR VEFE + D A+D ++ +EL GR IR+
Sbjct: 46 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 81
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKS 61
GL ERDL + YG I DV + GF FV FE+ DA +A NG
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 62 LLGERVTVEIA 72
L G R+ V+ +
Sbjct: 113 LDGRRIRVDFS 123
Score = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V LS + +DL++ + G + Y +R R V FE+ D K+A ++
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 171 DNAELNGRRIRL 182
+ EL+GRRIR+
Sbjct: 109 NGMELDGRRIRV 120
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 58 NGKSLLGERVTVEIA 72
N L G + V +A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++HR VEFE + D A+D ++ +EL GR IR+
Sbjct: 102 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
++Y+G L + + E L + +GRI + L G+GF+ F D A A+ +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 57 LNGKSLLGERVTV 69
LNG L G + V
Sbjct: 88 LNGFELAGRPMKV 100
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNG 59
+ GL ERDL + YG I DV + GF FV FE+ DA +A NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 60 KSLLGERVTVEIA 72
L G R+ V+ +
Sbjct: 77 MELDGRRIRVDFS 89
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V LS + +DL++ + G + Y +R R V FE+ D K+A ++
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 171 DNAELNGRRIRL 182
+ EL+GRRIR+
Sbjct: 75 NGMELDGRRIRV 86
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+YI GLP + ++D+E +GRI + L G F+ F+ +A++A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 58 NGKSLLG--ERVTVEIAKGID 76
NG G E +TV A ++
Sbjct: 151 NGHKPPGSSEPITVXFAANLE 171
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + +L G IRD + + G+GFV + +DA+ A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 58 NGKSLLGERVTVEIAK 73
N L G + V +AK
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 34.3 bits (77), Expect = 0.069, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++HR VEFE + D A+D ++ +EL GR IR+
Sbjct: 44 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRD--VILKNGFGFVEFEDYRDADDAVYELNGKS 61
VY GG+ G+ ++ + + +G+I + V + G+ FV F + A A+ +NG +
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTT 85
Query: 62 LLGERV 67
+ G V
Sbjct: 86 IEGHVV 91
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDV---------ILKNGFGFVEFEDYRDAD 51
M TKV+IG L V + + + YG+I+ + L G+ +VEFE+ +A+
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 52 DAVYELNGKSLLGERVT 68
A+ ++G + G+ +T
Sbjct: 62 KALKHMDGGQIDGQEIT 78
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
V++G L + D++ +GRI D ++K+ G+GFV F + DA++A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 58 NGKSLLGERVTVEIA 72
G+ L G ++ A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 11 LPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKSL 62
+P V E L + + YG I V + G+GFV+F+ A A+ LNG ++
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109
Query: 63 LGERVTVEIA 72
L +R+ V +A
Sbjct: 110 LNKRLKVALA 119
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
V+ L +R RDLE F G++RDV + G +VEF + + A+ L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 58 NGKSLLGERVTVEIAKG 74
G+ LLG + V+ ++
Sbjct: 87 TGQRLLGVPIIVQASQA 103
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKS 61
GL ERDL + YG I DV + GF FV FE+ DA +A NG
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 62 LLGERVTVE 70
L G R+ V
Sbjct: 82 LDGRRIRVS 90
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V LS + +DL++ + G + Y +R R V FE+ D K+A ++
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 171 DNAELNGRRIRL 182
+ EL+GRRIR+
Sbjct: 78 NGMELDGRRIRV 89
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 12/69 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV--- 54
++IGGL + ++DL+ + +G + D LK GFGFV F++ D +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 55 -YELNGKSL 62
++LNGK +
Sbjct: 62 EHKLNGKVI 70
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV--CYADAHK---RHRNEGVVEFESSSDMKKALDKL 170
+ + LS + +DLKD+ + GEV C R R G V F+ S + K +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 171 DNAELNGRRI 180
++ +LNG+ I
Sbjct: 62 EH-KLNGKVI 70
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
R+ L+ +NLS ++ +LK+ E+ + + +EF+S +D +K L++
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 171 DNAELNGRRIRL 182
AE++GR + L
Sbjct: 74 QGAEIDGRSVSL 85
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K++IGGL + E L + + +G++ D ++ GFGFV F + D A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
