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= 044184
(275 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 91.7 bits (226), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 53/175 (30%), Positives = 95/175 (54%), Gaps = 9/175 (5%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
R LYV NL + + +K F G + +++I+ K KN N+AFV +A A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 139 FDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSAN 198
+ +++ I+++ +A + Q+S+S + L+V +L+ V LR F
Sbjct: 61 LNGKQIENNIVKINWA-----FQSQQSSS----DDTFNLFVGDLNVNVDDETLRNAFKDF 111
Query: 199 FNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQK 253
+ +S V+++ G S GYGFVSF ++++A+ A+ S+ G++L GRPLR+ + K
Sbjct: 112 PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 49/173 (28%), Positives = 88/173 (50%), Gaps = 14/173 (8%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
L V LP + + E K+LF G + ++++ K G++ + FV + P +A A+N
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ ++ + I+V +A R +SA R+ LYVS L + + + FS
Sbjct: 67 NGLKLQTKTIKVSYA---------RPSSASIRDAN--LYVSGLPKTMSQKEMEQLFSQYG 115
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG--RPLRLKF 250
++S+++ + G S G GF+ F + EAE AI L+G++ +G P+ +KF
Sbjct: 116 RIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKF 168
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 45/79 (56%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
+++ L V+ L + + F + + S K+V + G+S GYGFV+++ +A+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 232 AISSLDGKELMGRPLRLKF 250
AI++L+G +L + +++ +
Sbjct: 62 AINTLNGLKLQTKTIKVSY 80
>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 = 75.1 bits (183), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 49/173 (28%), Positives = 87/173 (50%), Gaps = 14/173 (8%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
L V LP + + E ++LF G + ++++ K G++ + FV P++A+ A+N
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ + + I+V +A R +SA R+ LYVS L + L + FS
Sbjct: 65 NGLRLQTKTIKVSYA---------RPSSASIRDAN--LYVSGLPKTMTQKELEQLFSQYG 113
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG--RPLRLKF 250
++S+++ + G S G GF+ F + EAE AI L+G++ G P+ +KF
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
>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 = 68.6 bits (166), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 87/178 (48%), Gaps = 11/178 (6%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI------IKHKGGKNRNFAFVTMASPE 130
I ++YV ++ + I+ FAP G + +++ +KHKG FAFV PE
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG-----FAFVEYEVPE 81
Query: 131 EAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTH 190
AQ A+ Q ++ + GR I+V + +P A +++YV+++ +
Sbjct: 82 AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 141
Query: 191 LREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRL 248
++ F A S+ + + G+ GYGF+ + + ++ A+SS++ +L G+ LR+
Sbjct: 142 IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>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 = 67.8 bits (164), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 86/178 (48%), Gaps = 11/178 (6%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI------IKHKGGKNRNFAFVTMASPE 130
I ++YV ++ + I+ FAP G + +++ +KHKG FAFV PE
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG-----FAFVEYEVPE 66
Query: 131 EAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTH 190
AQ A+ Q ++ + GR I+V + +P A +++YV+++ +
Sbjct: 67 AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 126
Query: 191 LREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRL 248
++ F A S + + G+ GYGF+ + + ++ A+SS++ +L G+ LR+
Sbjct: 127 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>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 = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 84/165 (50%), Gaps = 12/165 (7%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
LYV +L + A + F+P G ++ + + + ++ +A+V P +A+ A++
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ + G+ +R+ ++++ P ++S +++ NL + + L + FSA
Sbjct: 73 NFDVIKGKPVRIMWSQR--DPSLRKSGVG-------NIFIKNLDKSIDNKALYDTFSAFG 123
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGR 244
N +S KVV + N S GYGFV F T+E AE AI ++G L R
Sbjct: 124 NILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 45/85 (52%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYV +L V L E FS +S +V + RS GY +V+F +AE A+ ++
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 237 DGKELMGRPLRLKFGQKNDDVSESN 261
+ + G+P+R+ + Q++ + +S
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSG 97
>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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 84/165 (50%), Gaps = 12/165 (7%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
LYV +L + A + F+P G ++ + + + ++ +A+V P +A+ A++
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ + G+ +R+ ++++ P ++S +++ NL + + L + FSA
Sbjct: 78 NFDVIKGKPVRIMWSQR--DPSLRKSGVG-------NIFIKNLDKSIDNKALYDTFSAFG 128
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGR 244
N +S KVV + N S GYGFV F T+E AE AI ++G L R
Sbjct: 129 NILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 45/85 (52%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYV +L V L E FS +S +V + RS GY +V+F +AE A+ ++
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 237 DGKELMGRPLRLKFGQKNDDVSESN 261
+ + G+P+R+ + Q++ + +S
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSG 102
>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 = 65.1 bits (157), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 36/153 (23%), Positives = 73/153 (47%), Gaps = 16/153 (10%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQ 138
K+++ L W + ++ F GTV D++I+K G++R F F++ P V
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 139 FDTQEV-SGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
TQ + G++I P+R+ ++ K++V + VR EFFS
Sbjct: 64 --TQHILDGKVID-----------PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQ 110
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
+ ++++ + + G+S G+GFV++ + + +
Sbjct: 111 WGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
K+++ L+W +LRE+F K++ + GRS G+GF+SF + + +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 236 ---LDGK 239
LDGK
Sbjct: 65 QHILDGK 71
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 83/178 (46%), Gaps = 11/178 (6%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVE------IIKHKGGKNRNFAFVTMASPE 130
I ++YV ++ + I+ FAP G + ++ KHKG FAFV PE
Sbjct: 11 IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKG-----FAFVEYEVPE 65
Query: 131 EAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTH 190
AQ A+ Q ++ + GR I+V + +P A +++YV+++ +
Sbjct: 66 AAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 125
Query: 191 LREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRL 248
++ F A S + + G+ GYGF+ + + ++ A+SS + +L G+ LR+
Sbjct: 126 IKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 59/191 (30%), Positives = 85/191 (44%), Gaps = 29/191 (15%)
Query: 70 EQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASP 129
E+T Q R L+V NLP + + K LF G +V I ++R F F+ + S
Sbjct: 16 EKTYTQRCR--LFVGNLPTDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLESR 68
Query: 130 EEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRST 189
A+ A + D + R +R+ FA +A L V NLS V +
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFAT---------HGAA--------LTVKNLSPVVSNE 111
Query: 190 HLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL-DGKELMG---RP 245
L + FS F PV VV + GR+ G GFV FA K A A+ DG L+ RP
Sbjct: 112 LLEQAFS-QFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRP 170
Query: 246 LRLKFGQKNDD 256
+ ++ ++ DD
Sbjct: 171 VIVEPMEQFDD 181
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 48/174 (27%), Positives = 86/174 (49%), Gaps = 16/174 (9%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
L++ NL + SVAE+K + D+ ++ + G NR F +V S E+ + A+ +
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 74
Query: 141 TQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFN 200
+V G I++E KP+ + S A T L NLS+ + L+E F +
Sbjct: 75 GLKVFGNEIKLE------KPKGRDSKKVRAART---LLAKNLSFNITEDELKEVFE---D 122
Query: 201 PVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF-GQK 253
+ ++V S +G+S G ++ F ++ +AE + G E+ GR + L + G+K
Sbjct: 123 ALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 29/77 (37%), Positives = 48/77 (62%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L+V +L+ V LR F + +S V+++ G S GYGFVSF ++++A+ A+ S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 237 DGKELMGRPLRLKFGQK 253
G++L GRPLR+ + K
Sbjct: 64 QGQDLNGRPLRINWAAK 80
Score = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 28/43 (65%)
Query: 116 GKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFK 158
G +R + FV+ S ++AQ A++ Q+++GR +R+ +A K +
Sbjct: 40 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 50/157 (31%), Positives = 69/157 (43%), Gaps = 23/157 (14%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVN 137
R +L+V NLP + E++ LF G +V I K KG F F+ + + A+ A
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKV 76
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+ D + G+ +RV FA SAS L V NL V + L E FS
Sbjct: 77 ELDNMPLRGKQLRVRFA--------CHSAS---------LTVRNLPQYVSNELLEEAFSV 119
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAIS 234
F V VV + GR +G G V F+ K A A+
Sbjct: 120 -FGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD 155
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 163 QRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVS 222
Q+ ++ P R LYV +L + + LR F S +++ +S GRS GYGF++
Sbjct: 20 QKGSAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
Query: 223 FATKEEAEAAISSLDGKELMGRPLRL 248
F+ E A+ A+ L+G EL GRP+++
Sbjct: 75 FSDSECAKKALEQLNGFELAGRPMKV 100
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKH-KGGKNRNFAFVTMASPEEAQAAVNQ 138
+LYV +L ++ + ++ +F P G + ++++ + G+++ + F+T + E A+ A+ Q
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 139 FDTQEVSGRIIRV 151
+ E++GR ++V
Sbjct: 88 LNGFELAGRPMKV 100
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 43/170 (25%), Positives = 79/170 (46%), Gaps = 15/170 (8%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
L+V NL ++ S E+K + D+ ++ + G R F +V S E+ + A+
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKAL---- 65
Query: 141 TQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFN 200
E++G + F + K +P+ S R+ + L NL +KV L+E F
Sbjct: 66 --ELTGLKV---FGNEIKLEKPKGKDSKKERDART-LLAKNLPYKVTQDELKEVFED--- 116
Query: 201 PVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
++++ S +G+S G ++ F T+ +AE G E+ GR + L +
Sbjct: 117 --AAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYY 164
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 4/86 (4%)
Query: 68 KPEQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMA 127
K + ++K+ R L NLP+ + E+K +F + V K GK++ A++
Sbjct: 83 KGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLV----SKDGKSKGIAYIEFK 138
Query: 128 SPEEAQAAVNQFDTQEVSGRIIRVEF 153
+ +A+ + E+ GR I + +
Sbjct: 139 TEADAEKTFEEKQGTEIDGRSISLYY 164
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 74 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 164 RSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSF 223
+S S E KL++ LS++ LR F V+ + N RS G+GFV++
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 224 ATKEEAEAAISS----LDGK 239
AT EE +AA+++ +DG+
Sbjct: 63 ATVEEVDAAMNARPHKVDGR 82
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 138 Q 138
Q
Sbjct: 165 Q 165
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 72 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 125
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 126 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 164 RSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSF 223
+S S E KL++ LS++ LR F V+ + N RS G+GFV++
Sbjct: 1 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
Query: 224 ATKEEAEAAISS----LDGK 239
AT EE +AA+++ +DG+
Sbjct: 61 ATVEEVDAAMNARPHKVDGR 80
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 162
Query: 138 Q 138
Q
Sbjct: 163 Q 163
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 67 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
E KL++ LS++ LR F V+ + N RS G+GFV++AT EE +A
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 232 AISS----LDGK 239
A+++ +DG+
Sbjct: 64 AMNARPHKVDGR 75
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157
Query: 138 Q 138
Q
Sbjct: 158 Q 158
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 74 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 164 RSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSF 223
+S S E KL++ LS++ LR F V+ + N RS G+GFV++
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 224 ATKEEAEAAISS----LDGK 239
AT EE +AA+++ +DG+
Sbjct: 63 ATVEEVDAAMNARPHKVDGR 82
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 138 Q 138
Q
Sbjct: 165 Q 165
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 73 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 126
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 127 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 164 RSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSF 223
+S S E KL++ LS++ LR F V+ + N RS G+GFV++
Sbjct: 2 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 61
Query: 224 ATKEEAEAAISS----LDGK 239
AT EE +AA+++ +DG+
Sbjct: 62 ATVEEVDAAMNARPHKVDGR 81
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 163
Query: 138 Q 138
Q
Sbjct: 164 Q 164
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVN 137
RKL++ L + + +++ F GT+ D +++ K +R F FVT A+ EE AA+N
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 138 QFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA 197
+V GR+ VE + + QR A T K++V + HLR++F
Sbjct: 75 A-RPHKVDGRV--VEPKRAVSREDSQRPG---AHLTVKKIFVGGIKEDTEEHHLRDYFEQ 128
Query: 198 NFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+++ + G+ G+ FV+F + + +
Sbjct: 129 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 164 RSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSF 223
+S S E KL++ LS++ LR F V+ + N RS G+GFV++
Sbjct: 4 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 63
Query: 224 ATKEEAEAAISS----LDGK 239
AT EE +AA+++ +DG+
Sbjct: 64 ATVEEVDAAMNARPHKVDGR 83
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVN 137
+K++V + +++ F G + +EI+ +G GK R FAFVT + V
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 165
Query: 138 Q 138
Q
Sbjct: 166 Q 166
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/158 (26%), Positives = 71/158 (44%), Gaps = 12/158 (7%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIK-HKGGKNRNFAFVTMASPEEAQAAVNQF 139
L V LP + E+ LF G + I++ +K G + +AFV S ++Q A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ V + ++V +A R ++T LYV+NL + L F
Sbjct: 66 NGITVRNKRLKVSYA---------RPGGESIKDTN--LYVTNLPRTITDDQLDTIFGKYG 114
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLD 237
+ V ++ + GR G FV + +EEA+ AIS+L+
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L V+ L + L F A P+++ +++ + G S GY FV F ++ +++ AI
Sbjct: 6 LIVNYLPQDMTDRELYALFRA-IGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 236 LDGKELMGRPLRLKFGQ 252
L+G + + L++ + +
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 55/95 (57%), Gaps = 5/95 (5%)
Query: 165 SASAPARETQHK---LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFV 221
S S+ R T+++ LYV NL + LR+ FS S+KV+ E GRS G+GFV
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFV 60
Query: 222 SFATKEEAEAAISSLDGKELMGRPLRLKFGQKNDD 256
F++ EEA A++ ++G+ + +PL + Q+ ++
Sbjct: 61 CFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
LYV NL ++ F+P GT+ +++ +GG+++ F FV +SPEEA AV + +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM-MEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 141 TQEVSGRIIRVEFAKK 156
+ V+ + + V A++
Sbjct: 77 GRIVATKPLYVALAQR 92
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 51/88 (57%), Gaps = 5/88 (5%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
++V N+ ++ L++ FS VS ++V++ G+ GYGF + +E A +A+ +L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 237 DGKELMGRPLRLKFGQKNDDVSESNKEE 264
+G+E GR LR+ ++ SE NKEE
Sbjct: 71 NGREFSGRALRV-----DNAASEKNKEE 93
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEII-KHKGGKNRNFAFVTMASPEEAQAAVN 137
R ++V N+P+ + ++K++F+ G VV ++ + GK + + F E A +A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 138 QFDTQEVSGRIIRVEFA 154
+ +E SGR +RV+ A
Sbjct: 69 NLNGREFSGRALRVDNA 85
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 50/203 (24%), Positives = 90/203 (44%), Gaps = 33/203 (16%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLF-----------APCGTVVDVEIIKHKGGKNRNFAFVT 125
+ R+LYV N+P+ + + + F AP V+ V+I +++NFAF+
Sbjct: 3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLE 57