+ +Y+G L + + E L + +G+I +++L G+GF+ F D A A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 56 ELNGKSLLGERVTV 69
+LNG L G + V
Sbjct: 66 QLNGFELAGRPMRV 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 8/91 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
V++G +PY E L+ G + R+ G+GF E++D A A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
NG+ G + V+ A +E G G+
Sbjct: 71 NGREFSGRALRVDNAASEKNKEELKSLGTGA 101
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKK 165
RS + V N+ + + LKD +VG V Y + + G E++
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 166 ALDKLDNAELNGRRIRL 182
A+ L+ E +GR +R+
Sbjct: 66 AMRNLNGREFSGRALRV 82
>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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+Y+GGL V ++ L +G I D+ + GF FVEFE DA A+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 58 NGKSLLGERVTVEIA 72
N L G + V +A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 34.3 bits (77), Expect = 0.070, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
++HR VEFE + D A+D ++ +EL GR IR+
Sbjct: 41 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 76
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNG 59
G+KV++G + +L++F YG + DV + F FV F D D L G
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFAD----DKVAQSLCG 66
Query: 60 KSLLGERVTVEIAKG 74
+ L+ + ++V I+
Sbjct: 67 EDLIIKGISVHISNA 81
>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 = 0.018, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVYE 56
T +YI LP + E++LE +K +G++ IL++ G GF E + +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 57 LNGK 60
NGK
Sbjct: 86 FNGK 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
V++G L + D++ +G+I D ++K+ G+GFV F + DA++A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 58 NGKSLLGERVTVEIA 72
G+ L G ++ A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRD-----------VILKNGFGFVEFEDYRDADDAV 54
++I L + E L+ G I+ V+L GFGFVE++ A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 55 YELNGKSLLGERVTVEIA 72
+L G ++ G ++ V I+
Sbjct: 68 KQLQGHTVDGHKLEVRIS 85
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV--------VEFESSSDMKKAL 167
L ++NL+ + + LK +VG + K+ GV VE++ +KAL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 168 DKLDNAELNGRRIRL 182
+L ++G ++ +
Sbjct: 68 KQLQGHTVDGHKLEV 82
>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 = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 13/78 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR--DVI------LKNGFGFVEFEDYRDADDAVYE 56
K++IGGLP + + +++ + +G ++ +++ L G+ F E+ D D A+
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 57 LNG-----KSLLGERVTV 69
LNG K LL +R +V
Sbjct: 176 LNGMQLGDKKLLVQRASV 193
>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 = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+++ + Y E L + + YG I+ + + G+ F+E+E RD A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 58 NGKSLLGERVTVEIAKG 74
+GK + G RV V++ +G
Sbjct: 165 DGKKIDGRRVLVDVERG 181
>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 = 0.032, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---------GFGFVEFEDYRDADDAV 54
+K+ + +P+ +R++ + +G ++ V L GFGFV+F +DA A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 55 YEL-NGKSLLGERVTVEIA 72
L + L G R+ +E A
Sbjct: 76 NALCHSTHLYGRRLVLEWA 94
Score = 34.7 bits (78), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKR------HRNEGVVEFESSS 161
P ++ +++V N+ + + +++++ GE+ K+ HR G V+F +
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 162 DMKKALDKL-DNAELNGRRIRL 182
D KKA + L + L GRR+ L
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVL 91
>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 = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR--DVI------LKNGFGFVEFEDYRDADDAVYE 56
K++IGGLP + + +++ + +G ++ +++ L G+ F E+ D D A+
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 57 LNGKSLLGERVTVE 70
LNG L +++ V+
Sbjct: 158 LNGMQLGDKKLLVQ 171
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR--DVI------LKNGFGFVEFEDYRDADDAVYE 56
K++IGGLP + + +++ + +G ++ +++ L G+ F E+ D D A+
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 57 LNGKSLLGERVTVE 70
LNG L +++ V+
Sbjct: 156 LNGMQLGDKKLLVQ 169
>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 = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 11/70 (15%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV- 54