Query: 126 MASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRS----------ASAPARETQH 175
S +E A+ FD G+ +++ ++ P P S S ++ H
Sbjct: 58 FRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQ-PLPGMSENPSVYVPGVVSTVVPDSAH 115
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAIS 234
KL++ L + ++E ++ F P+ + +V +S G S GY F + + AI+
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
Query: 235 SLDGKELMGRPL---RLKFGQKN 254
L+G +L + L R G KN
Sbjct: 175 GLNGMQLGDKKLLVQRASVGAKN 197
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 48/183 (26%), Positives = 77/183 (42%), Gaps = 24/183 (13%)
Query: 65 VETKPEQTQKQ-NIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAF 123
+ + E T++Q RRK+ + LP + E+ +L + D E+ K + AF
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCFVDKYKGTAF 61
Query: 124 VTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLS 183
VT+ + E+A+AA+N F + R + V+ + T L V+NL
Sbjct: 62 VTLLNGEQAEAAINAFHQSRLRERELSVQL-----------------QPTDALLCVANLP 104
Query: 184 WKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG 243
+ E + +V+ G+S GYGF + K+ A A S L GK L
Sbjct: 105 PSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164
Query: 244 RPL 246
R L
Sbjct: 165 RTL 167
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 48/183 (26%), Positives = 77/183 (42%), Gaps = 24/183 (13%)
Query: 65 VETKPEQTQKQ-NIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAF 123
+ + E T++Q RRK+ + LP + E+ +L + D E+ K + AF
Sbjct: 6 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCFVDKYKGTAF 59
Query: 124 VTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLS 183
VT+ + E+A+AA+N F + R + V+ + T L V+NL
Sbjct: 60 VTLLNGEQAEAAINAFHQSRLRERELSVQL-----------------QPTDALLCVANLP 102
Query: 184 WKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG 243
+ E + +V+ G+S GYGF + K+ A A S L GK L
Sbjct: 103 PSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 162
Query: 244 RPL 246
R L
Sbjct: 163 RTL 165
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 48/183 (26%), Positives = 77/183 (42%), Gaps = 24/183 (13%)
Query: 65 VETKPEQTQKQ-NIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAF 123
+ + E T++Q RRK+ + LP + E+ +L + D E+ K + AF
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCFVDKYKGTAF 61
Query: 124 VTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLS 183
VT+ + E+A+AA+N F + R + V+ + T L V+NL
Sbjct: 62 VTLLNGEQAEAAINAFHQSRLRERELSVQL-----------------QPTDALLCVANLP 104
Query: 184 WKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG 243
+ E + +V+ G+S GYGF + K+ A A S L GK L
Sbjct: 105 PSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164
Query: 244 RPL 246
R L
Sbjct: 165 RTL 167
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 82/183 (44%), Gaps = 30/183 (16%)
Query: 79 RKLYVFNLPWSFSVAEIKNLF-----------APCGTVVDVEIIKHKGGKNRNFAFVTMA 127
R+LYV N+P+ + + + F AP V+ V+I +++NFAF+
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFR 61
Query: 128 SPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVR 187
S +E A+ FD G+ +++ RP P HKL++ L +
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKIR--------RPHDYQPLPG---AHKLFIGGLPNYLN 109
Query: 188 STHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPL 246
++E ++ F P+ + +V +S G S GY F + + AI+ L+G +L + L
Sbjct: 110 DDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 168
Query: 247 RLK 249
++
Sbjct: 169 LVQ 171
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 82/183 (44%), Gaps = 30/183 (16%)
Query: 79 RKLYVFNLPWSFSVAEIKNLF-----------APCGTVVDVEIIKHKGGKNRNFAFVTMA 127
R+LYV N+P+ + + + F AP V+ V+I +++NFAF+
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFR 59
Query: 128 SPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVR 187
S +E A+ FD G+ +++ RP P HKL++ L +
Sbjct: 60 SVDETTQAM-AFDGIIFQGQSLKIR--------RPHDYQPLPG---AHKLFIGGLPNYLN 107
Query: 188 STHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPL 246
++E ++ F P+ + +V +S G S GY F + + AI+ L+G +L + L
Sbjct: 108 DDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Query: 247 RLK 249
++
Sbjct: 167 LVQ 169
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 2/73 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVF-ESNEGRSAGYGFVSFATKEEAEAAISS 235
LYV +L + + LR F F + + V+ +S+ GRS GYGF++F+ E A A+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEP-FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 236 LDGKELMGRPLRL 248
L+G EL GRP+R+
Sbjct: 67 LNGFELAGRPMRV 79
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQF 139
LYV +L ++ + ++ +F P G + ++ ++K G+++ + F+T + E A+ A+ Q
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 140 DTQEVSGRIIRV 151
+ E++GR +RV
Sbjct: 68 NGFELAGRPMRV 79
>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 = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 42/158 (26%), Positives = 70/158 (44%), Gaps = 12/158 (7%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIK-HKGGKNRNFAFVTMASPEEAQAAVNQF 139
L V LP + E+ LF G + I + +K G + +AFV S ++Q A+
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANF 199
+ V + ++V +A R ++T LYV+NL + L F
Sbjct: 77 NGITVRNKRLKVSYA---------RPGGESIKDTN--LYVTNLPRTITDDQLDTIFGKYG 125
Query: 200 NPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLD 237
+ V ++ + GR G FV + +EEA+ AIS+L+
Sbjct: 126 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 171 RETQHKLYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEA 229
R + L V+ L L F A P+++ ++ + G S GY FV F ++ ++
Sbjct: 11 RASNTNLIVNYLPQDXTDRELYALFRA-IGPINTCRIXRDYKTGYSFGYAFVDFTSEXDS 69
Query: 230 EAAISSLDGKELMGRPLRLKFGQ 252
+ AI L+G + + L++ + +
Sbjct: 70 QRAIKVLNGITVRNKRLKVSYAR 92
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 58 STLQDTTVETKPEQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK 117
S L+ + V+ + + Q+Q+ LY+ NLP S E++N+ P G V+ I++ G
Sbjct: 6 SGLKASGVQAQMAKQQEQD-PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64
Query: 118 NRNFAFVTMASPEEAQAAVNQFD 140
+R F M S E+ +A + F+
Sbjct: 65 SRGVGFARMESTEKCEAVIGHFN 87
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LY+SNL + L F V S + + G S G GF + E+ EA I
Sbjct: 28 LYISNLPLSMDEQELENMLKP-FGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 237 DGK 239
+GK
Sbjct: 87 NGK 89
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
++YV NLP +I+++F G + D+++ +GG FAFV P +A+ AV
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP--PFAFVEFEDPRDAEDAVYGR 81
Query: 140 DTQEVSGRIIRVEFAK 155
D + G +RVEF +
Sbjct: 82 DGYDYDGYRLRVEFPR 97
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 3/83 (3%)
Query: 168 APARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKE 227
PA ++YV NL +R+ + + F + + + + N + FV F
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVF---YKYGAIRDIDLKNRRGGPPFAFVEFEDPR 72
Query: 228 EAEAAISSLDGKELMGRPLRLKF 250
+AE A+ DG + G LR++F
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEF 95
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAV 136
+R LYV L + F P G + D++I + ++ K+R FAFV E+A AA+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 137 NQFDTQEVSGRIIRVEFAKKFK 158
+ + E+ GR IRV AK +
Sbjct: 72 DNMNESELFGRTIRVNLAKPMR 93
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 165 SASAPARETQHKLYVSNLSWKVRSTHLREFFS--ANFNPVSSKVVFESNEGRSAGYGFVS 222
S S+ T+ LYV L+ +V L F + + + +E+ + R G+ FV
Sbjct: 3 SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR--GFAFVE 60
Query: 223 FATKEEAEAAISSLDGKELMGRPLRLKFGQ 252
F E+A AAI +++ EL GR +R+ +
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 50/94 (53%), Gaps = 4/94 (4%)
Query: 73 QKQNIRRKLYVF--NLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASP 129
QK++ +VF +L + +IK FAP G + D ++K GK++ + FV+ +
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 130 EEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQ 163
+A+ A+ Q Q + GR IR +A + K P P+
Sbjct: 68 WDAENAIQQMGGQWLGGRQIRTNWATR-KPPAPK 100
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 2/75 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVS-SKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
++V +LS ++ + ++ F A F +S ++VV + G+S GYGFVSF K +AE AI
Sbjct: 18 VFVGDLSPEITTEDIKAAF-APFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 236 LDGKELMGRPLRLKF 250
+ G+ L GR +R +
Sbjct: 77 MGGQWLGGRQIRTNW 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 44/77 (57%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL++ L + +K +F G + +V +IK + K+R FAF+T +P +A+ A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 140 DTQEVSGRIIRVEFAKK 156
+ + + G+ I+VE AKK
Sbjct: 69 NGKSLHGKAIKVEQAKK 85
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 172 ETQH--KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEA 229
E H KL++ L+ + L+ F + P+S ++ + +S G+ F++F +A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKH-GPISEVLLIKDRTSKSRGFAFITFENPADA 61
Query: 230 EAAISSLDGKELMGRPLRLKFGQK 253
+ A ++GK L G+ ++++ +K
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKK 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 48/80 (60%), Gaps = 7/80 (8%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
K++V N+ + + E+++LF G V++ +++K ++AFV M +A+AA+ Q
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQL 63
Query: 140 DTQEVSGRIIRVEFAKKFKK 159
+ +EV G+ I VE + K +K
Sbjct: 64 NGKEVKGKRINVELSTKGQK 83
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 11/81 (13%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
K++V N+S S LR F + VV + Y FV + +A+AAI+
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 236 LDGKELMGRPLRLKF---GQK 253
L+GKE+ G+ + ++ GQK
Sbjct: 63 LNGKEVKGKRINVELSTKGQK 83
>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 = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAV 136
+R LYV L + F P G + D++I + ++ K+R FAFV E+A AA+
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 137 NQFDTQEVSGRIIRVEFAK 155
+ + E+ GR IRV AK
Sbjct: 67 DNMNESELFGRTIRVNLAK 85
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 38/80 (47%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
T+ LYV L+ +V L F + ++ + + G+ FV F E+A AA
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 233 ISSLDGKELMGRPLRLKFGQ 252
I +++ EL GR +R+ +
Sbjct: 66 IDNMNESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAV 136
+R LYV L + F P G + D++I + ++ K+R FAFV E+A AA+
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 137 NQFDTQEVSGRIIRVEFAK 155
+ + E+ GR IRV AK
Sbjct: 65 DNMNESELFGRTIRVNLAK 83
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 38/80 (47%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
T+ LYV L+ +V L F + ++ + + G+ FV F E+A AA
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 233 ISSLDGKELMGRPLRLKFGQ 252
I +++ EL GR +R+ +
Sbjct: 64 IDNMNESELFGRTIRVNLAK 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAV 136
+R LYV L + F P G + D++I + ++ K+R FAFV E+A AA+
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 137 NQFDTQEVSGRIIRVEFA 154
+ + E+ GR IRV A
Sbjct: 123 DNMNESELFGRTIRVNLA 140
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFS--ANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
T+ LYV L+ +V L F + + + +E+ + R G+ FV F E+A
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR--GFAFVEFELAEDAA 119
Query: 231 AAISSLDGKELMGRPLRLKFG 251
AAI +++ EL GR +R+
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 39/177 (22%), Positives = 82/177 (46%), Gaps = 14/177 (7%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGG---KNRNFAFVTMASPEEAQAAV 136
K++V +P ++S +++ LF G V ++ +++ + +++ FVT + + A A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 137 NQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFS 196
N +V + + + K +++ + R KL++ +S K +R FS
Sbjct: 77 NALHNMKV---LPGMHHPIQMKPADSEKNNAVEDR----KLFIGMISKKCTENDIRVMFS 129
Query: 197 ANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELM---GRPLRLKF 250
+ F + + +G S G FV+F T+ A+ AI ++ + M P+ +KF
Sbjct: 130 S-FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 185
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 2/84 (2%)
Query: 174 QHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEG-RSAGYGFVSFATKEEAEAA 232
+ KL+V LS+ L + FS + +S VV + E RS G+GFV+F ++A+ A
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFS-KYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 233 ISSLDGKELMGRPLRLKFGQKNDD 256
+ +++GK + GR +R+ K+ D
Sbjct: 71 MMAMNGKSVDGRQIRVDQAGKSSD 94
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQ 138
KL+V L + + ++ +F+ G + +V ++K + ++R F FVT + ++A+ A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 139 FDTQEVSGRIIRVEFAKKFKKPR 161
+ + V GR IRV+ A K R
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNR 96
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 73 QKQNIRRKLYVF--NLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASP 129
QK++ +VF +L + +IK+ FAP G + D ++K GK++ + FV+ +
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 130 EEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASA 168
+A+ A+ Q + GR IR +A + K P P +S
Sbjct: 68 LDAENAIVHMGGQWLGGRQIRTNWATR-KPPAPSGPSSG 105
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 2/75 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVS-SKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
++V +LS ++ + ++ F A F +S ++VV + G+S GYGFVSF K +AE AI
Sbjct: 18 VFVGDLSPEITTEDIKSAF-APFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 236 LDGKELMGRPLRLKF 250
+ G+ L GR +R +
Sbjct: 77 MGGQWLGGRQIRTNW 91
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 47/81 (58%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L V+ L + LR FS+ S+K++ + G S GYGFV++ T ++AE AI++L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 237 DGKELMGRPLRLKFGQKNDDV 257
+G L + +++ + + + +V
Sbjct: 65 NGLRLQSKTIKVSYARPSSEV 85
Score = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 31/135 (22%), Positives = 62/135 (45%), Gaps = 12/135 (8%)
Query: 32 KLLHSSNSTPSLSY---NFPTRNLCLQVCSTL-----QDTTVETKPEQTQKQNIRR-KLY 82
KL+ + SL Y N+ T + +TL Q T++ + + I+ LY
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLY 92
Query: 83 VFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQFDT 141
+ LP + + +++++F+ G +++ + + G +R AF+ EA+ A+ F+
Sbjct: 93 ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Query: 142 QEVSGRI--IRVEFA 154
+ G I V+FA
Sbjct: 153 HKPPGSSEPITVKFA 167
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 47/81 (58%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L V+ L + LR FS+ S+K++ + G S GYGFV++ T ++AE AI++L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 237 DGKELMGRPLRLKFGQKNDDV 257
+G L + +++ + + + +V
Sbjct: 65 NGLRLQSKTIKVSYARPSSEV 85
Score = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 27/125 (21%), Positives = 57/125 (45%), Gaps = 10/125 (8%)
Query: 32 KLLHSSNSTPSLSY---NFPTRNLCLQVCSTL-----QDTTVETKPEQTQKQNIRR-KLY 82
KL+ + SL Y N+ T + +TL Q T++ + + I+ LY
Sbjct: 33 KLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLY 92
Query: 83 VFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQFDT 141
+ LP + + +++++F+ G +++ + + G +R AF+ EA+ A+ F+
Sbjct: 93 ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Query: 142 QEVSG 146
+ G
Sbjct: 153 HKPPG 157
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 10/91 (10%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+++V NLP+ F+ +K+ F CG V+ +I K + GK++ V SPE A+ A
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPA 170
+ ++SGR I V R R+AS P+
Sbjct: 69 NGMKLSGREIDV---------RIDRNASGPS 90
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 39/178 (21%), Positives = 82/178 (46%), Gaps = 14/178 (7%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGG---KNRNFAFVTMASPEEAQAAV 136
K++V +P ++S +++ LF G V ++ +++ + +++ FVT + + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 137 NQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFS 196
N +V + + + K +++ + R KL++ +S K +R FS
Sbjct: 65 NALHNMKV---LPGMHHPIQMKPADSEKNNAVEDR----KLFIGMISKKCTENDIRVMFS 117
Query: 197 ANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELM---GRPLRLKFG 251
+ F + + +G S G FV+F T+ A+ AI ++ + M P+ +KF
Sbjct: 118 S-FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>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 = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAV 136
+R LYV L + F P G + D++I + ++ K+R FAFV E+A AA+
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 137 NQFDTQEVSGRIIRVEFA 154
+ + E+ GR IRV A
Sbjct: 62 DNMNESELFGRTIRVNLA 79
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 37/79 (46%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
++ LYV L+ +V L F + ++ + + G+ FV F E+A AA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 233 ISSLDGKELMGRPLRLKFG 251
I +++ EL GR +R+
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 169 PARETQHK-LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKE 227
PA+E + ++V NL +VR L E F P++ + + EG+ +GFV F E