K++IGGL + E +L ++ YG + D+ I+K+ GFGF+ FE D+ V
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 55 --YELNGKSL 62
+ L+GK +
Sbjct: 64 TQHILDGKVI 73
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ VR ++ E+F +G I D L GFGFV + D DA D V +
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDRVCQ 147
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.0 bits (79), Expect = 0.042, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR--DVI------LKNGFGFVEFEDYRDADDAVYE 56
K++IGGLP + + +++ + +G ++ +++ L G+ F E+ D D A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 57 LNGKSLLGERVTVEIA 72
LNG L +++ V+ A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 29 RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDR 77
+IRD + FV F + DA +A+ LNGK L G + V +AK +D+
Sbjct: 49 KIRD------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFED 46
K+++GGL + + L + YG + D VI+K+ GFGFV+F+D
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 12/91 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV-- 54
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 55 --YELNGKSLLGERVTVEIAKGIDRSQERGR 83
+ +NG + + + S +RGR
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 34.7 bits (78), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 12/91 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV-- 54
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 55 --YELNGKSLLGERVTVEIAKGIDRSQERGR 83
+ +NG + + + S +RGR
Sbjct: 165 KYHTVNGHNCEVRKALSKQEMASASSSQRGR 195
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.7 bits (78), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 12/91 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV-- 54
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 55 --YELNGKSLLGERVTVEIAKGIDRSQERGR 83
+ +NG + + + S +RGR
Sbjct: 167 KYHTVNGHNCEVRKALSKQEMASASSSQRGR 197
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + + + G I RD I G+GFV + D DAD A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>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 = 34.3 bits (77), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+++ + Y E L + + YG I+ + + G+ F+E+E RD A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 58 NGKSLLGERVTVEIAKG 74
+GK + G RV V++ +G
Sbjct: 165 DGKKIDGRRVLVDVERG 181
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.9 bits (76), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
VY+G +PY E + G + ++ + G+ F+EF D + AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 58 NGKSL 62
NG L
Sbjct: 65 NGYQL 69
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KNGFGFVEFEDYRDADDAVYELNG 59
+Y+ L G+ + L K +G I + GFGFV F +A AV E+NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 60 KSLLGERVTVEIAKGIDRSQER 81
+ + + + V +A+ R +ER
Sbjct: 78 RIVATKPLYVALAQ---RKEER 96
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDY 47
+ + GLP+ E+DL+++ +G + V +K GFGFV F +Y
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFED 46
K ++GGL + ++DL+ + +G + D +K GFGF+ F+D
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDK 169
+ V LS S +DLKD+ + GEV R R G + F+ ++ ++K LD+
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 170 LDNAELNGRRI 180
++ L+GR I
Sbjct: 73 KEH-RLDGRVI 82
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
VY+G +PY E + G + ++ + G+ F+EF D + AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 58 NGKSL 62
NG L
Sbjct: 66 NGYQL 70
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGE 65
+++ L V E LEK +G++ V + FV FED A A+ E+NGK + GE
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMNGKEIEGE 77
Query: 66 RVTVEIAKGIDR 77
+ + +AK D+
Sbjct: 78 EIEIVLAKPPDK 89
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV-CYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
L++ NLS + + L++ + + + + + + +EF S D K+AL+ + E
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE 77
Query: 175 LNGRRIRL 182
+ GR IRL
Sbjct: 78 IEGRAIRL 85
>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 = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
D + V++ + R +++D ++ G V + R G V F S D + A+D +
Sbjct: 8 DLNVNVDDETLRNAFKDFPSYLS--GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 65
Query: 173 AELNGRRIRL 182
+LNGR +R+
Sbjct: 66 QDLNGRPLRI 75
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELNGK 60
+YI LPY + ++ YG IR + + N G +V +ED DA +A L+G