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELF-LQAGPLTKVTICKDREGKPKSFGFVCFKHPE 68
Query: 228 EAEAAISSLDGKELMGRPLRL 248
AI+ L+G L GRP+ +
Sbjct: 69 SVSYAIALLNGIRLYGRPINV 89
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 32/73 (43%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
R ++V NL + LF G + V I K + GK ++F FV PE A+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 139 FDTQEVSGRIIRV 151
+ + GR I V
Sbjct: 77 LNGIRLYGRPINV 89
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+++ NL + + L + FSA N +S KVV + N S GYGFV F T+E AE AI +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
Query: 237 DGKELMGRPL 246
+G L R +
Sbjct: 72 NGMLLNDRKV 81
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%)
Query: 171 RETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
R +YV L KV L E F V++ + + G+ GYGFV F ++E+A+
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 231 AAISSLDGKELMGRPLRL 248
AI +D +L G+P+R+
Sbjct: 72 YAIKIMDMIKLYGKPIRV 89
Score = 35.0 bits (79), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
+YV L S + LF G VV+ + K + G+++ + FV S E+A A+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 140 DTQEVSGRIIRVEFAKKFKK 159
D ++ G+ IRV A K
Sbjct: 78 DMIKLYGKPIRVNKASAHNK 97
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 1/89 (1%)
Query: 165 SASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFA 224
S + A ++V+NL +KV L+E FS V + ++ E +G+S G G V+F
Sbjct: 6 SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADIL-EDKDGKSRGIGTVTFE 64
Query: 225 TKEEAEAAISSLDGKELMGRPLRLKFGQK 253
EA AIS +G+ L RP+ +K ++
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHVKMDER 93
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 49/81 (60%), Gaps = 3/81 (3%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPV--SSKVVFESNEGRSAGYGFVSFATKEEAEAAIS 234
+++ NL ++ L + FSA F + + K++ + + G S GY F++FA+ + ++AAI
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSA-FGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 235 SLDGKELMGRPLRLKFGQKND 255
+++G+ L RP+ + + K D
Sbjct: 67 AMNGQYLCNRPITVSYAFKKD 87
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 116 GKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKK 159
G ++ +AF+ AS + + AA+ + Q + R I V +A FKK
Sbjct: 45 GNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA--FKK 86
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 44/76 (57%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L V+ L + LR FS+ S+K++ + G S GYGFV++ T ++AE AI++L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 237 DGKELMGRPLRLKFGQ 252
+G L + +++ + +
Sbjct: 67 NGLRLQSKTIKVSYAR 82
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+++ NL + + L + FSA N +S KVV + N S GYGFV F T+E AE AI +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 237 DGKELMGRPL 246
+G L R +
Sbjct: 66 NGMLLNDRKV 75
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
++L+V N+P+ F +++ +F G ++DVEII ++ G ++ F FVT + +A A +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 88
Query: 139 FDTQEVSGRIIRV 151
V GR I V
Sbjct: 89 LHGTVVEGRKIEV 101
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
+L+VSN+ ++ R LR+ F + +++F NE S G+GFV+F +A+ A
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRAREK 88
Query: 236 LDGKELMGRPLRL 248
L G + GR + +
Sbjct: 89 LHGTVVEGRKIEV 101
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L V+ L LR FS+ S+K++ + G S GYGFV++ T ++AE AI++L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 237 DGKELMGRPLRLKFGQ 252
+G L + +++ + +
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
++L+V N+P+ F +++ +F G ++DVEII ++ G ++ F FVT + +A A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 74
Query: 139 FDTQEVSGRIIRV 151
V GR I V
Sbjct: 75 LHGTVVEGRKIEV 87
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
T +L+VSN+ ++ R LR+ F + +++F NE S G+GFV+F +A+ A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRA 71
Query: 233 ISSLDGKELMGRPLRL 248
L G + GR + +
Sbjct: 72 REKLHGTVVEGRKIEV 87
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 10/90 (11%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
++V NLP+ F+ +K+ F CG V+ +I K + GK++ V SPE A+ A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMN 66
Query: 141 TQEVSGRIIRVEFAKKFKKPRPQRSASAPA 170
++SGR I V R R+AS P+
Sbjct: 67 GMKLSGREIDV---------RIDRNASGPS 87
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYVS L + + + FS ++S+++ + G S G GF+ F + EAE AI L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 237 DGKELMG--RPLRLKFG 251
+G++ +G P+ +KF
Sbjct: 64 NGQKPLGAAEPITVKFA 80
Score = 31.2 bits (69), Expect = 0.72, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQF 139
LYV LP + S E++ LF+ G ++ I+ + G +R F+ EA+ A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 140 DTQEVSGRI--IRVEFA 154
+ Q+ G I V+FA
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVN 137
+ KL++ LP+S + E++ + GTV D+ ++ ++ GK + A+V + +A AV
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 138 QFDTQEVSGRIIRVEFA 154
+ D + II+V +
Sbjct: 77 KMDGMTIKENIIKVAIS 93
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 177 LYVSNLSWKVRSTHLREFFS-ANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L +SNLS+ L+E F A F V ++ G+S GY F+ FA+ E+A+ A++S
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKVP-----QNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 236 LDGKELMGRPLRLKF 250
+ +E+ GR +RL+
Sbjct: 73 CNKREIEGRAIRLEL 87
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 45/75 (60%), Gaps = 3/75 (4%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
+ L + NL +S + ++ +F +++ +++ GK++ +AF+ AS E+A+ A+N
Sbjct: 16 KTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 139 FDTQEVSGRIIRVEF 153
+ +E+ GR IR+E
Sbjct: 73 CNKREIEGRAIRLEL 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGG-KNRNFAFVTMASPEEAQAAVNQF 139
+YV NLP+S + ++ +F+ G VV V I+K K K++ AF+ + AQ
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 140 DTQEVSGRIIRVEFA 154
+ +++ GR+I+ A
Sbjct: 79 NNKQLFGRVIKASIA 93
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 168 APARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKE 227
AP++ T +YVSNL + + + L FS V ++ + + +S G F+ F K+
Sbjct: 13 APSKST---VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
Query: 228 EAEAAISSLDGKELMGRPLR 247
A+ +++ K+L GR ++
Sbjct: 70 SAQNCTRAINNKQLFGRVIK 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+YV NL + S ++E FS + K++++ + G+GFV +E AI+ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Query: 237 DGKELMGRPLRL 248
D + MGR +R+
Sbjct: 63 DNTDFMGRTIRV 74
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKN-RNFAFVTMASPEEAQAAVN 137
R +YV NL +S + ++K LF+ G V +V++I + K + F FV M E A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 138 QFDTQEVSGRIIRV 151
+ D + GR IRV
Sbjct: 61 KLDNTDFMGRTIRV 74
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 56/99 (56%), Gaps = 10/99 (10%)
Query: 66 ETKPEQ--TQKQNIRRKLYVFNLPWS-FSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFA 122
E KP+Q QKQ + R +++ NLP S +S + + L P G + + +++ K + A
Sbjct: 11 EGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK-----SQA 65
Query: 123 FVTMASPEEAQAAVNQFDTQEV--SGRIIRVEFAKKFKK 159
F+ M + E+A A V+ + + GR ++V+ ++K+KK
Sbjct: 66 FIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK 104
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
ET KL VSNL + V ++E F A F + V GRS G V F + +A
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 144
Query: 232 AISSLDGKELMGRPLRLKF 250
A+ G L GRP+ ++
Sbjct: 145 AMKQYKGVPLDGRPMDIQL 163
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL V NL + S A+I+ LFA GT+ + + G++ A V +A A+ Q+
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 149
Query: 140 DTQEVSGRIIRVEF 153
+ GR + ++
Sbjct: 150 KGVPLDGRPMDIQL 163
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 31/50 (62%)
Query: 204 SKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQK 253
++VV + G+S GYGFVSF K +AE AI + G+ L GR +R + +
Sbjct: 36 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85
Score = 35.8 bits (81), Expect = 0.029, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 101 PCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKK 156
P G + D ++K GK++ + FV+ + +A+ A+ Q Q + GR IR +A +
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
KL VSNL + V ++E F A F + V GRS G V F K +A A+
Sbjct: 30 KLLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 88
Query: 236 LDGKELMGRPLRLKF 250
+G L GRP+ ++
Sbjct: 89 YNGVPLDGRPMNIQL 103