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 61 SLLGERVTV 69
++ + V
Sbjct: 81 NVCNRYLVV 89
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELNG 59
+YI LPY + ++ YG IR + + N G +V +ED DA +AV L+G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 7/85 (8%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K+++G L E D+ + + +G I + + G FV+F + +A A++ L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 58 NGKSLLGERVTVEIAKGIDRSQERG 82
+G + + + K D +E G
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKESG 101
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGVVEFESSSDMKKA 166
R + V NL +V W+ LK+ G V AD + + R G V FE S + +A
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQA 72
Query: 167 LDKLDNAELNGRRIRLIED 185
+ + L R + + D
Sbjct: 73 ISMFNGQLLFDRPMHVKMD 91
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.7 bits (73), Expect = 0.20, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN-----GFGFVEFEDYRDADDAVYEL 57
+YI GL G ++DL K + YG+I + ++ K G+GFV+F+ A AV L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 58 NGKSL 62
+
Sbjct: 68 KASGV 72
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 35/71 (49%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKS 61
TK+++G + ++L + YG + + + + FV E DA +A+ L+
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTE 68
Query: 62 LLGERVTVEIA 72
G+R+ V+++
Sbjct: 69 FQGKRMHVQLS 79
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
++ +L V N+S + Q+L+ + G V D K + V E + D +A+ L
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGL 64
Query: 171 DNAELNGRRIRL 182
DN E G+R+ +
Sbjct: 65 DNTEFQGKRMHV 76
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KNGFGFVEFEDYRDADDAVYELNG 59
+Y+G L V E + + G + + + + FVEF ++RDA A+ +NG
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 60 KSLLGERVTVEIAKGIDRSQERG 82
+ +LG+ V V A SQ+ G
Sbjct: 78 RKILGKEVKVNWAT-TPSSQKSG 99
>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 = 32.7 bits (73), Expect = 0.21, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
VY+G +PY E + G + ++ + G+ F+EF D + AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 58 NGKSL 62
NG L
Sbjct: 67 NGYQL 71
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
G +++ + +E ++++ YG I+++ L G+ VE+E ++ A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 55 YELNGKSLLGERVTVE 70
LNG ++G+ + V+
Sbjct: 86 EALNGAEIMGQTIQVD 101
>pdb|3ITG|A Chain A, Structure The Proline Utilization A Proline Dehydrogenase
Domain (Puta86-630) Inactivated With N-Propargylglycine
pdb|3ITG|B Chain B, Structure The Proline Utilization A Proline Dehydrogenase
Domain (Puta86-630) Inactivated With N-Propargylglycine
Length = 602
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 78 SQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRV------SWQDLK 131
+Q+ G+ G + P PR +GH RD+ G ++HRL +LSS + WQ L
Sbjct: 507 AQQEGQTGLPHPKIPLPRDLYGHGRDNSAGLDLANEHRL--ASLSSALLNSALQKWQALP 564
Query: 132 DFMRQVG 138
+ V
Sbjct: 565 MLEQPVA 571
>pdb|1TIW|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With
L-Tetrahydro-2-Furoic Acid
pdb|1TJ0|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Co-Crystallized With L-Lactate
pdb|1TJ1|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With L-Lactate
pdb|2FZN|A Chain A, Structure Of The E. Coli Puta Proline Dehydrogenase Domain
Reduced By Dithionite And Complexed With Proline
pdb|2FZM|A Chain A, Structure Of The E. Coli Puta Proline Dehydrogenase Domain
Reduced By Dithionite And Complexed With So2
Length = 602
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 78 SQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRV------SWQDLK 131
+Q+ G+ G + P PR +GH RD+ G ++HRL +LSS + WQ L
Sbjct: 507 AQQEGQTGLPHPKIPLPRDLYGHGRDNSAGLDLANEHRL--ASLSSALLNSALQKWQALP 564
Query: 132 DFMRQVG 138
+ V
Sbjct: 565 MLEQPVA 571
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAV 54
G ++I LP + DL +G + + L FGFV F++ A A+
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 55 YELNGKSLLGERVTVEIAK 73
+NG + +R+ V++ K
Sbjct: 100 KAMNGFQVGTKRLKVQLKK 118
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 4 TKVYIGGLP-YGVRERDLEKFVKGYGRIRDVI--------LKN-GFGFVEFEDYRDADDA 53
+++IGG+P RE LE+ K + DVI +KN GF FVE+E +R A A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
+Y+G L + E + + G I+ +I+ GF FVE+ DA++A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 56 ELNGKSL 62