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL V NL + S A+I+ LFA GT+ + + G++ A V +A A+ Q+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 140 DTQEVSGRIIRVEF 153
+ + GR + ++
Sbjct: 90 NGVPLDGRPMNIQL 103
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEII-KHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L VF L + +++ +F+ G + DV I+ + ++R FAFV + ++A+ A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 140 DTQEVSGRIIRVEFA 154
+ E+ GR IRV+F+
Sbjct: 78 NGMELDGRRIRVDFS 92
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 174 QHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAI 233
+KLY+ NLS V + LR+ F P++ +V+ +S GY FV + + A AI
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAI 61
Query: 234 SSLDGK-ELMGRPLRLKF 250
+L GK EL G+ + + +
Sbjct: 62 ETLSGKVELHGKIMEVDY 79
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVNQF 139
L V NL + S ++ +F G V DV I + + K +R FAFV +A+ A++
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 140 DTQEVSGRIIRVEFAKKFKKP 160
D + GR +RV+ A+ + P
Sbjct: 110 DGAVLDGRELRVQMARYGRPP 130
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 169 PARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEE 228
P E L V NL+++ LR F + + S G+ FV F K +
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 229 AEAAISSLDGKELMGRPLRL---KFGQKND 255
AE A+ ++DG L GR LR+ ++G+ D
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRPPD 131
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
ET KL VSNL + V ++E F A F + V GRS G V F + +A
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 232 AISSLDGKELMGRPLRLKF 250
A+ G L GRP+ ++
Sbjct: 92 AMKQYKGVPLDGRPMDIQL 110
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL V NL + S A+I+ LFA GT+ + + G++ A V +A A+ Q+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 140 DTQEVSGRIIRVEF 153
+ GR + ++
Sbjct: 97 KGVPLDGRPMDIQL 110
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
ET KL VSNL + V ++E F A F + V GRS G V F + +A
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 232 AISSLDGKELMGRPLRLKF 250
A+ G L GRP+ ++
Sbjct: 92 AMKQYKGVPLDGRPMDIQL 110
Score = 33.9 bits (76), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL V NL + S A+I+ LFA GT+ + + G++ A V +A A+ Q+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 140 DTQEVSGRIIRVEF 153
+ GR + ++
Sbjct: 97 KGVPLDGRPMDIQL 110
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEII-KHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L VF L + +++ +F+ G + DV I+ + ++R FAFV + ++A+ A +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 140 DTQEVSGRIIRVEFA 154
+ E+ GR IRV+F+
Sbjct: 109 NGMELDGRRIRVDFS 123
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEII-KHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L VF L + +++ +F+ G + DV I+ + ++R FAFV + ++A+ A +
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 140 DTQEVSGRIIRVEFA 154
+ E+ GR IRV+F+
Sbjct: 75 NGMELDGRRIRVDFS 89
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 1/86 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGK-NRNFAFVTMASPEEAQAAVNQF 139
L V NL + S ++ +F G V DV I + + K +R FAFV +A+ A++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRS 165
D + GR +RV+ A+ + P S
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDSHHS 158
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
E L V NL+++ LR F + + S G+ FV F K +AE
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 232 AISSLDGKELMGRPLRLKFGQ 252
A+ ++DG L GR LR++ +
Sbjct: 128 AMDAMDGAVLDGRELRVQMAR 148
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L++++LP F+ ++ + F P G V+ ++ I + ++ F FV+ +P+ AQ A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 140 DTQEVSGRIIRVEFAK 155
+ +V + ++V+ K
Sbjct: 103 NGFQVGTKRLKVQLKK 118
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L++ +L + T L F N +S+KV + S +GFVSF + A+ AI ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 237 DGKELMGRPLRLKF 250
+G ++ + L+++
Sbjct: 103 NGFQVGTKRLKVQL 116
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 169 PARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKE 227
P + L V+ + V LR+ F + P+ S K+V + +S GYGFV F +
Sbjct: 37 PEPDVLRNLMVNYIPTTVDEVQLRQLFE-RYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 228 EAEAAISSLDGKELMGRPLRLKF 250
A+ AI+ L+G ++ + L++
Sbjct: 96 SAQQAIAGLNGFNILNKRLKVAL 118
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 72/159 (45%), Gaps = 11/159 (6%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGG---KNRNFAFVTMASPEEAQAAV 136
K +V +P ++S +++ LF G V ++ +++ + +++ FVT + + A A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 137 NQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFS 196
N +V + + +P S A E + KL++ +S K +R FS
Sbjct: 65 NALHNXKV------LPGXHHPIQXKPADSEKNNAVEDR-KLFIGXISKKCTENDIRVXFS 117
Query: 197 ANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
+ F + + +G S G FV+F T+ A+ AI +
Sbjct: 118 S-FGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 43/92 (46%), Gaps = 6/92 (6%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
K+YV NL E++ F+ G + V I ++ G FAFV P +A+ AV
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGL 57
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPAR 171
D + + G +RVE + PR R PAR
Sbjct: 58 DGKVICGSRVRVELSTGM--PRRSRFDRPPAR 87
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
K+YV NL L FS + P+ + + + G+ FV F +AE A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSY-YGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRG 56
Query: 236 LDGKELMGRPLRLKF 250
LDGK + G +R++
Sbjct: 57 LDGKVICGSRVRVEL 71
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 78 RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVN 137
R +L+V NLP + E++ LF G +V I K KG F F+ + + A+ A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKV 69
Query: 138 QFDTQEVSGRIIRVEFA 154
+ D + G+ +RV FA
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 159 KPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGY 218
+P PQRS L+V+ + + + + F+ + + + G GY
Sbjct: 13 EPGPQRSVEGWI------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 219 GFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
V + T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 47/89 (52%), Gaps = 4/89 (4%)
Query: 165 SASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSA--GYGFVS 222
S P ++T K+ V N+ ++ +RE FS F + + + + G A G+GFV
Sbjct: 6 SGQVPKKQTTSKILVRNIPFQANQREIRELFS-TFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 223 FATKEEAEAAISSL-DGKELMGRPLRLKF 250
F TK++A+ A ++L L GR L L++
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEW 93
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 71 QTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKH--KGGKNRNFAFVTMAS 128
Q K+ K+ V N+P+ + EI+ LF+ G + V + K G +R F FV +
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 129 PEEAQAAVNQF-DTQEVSGRIIRVEFA 154
++A+ A N + + GR + +E+A
Sbjct: 68 KQDAKKAFNALCHSTHLYGRRLVLEWA 94
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L++++LP F ++ +F P G VV ++ I + ++ F FV+ +P AQAA+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 140 DTQEVSGRIIRVEFAK 155
+ ++ + ++V+ +
Sbjct: 88 NGFQIGMKRLKVQLKR 103
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 42/80 (52%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L++ +L + L + F N VS+KV + S +GFVS+ A+AAI S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 237 DGKELMGRPLRLKFGQKNDD 256
+G ++ + L+++ + +D
Sbjct: 88 NGFQIGMKRLKVQLKRSKND 107
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 5/88 (5%)
Query: 165 SASAPARETQ--HKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVS 222
+S P +Q L+V LS L+E F + V +++V + G S G+GFV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVD 60
Query: 223 FATKEEAEAAISSLDGKELMGRPLRLKF 250
F ++E+A+AA +++ E+ G + L +
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDW 88
Score = 30.8 bits (68), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
+ L+V L + +K F G+V + + G ++ F FV S E+A+AA
Sbjct: 16 KTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 139 FDTQEVSGRIIRVEFAK 155
+ E+ G + +++AK
Sbjct: 74 MEDGEIDGNKVTLDWAK 90
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 159 KPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGY 218
+P PQRS L+V+ + + + + F+ + + + G GY
Sbjct: 14 EPGPQRSVEGWI------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67
Query: 219 GFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