+NG L
Sbjct: 78 YINGTRL 84
>pdb|1TJ2|A Chain A, Crystal Structure Of E. Coli Puta Proline Dehydrogenase
Domain (Residues 86-669) Complexed With Acetate
Length = 584
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 78 SQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRV------SWQDLK 131
+Q+ G+ G + P PR +GH RD+ G ++HRL +LSS + WQ L
Sbjct: 507 AQQEGQTGLPHPKIPLPRDLYGHGRDNSAGLDLANEHRL--ASLSSALLNSALQKWQALP 564
Query: 132 DFMRQVG 138
+ V
Sbjct: 565 MLEQPVA 571
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+Y+G L Y +++ +G++ +V L GFGFVE ++ +A+ +L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 58 NGKSLLGERVTV 69
+ +G + V
Sbjct: 63 DNTDFMGRTIRV 74
>pdb|1K87|A Chain A, Crystal Structure Of E.coli Puta (residues 1-669)
Length = 669
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 78 SQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRV------SWQDLK 131
+Q+ G+ G + P PR +GH RD+ G ++HRL +LSS + WQ L
Sbjct: 592 AQQEGQTGLPHPKIPLPRDLYGHGRDNSAGLDLANEHRL--ASLSSALLNSALQKWQALP 649
Query: 132 DFMRQVG 138
+ V
Sbjct: 650 MLEQPVA 656
>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 = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAV 54
GT + + LP + +L G IRD + + G+GFV + +DA+ A+
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 55 YELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 79 NTLNGLRLQSKTIKVSYAR 97
>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 = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 10/92 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV 54
G +++ + +E ++++ YG I+++ L G+ VE+E ++ A A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 55 YELNGKSLLGERVTVE--IAKGIDRSQERGRR 84
LNG ++G+ + V+ KG R ++ +R
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163
>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 = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
VY+G + YG +DLE G I + + G+ ++EF + D AV
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K+++G L E D+ + + +G I + + G FV++ + +A A+ L
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 58 NGKSLLGERVTVEIAKGIDRSQERG 82
+G + + + K D +E G
Sbjct: 77 HGSQTMPGASSSLVVKFADTDKESG 101
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 5 KVYIGGLPYGVRERDLEKFV--KGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
K+YIG L V DL + + V+LK+G+ FV++ D A A+ L+GK
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 11/58 (18%)
Query: 35 LKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAP 92
+ G+ FVEF D A+ ++++NGK L G +R + Y +Y P
Sbjct: 50 IPAGYCFVEFADLATAEKCLHKINGKPLPGA-----------TPAKRFKLNYATYSGP 96
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVI-----LKNGFGFVEFEDYRDADDAVYELNGK 60
+++ GL E L++ G R R V GFGFV+F DA A +
Sbjct: 18 LFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG 77
Query: 61 SLLGERVTVEIAK 73
+ G +VT++ AK
Sbjct: 78 EIDGNKVTLDWAK 90
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.6 bits (70), Expect = 0.42, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELNG 59
+YI LPY + ++ YG IR + + N G +V +ED DA +A L+G
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 73
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR------DVILK--NGFGFVEFEDYRDADDAVYE 56
++++ L Y E DLEK YG + D + K GF FV F A A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 57 LNGKSLLGERVTV 69
++G+ G + V
Sbjct: 70 VDGQVFQGRMLHV 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 31.2 bits (69), Expect = 0.55, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFE 45
+++GGL D++ + + +G++ D +L GFGFV FE
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE 49
Score = 28.5 bits (62), Expect = 4.0, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALD 168
+ V LS + +D+K + Q G+V + RHR G V FES ++K +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
+Y+G L + E + + G I+ +I+ GF FVE+ DA++A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGR 83
+NG L + + G ++ GR
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKEGRQYGR 127
>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 = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAV 54
G ++I LP ++DL + +G + + L FGFV +++ A A+
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 55 YELNGKSLLGERVTVEI 71
+NG + +R+ V++
Sbjct: 85 QSMNGFQIGMKRLKVQL 101
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNGK 60
+ V++G + E +L +F YG + DV + F FV F D D L G+
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFAD----DQIAQSLCGE 61
Query: 61 SLLGERVTVEIAK 73
L+ + ++V I+
Sbjct: 62 DLIIKGISVHISN 74
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 14/85 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK---------NGFGFVEFEDYRDADDAVYE 56
++G LPY V E +++F +G I V L GFG+ EFED D+ +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED-LDSLLSALS 75
Query: 57 LNGKSLLGERVTVEIAKGIDRSQER 81
LN +SL +R+ V++A D++Q++
Sbjct: 76 LNEESLGNKRIRVDVA---DQAQDK 97
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGF---GFVEFEDYRDADDAVYELN 58
+ VY+G LP R DL++ ++ G + + G F+ + D A AV L
Sbjct: 18 LAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQ 77
Query: 59 GKSLLGERVTVEIAK 73
G L + + V +A+
Sbjct: 78 GLRLGTDTLRVALAR 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.8 bits (68), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVY 55
T + + LP + +R+L + G I I+++ G+ FV+F D+ A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG ++ +R+ V A+
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVY 55
VY+GGL V E L + G + + + G+GFVEF DAD A+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 56 ELNGKSLLGERVTVEIAKGIDRS 78
++ L G+ + V A +++
Sbjct: 76 IMDMIKLYGKPIRVNKASAHNKN 98
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH--KRHRNEGV--VEFESSSDMKKALDKL 170
+L+V NL VS D+++ + G + A H + R+ G V FE +D KA+ +
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 171 DNAELNGRRIRL 182
+ L+GR + +
Sbjct: 90 NGVPLDGRPMNI 101
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYEL 57
K+ + L +GV + D+++ +G ++ + G V FE DA A+ +
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 58 NGKSLLGERVTVEI 71
NG L G + +++
Sbjct: 90 NGVPLDGRPMNIQL 103
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 9/76 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI-------RDVILKN--GFGFVEFEDYRDADDAVYE 56
++IG L + E+ L +G I RD N G+ F+ F + +D A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 57 LNGKSLLGERVTVEIA 72
+NG+ L +TV A
Sbjct: 68 MNGQYLCNRPITVSYA 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVY 55
T + + LP + +R+L + G I I+++ G+ FV+F D+ A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG ++ +R+ V A+
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
>pdb|3E2Q|A Chain A, Crystal Structure Reduced Puta86-630 Mutant Y540s
Complexed With Trans-4-Hydroxy-L-Proline
pdb|3E2R|A Chain A, Crystal Structure Puta86-630 Mutant Y540s Complexed With
L-Tetrahydro- 2-Furoic Acid
pdb|3E2S|A Chain A, Crystal Structure Reduced Puta86-630 Mutant Y540s
Complexed With L- Proline
Length = 551
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 78 SQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRL 116
+Q+ G+ G + P PR +GH RD+ G ++HRL
Sbjct: 507 AQQEGQTGLPHPKIPLPRDLYGHGRDNSAGLDLANEHRL 545
>pdb|3LKU|A Chain A, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
N-Terminal Fragment Of Get5
pdb|3LKU|C Chain C, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
N-Terminal Fragment Of Get5
pdb|3LKU|E Chain E, Crystal Structure Of S. Cerevisiae Get4 In Complex With An
N-Terminal Fragment Of Get5
Length = 292
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 1 MVGTKVYIGGLPYGVRERD--LEKFVKGYGRIRDVILKNGFGFVEFEDYRDAD 51
+V ++I + + +D LE+F++ + + I KNG+ V FEDY D +
Sbjct: 186 LVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLN 238
>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 = 30.4 bits (67), Expect = 0.99, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + +L G IRD + + G+GFV + +DA+ A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|2WPV|A Chain A, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
pdb|2WPV|C Chain C, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
pdb|2WPV|E Chain E, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
pdb|2WPV|G Chain G, Crystal Structure Of S. Cerevisiae Get4-Get5 Complex
Length = 312
Score = 30.4 bits (67), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 1 MVGTKVYIGGLPYGVRERD--LEKFVKGYGRIRDVILKNGFGFVEFEDYRDAD 51
+V ++I + + +D LE+F++ + + I KNG+ V FEDY D +
Sbjct: 194 LVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLN 246
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELNGKSL 62
I LPY + ++ YG IR + + N G +V +ED DA +A L+G ++
Sbjct: 23 IRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNV 82
Query: 63 LGERVTV 69
+ V
Sbjct: 83 CNRYLVV 89
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 7/92 (7%)
Query: 98 WGHDRDDRY---GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHR 150
W HD D G + +L+V NL VS D+++ + G + A D R
Sbjct: 17 WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76
Query: 151 NEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
V FE +D KA+ + L+GR + +
Sbjct: 77 GTADVHFERRADALKAMKQYKGVPLDGRPMDI 108
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 7/92 (7%)
Query: 98 WGHDRDDRY---GPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHR 150
W HD D G + +L+V NL VS D+++ + G + A D R
Sbjct: 17 WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76
Query: 151 NEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
V FE +D KA+ + L+GR + +
Sbjct: 77 GTADVHFERRADALKAMKQYKGVPLDGRPMDI 108
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 11/76 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK---------NGFGFVEFEDYRDADDAVYE 56
++G LPY V E +++F +G I V L GFG+ EFED D+ +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED-LDSLLSALS 79
Query: 57 LNGKSLLGERVTVEIA 72
LN +SL R+ V++A
Sbjct: 80 LNEESLGNRRIRVDVA 95
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFED 46
+Y+G + YG +LE G G + V + GF ++EF D
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 56
>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 = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFED 46
+Y+G + YG +LE G G + V + GF ++EF D
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 57
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 15/95 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVI--------LKNGFGFVEF---EDYRDADDA 53
K+++G +P G+ E+DL+ + +GRI ++ L G F+ + + A A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 54 VYELNGKSLLGERVTVEIAKGIDRSQERGRRGYGS 88
++E K+L G +++ S+ RG G S
Sbjct: 77 LHEQ--KTLPGMNRPIQVKPAA--SEGRGESGPSS 107
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH--KRHRNEGV--VEFESSSDMKKALDKL 170
+L+V NL VS D+++ + G + A H + R+ G V FE +D KA +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 171 DNAELNGR--RIRLI 183
+ L+GR I+L+
Sbjct: 91 NGVPLDGRPXNIQLV 105
>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 = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
T + + LP +R+L + G I + G+ FV+F D+ A+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG ++ +R+ V A+
Sbjct: 75 VLNGITVRNKRLKVSYAR 92
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 101 DRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRN-----EGVV 155
+ DD P S+ LIV L + ++L R +G + + ++ V
Sbjct: 2 ESDDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFV 61
Query: 156 EFESSSDMKKALDKLDNAELNGRRIRL 182
+F S D ++A+ L+ + +R+++
Sbjct: 62 DFTSEXDSQRAIKVLNGITVRNKRLKV 88
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 15 VRERDLEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
+RE DL +G+IR ++L +G V F D +AD + L+G+ G ++T +
Sbjct: 39 IRE-DLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
Query: 71 IAKG 74
G
Sbjct: 98 AWDG 101
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 49/131 (37%), Gaps = 25/131 (19%)
Query: 75 IDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPP---------------------TRSD 113
++R+Q R RG G R P G +R Y P +
Sbjct: 29 LNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETG 88
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
+L+V NL VS D+++ + G + A D R V FE +D KA+ +
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 170 LDNAELNGRRI 180
L+GR +
Sbjct: 149 YKGVPLDGRPM 159
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAV 54
G K+ + L +GV + D+++ +G ++ + G V FE DA A+
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 146
Query: 55 YELNGKSLLGERVTVE-IAKGID 76
+ G L G + ++ +A ID
Sbjct: 147 KQYKGVPLDGRPMDIQLVASQID 169
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 103 DDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQV---GEVCYADAHK-RHRNEGVVEFE 158
D G + + L + NL+ S +LK + ++ ++ D +R G V+FE
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66
Query: 159 SSSDMKKALDKLDNAELNGRRIRL 182
S+ D++KAL+ L ++ G I+L
Sbjct: 67 SAEDLEKALE-LTGLKVFGNEIKL 89
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 39 FGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGID 76
FG+V+FE D + A+ EL G + G + +E KG D
Sbjct: 60 FGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRD 96
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFGFVE----FEDYRDADDAVYEL 57
K++IG +P + E+DL+ + +G+I ++ +LK+ F + F Y + + A L
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA---L 69
Query: 58 NGKSLLGERVTV 69
+S L E+ T+
Sbjct: 70 KAQSALHEQKTL 81
>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 = 28.5 bits (62), Expect = 4.4, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 30/49 (61%), Gaps = 8/49 (16%)
Query: 27 YGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
+GRI D ++K+ G+GFV F + DA++A+ ++ G+ L G ++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>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 = 27.7 bits (60), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KNGFGFVEFEDYRDADDAVYELNG 59
++I L + + L +G I + G+GFV FE A+ A+ ++NG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 60 KSLLGERVTV 69
L +V V
Sbjct: 161 MLLNDRKVFV 170
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 27.7 bits (60), Expect = 6.8, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIR--DVILKNGFGFVEFEDYRDADDAVYELNGKS 61
T +Y+GGL + E DL +G IR V+ + F++F + A+ A + K
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 62 LL-GERVTVE 70
++ G R+ V+
Sbjct: 73 IVNGRRLNVK 82
>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 = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDAD 51
++ V++GG+ + E ++ F YG +++V + G+GFV F Y D D
Sbjct: 7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF--YNDVD 62
>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 = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDAD 51
V++GG+ + E ++ F YG +++V + G+GFV F Y D D
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF--YNDVD 62
>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 = 27.3 bits (59), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KNGFGFVEFEDYRDADDAVYELNG 59
++I L + + L +G I + G+GFV FE A+ A+ ++NG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 60 KSLLGERVTV 69
L +V V
Sbjct: 166 MLLNDRKVFV 175
>pdb|4GVQ|A Chain A, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
Tetrahydromethanpterin
pdb|4GVQ|B Chain B, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
Tetrahydromethanpterin
pdb|4GVQ|C Chain C, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
Tetrahydromethanpterin
Length = 316
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 23 FVKGYGRIRDVILKNGFGF--VEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQE 80
F G G R + LK + +E+ED DAD AV L L E+V IAK D E
Sbjct: 105 FAMGSGPARALALKPKKTYERIEYED--DADVAVIALEANQLPDEKVMEFIAKECDVDPE 162
Query: 81 R 81
Sbjct: 163 N 163
>pdb|4GVR|A Chain A, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase
pdb|4GVR|B Chain B, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase
pdb|4GVR|C Chain C, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase
pdb|4GVS|A Chain A, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
N5-Formyl- Tetrahydromethanopterin
pdb|4GVS|B Chain B, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
N5-Formyl- Tetrahydromethanopterin
pdb|4GVS|C Chain C, X-Ray Structure Of The Archaeoglobus Fulgidus Methenyl-
Tetrahydromethanopterin Cyclohydrolase In Complex With
N5-Formyl- Tetrahydromethanopterin
Length = 316
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 23 FVKGYGRIRDVILKNGFGF--VEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQE 80
F G G R + LK + +E+ED DAD AV L L E+V IAK D E
Sbjct: 105 FAMGSGPARALALKPKKTYERIEYED--DADVAVIALEANQLPDEKVMEFIAKECDVDPE 162
Query: 81 R 81
Sbjct: 163 N 163
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDAD 51
V++GG+ + E ++ F YG +++V + G+GFV F Y D D
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF--YNDVD 63
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
0.319 0.141 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,178,245
Number of Sequences: 62578
Number of extensions: 272368
Number of successful extensions: 1034
Number of sequences better than 100.0: 171
Number of HSP's better than 100.0 without gapping: 110
Number of HSP's successfully gapped in prelim test: 61
Number of HSP's that attempted gapping in prelim test: 804
Number of HSP's gapped (non-prelim): 244
length of query: 262
length of database: 14,973,337
effective HSP length: 97
effective length of query: 165
effective length of database: 8,903,271
effective search space: 1469039715
effective search space used: 1469039715
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)