V + T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 68 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
+L+V NL ++ S +++ LF+ G + ++ I K + FAFVT PE A A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 139 FDTQEVSGRIIRV 151
D Q GR++ V
Sbjct: 70 VDGQVFQGRMLHV 82
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAIS 234
+L+V NLS+ L + FSA + P+S +S + G+ FV+F E A A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSA-YGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 235 SLDGKELMGRPLRL 248
+DG+ GR L +
Sbjct: 69 EVDGQVFQGRMLHV 82
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVNQF 139
LYV NLP + + ++ +F G++V I++ K G+ R AFV EEAQ A++
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 140 D 140
+
Sbjct: 76 N 76
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYV+NL + L F + V ++ + GR G FV + +EEA+ AIS+L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 237 D 237
+
Sbjct: 76 N 76
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 9/94 (9%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKN----RNFAFVTMASPEEAQAAV 136
L++ NL +S + +K +F+ G + I K K F FV PE+AQ A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 137 NQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPA 170
Q V G + V +++ KP AS P+
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKP-----ASGPS 96
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGR---SAGYGFVSFATKEEAEAAI 233
L++ NL++ L+ FS S + + N+ S G+GFV + E+A+ A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 234 SSLDGKELMGRPLRLKFGQK 253
L G + G L ++ ++
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVN 137
RKL+V L + +++ +F P GT+ + +++ G ++ AFV + EAQAA+N
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 171 RETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
R KL+V L + +R+ F F + V +G S G FV F T EA+
Sbjct: 9 RGEDRKLFVGMLGKQQTDEDVRKMFEP-FGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQ 67
Query: 231 AAISSL 236
AAI++L
Sbjct: 68 AAINTL 73
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL++ NLP + EI++LF G V++ +IIK N+ FV + A+ A+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIK-------NYGFVHIEDKTAAEDAIRNL 62
Query: 140 DTQEVSGRIIRVEFAK 155
++ G I VE +K
Sbjct: 63 HHYKLHGVNINVEASK 78
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKN-RNFAFVTMASPEEAQAAVNQF 139
L V NL + S ++ +F G V DV I + K R FAFV +AQ A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 140 DTQEVSGRIIRVEFAKKFKK 159
D E+ GR +RV+ A+ ++
Sbjct: 76 DGAELDGRELRVQVARYGRR 95
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
KL VSNL + V ++E F A F + V GRS G V F K +A A
Sbjct: 31 KLLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQ 89
Query: 236 LDGKELMGRPLRLKF 250
+G L GRP ++
Sbjct: 90 YNGVPLDGRPXNIQL 104
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL V NL + S A+I+ LFA GT+ + + G++ A V +A A Q+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 140 DTQEVSGRIIRVEF 153
+ + GR ++
Sbjct: 91 NGVPLDGRPXNIQL 104
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 166 ASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFAT 225
S+ + ++ L+V +L+ V L EFF + V G S GYGFV F
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 226 KEEAEAAISSLDGKELMG-RPLRL 248
+ E + A++ G +G +P+RL
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRL 84
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 1/90 (1%)
Query: 169 PARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFATKE 227
P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 60
Query: 228 EAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 61 SATNALRSMQGFPFYDKPMRIQYAKTDSDI 90
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 197 ANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQKND 255
+N PV + K++F+ GRS GY F+ F E + +A+ +L+G +L R L+ + N
Sbjct: 24 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY-SSNS 82
Query: 256 DVS 258
D+S
Sbjct: 83 DIS 85
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S+ G +P+R+++ + + D+
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 197 ANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQKND 255
+N PV + K++F+ GRS GY F+ F E + +A+ +L+G +L R L+ + N
Sbjct: 25 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY-SSNS 83
Query: 256 DVS 258
D+S
Sbjct: 84 DIS 86
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 3/87 (3%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
RKL+V L S +++ LF G + + I++ G ++ AFV +S EAQAA+N
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 139 F-DTQEVSG--RIIRVEFAKKFKKPRP 162
+Q + G + V+FA K+ P
Sbjct: 76 LHGSQTMPGASSSLVVKFADTDKESGP 102
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
+ KL+V L+ + +R F A F + + +G S G FV +++ EA+AA
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEA-FGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAA 72
Query: 233 ISSLDGKELM 242
I++L G + M
Sbjct: 73 INALHGSQTM 82
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 162 PQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFV 221
P S+ P E LY+ NLS +V L F+ + F GR G F+
Sbjct: 14 PMFSSYNPG-EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 72
Query: 222 SFATKEEAEAAISSLDGKELMGRPLRLKFGQ 252
+F KE A A+ ++G +L G+ L ++FG+
Sbjct: 73 TFPNKEIAWQALHLVNGYKLYGKILVIEFGK 103
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 116 GKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSAS 167
G+ R AF+T + E A A++ + ++ G+I+ +EF K K QRS+
Sbjct: 64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK----QRSSG 111
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 46/81 (56%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
+++ L V+ L + + F + + S K+V + G+S GYGFV+++ +A+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 232 AISSLDGKELMGRPLRLKFGQ 252
AI++L+G +L + +++ + +
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR 82
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEII-KHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L VF L + +++ +F+ G + DV I+ + ++R FAFV + ++A+ A +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 140 DTQEVSGRIIRV 151
+ E+ GR IRV
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 73 QKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVD-VEIIKHKGGKNRNFAFVTMASPEE 131
QK K++V LP+ + A ++ F G + + V I + GK+R + FVTMA
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 132 AQAAVNQFDTQEVSGRIIRVEFAKKFKKPR 161
A+ A + GR V A KPR
Sbjct: 72 AERACKD-PNPIIDGRKANVNLAYLGAKPR 100
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
K++V L + LR++F + + V+ + G+S GYGFV+ A + AE A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 236 ----LDGKE 240
+DG++
Sbjct: 79 PNPIIDGRK 87
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 175 HKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFATKEEAEAAI 233
H +Y++NL+ K++ L++ A F+ + + S + G FV F A A+
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 234 SSLDGKELMGRPLRLKFGQKNDDV 257
S+ G +P+R+++ + + D+
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDI 89
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 159 KPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGY 218
+P PQRS L+V+++ + + ++E F + + + G S GY
Sbjct: 17 EPGPQRSVEGWI------LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY 70
Query: 219 GFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
V + T ++A AA +L+G E+MG+ +++ +
Sbjct: 71 ALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEA 231
E K +V LSW L+++F+ V + + N GRS G+GF+ F ++A +
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAAS 65
Query: 232 AISSLDGKE 240
LD KE
Sbjct: 66 VEKVLDQKE 74
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQ 138
K +V L W S ++K+ F G VVD I G++R F F+ + ++Q
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 139 FDTQEVSGRII 149
+ GR+I
Sbjct: 73 -KEHRLDGRVI 82
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 45/91 (49%), Gaps = 12/91 (13%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
KL+V N+ + + E++ F G V++ +I+K ++AFV M E+A A+
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGL 64
Query: 140 DTQEVSGRIIRVEFAKKFKKPRPQRSASAPA 170
D E G+ + V+ + R+AS P+
Sbjct: 65 DNTEFQGKRMHVQLSTS-----RLRTASGPS 90
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
KL+V N+S + LR F + PV + + Y FV E+A AI
Sbjct: 12 KLHVGNISPTCTNQELRAKFE-EYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63
Query: 236 LDGKELMGRPLRLKF 250
LD E G+ + ++
Sbjct: 64 LDNTEFQGKRMHVQL 78
>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: Composition-based stats.
Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 160 PRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYG 219
P PQRS L+V+ + + + + F+ + + + G GY
Sbjct: 1 PGPQRSVEGWI------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 54
Query: 220 FVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
V + T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 55 LVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>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 = 22/89 (24%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 162 PQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFV 221
PQRS L+V+ + + + + F+ + + + G GY V
Sbjct: 1 PQRSVEGWI------LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 54
Query: 222 SFATKEEAEAAISSLDGKELMGRPLRLKF 250
+ T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 55 EYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 3/87 (3%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
RKL+V L S ++ LF P G + + +++ G ++ AFV +S EAQAA++
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 139 F-DTQEVSG--RIIRVEFAKKFKKPRP 162
+Q + G + V+FA K+ P
Sbjct: 76 LHGSQTMPGASSSLVVKFADTDKESGP 102
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
KL+V L+ + + F F + V +G S G FV F++ EA+AAI +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQP-FGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 236 LDGKELM 242
L G + M
Sbjct: 76 LHGSQTM 82
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 48/95 (50%), Gaps = 4/95 (4%)
Query: 58 STLQDTTVETKPEQTQKQNIR--RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG 115
S+ + T+ET P + +K+ RKL++ L + + ++N + G + D +++
Sbjct: 5 SSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64
Query: 116 GK-NRNFAFVTMASPEEAQAAVNQFDTQEVSGRII 149
K +R F FVT +S E AA+ + GR++
Sbjct: 65 SKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVV 98
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 171 RETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
+E KL++ LS++ LR ++ V+ + RS G+GFV+F++ E +
Sbjct: 24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 83
Query: 231 AAIS----SLDGK 239
AA++ S+DG+
Sbjct: 84 AAMAARPHSIDGR 96
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 175 HKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFATKEEAEAAI 233
H +Y++NL+ K++ L++ A F+ + + S + G FV F A A+
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 234 SSLDGKELMGRPLRLKFGQKNDDV 257
S+ G +P+R+++ + + D+
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTDSDI 87
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 159 KPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGY 218
+P PQRS L+V+++ + + ++E F + + + G S GY
Sbjct: 63 EPGPQRSVEGWI------LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY 116
Query: 219 GFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
V + T ++A AA +L+G E+MG+ +++ +
Sbjct: 117 ALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 175 HKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFATKEEAEAAI 233
H +Y++NL+ K++ L++ A F+ + + S + G FV F A A+
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 234 SSLDGKELMGRPLRLKFGQKNDDV 257
S+ G +P+R+++ + + D+
Sbjct: 65 RSMQGFPFYDKPMRIQYAKTDSDI 88
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 197 ANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQKN 254
+N PV + K++F+ GRS GY F+ F E + +A+ +L+G +L R L+ + +
Sbjct: 26 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS 84
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+++ LSW L+++FS V + + GRS G+GFV F +E+E+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF---KESESVDKVM 58
Query: 237 DGKE 240
D KE
Sbjct: 59 DQKE 62
Score = 32.7 bits (73), Expect = 0.25, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+++ L W + ++K+ F+ G VVD + + G++R F FV E ++Q
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60
Query: 140 DTQEVSGRII 149
+++G++I
Sbjct: 61 KEHKLNGKVI 70
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKE 60
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S G +P R+++ + + D+
Sbjct: 61 VSSATNALRSXQGFPFYDKPXRIQYAKTDSDI 92
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 1/92 (1%)
Query: 167 SAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFAT 225
+ P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKE 61
Query: 226 KEEAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S G +P R+++ + + D+
Sbjct: 62 VSSATNALRSXQGFPFYDKPXRIQYAKTDSDI 93
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
KL+V L W LR +FS V ++ + +S G+GFV F ++S
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 236 ----LDGKELMGRP 245
LDG+ + +P
Sbjct: 78 RPHTLDGRNIDPKP 91
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASP 129
KL+V L WS + +++ F+ G VVD I+K K ++R F FV P
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L+V+ +++ + LR F + P+ +V+ G+ GY F+ + + + +A
Sbjct: 105 LFVARVNYDTTESKLRREFEV-YGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 236 LDGKELMGR 244
DGK++ GR
Sbjct: 164 ADGKKIDGR 172
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVN 137
+ L+V + + + ++++ F G + + ++ K GK R +AF+ + +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 138 QFDTQEVSGRIIRVEFAK 155
D +++ GR + V+ +
Sbjct: 163 HADGKKIDGRRVLVDVER 180
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 169 PARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKV-VFESNEGRSAGYGFVSFATKE 227
P H +Y++NL+ K++ L++ A F+ + + S + G FV F
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVS 60
Query: 228 EAEAAISSLDGKELMGRPLRLKFGQKNDDV 257
A A+ S G +P R+++ + + D+
Sbjct: 61 SATNALRSXQGFPFYDKPXRIQYAKTDSDI 90
>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 = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 26/38 (68%)
Query: 213 GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
G GY V + T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 46 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 26/38 (68%)
Query: 213 GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
G GY V + T +EA+AA+ L+G++LMG+P+ + +
Sbjct: 46 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 11/95 (11%)
Query: 85 NLPWSFSVAEIKNLFAPC---GTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFDT 141
LPWS S+ +++N + C V V I + G+ AFV + S ++ + A+ + D
Sbjct: 24 GLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKK-DR 82
Query: 142 QEVSGRII------RVEFAKKFKKPRPQRSASAPA 170
+ + R I R E K P SAS P+
Sbjct: 83 ESMGHRYIEVFKSHRTEMDWVLKHSGPN-SASGPS 116
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 11/86 (12%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTV----------VDVEIIKHKGGKNRNFAFVTMASPE 130
+YV L S ++ ++ + F CG V + + + K G K + A V+ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG-KPKGDATVSYEDPP 76
Query: 131 EAQAAVNQFDTQEVSGRIIRVEFAKK 156
A+AAV FD ++ G ++V A+K
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLARK 102
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 9/98 (9%)
Query: 165 SASAPARETQHK-LYVSNLSWKVRSTHLREFFS----ANFNPVSSK----VVFESNEGRS 215
S+ P ++ + +YV L+ V L +FF N + + + + G+
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 216 AGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQK 253
G VS+ A+AA+ DGK+ G L++ +K
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 43/200 (21%), Positives = 86/200 (43%), Gaps = 18/200 (9%)
Query: 9 TSIFLTNHPFSFSC--LFPKLPHCIKLLHSSNSTPSLSYNFPTRNLCLQVCSTLQDTTVE 66
T++ + N P S++ ++ HC ++H + SL NF R ++
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV-DVADSLKKNF--RFARIEFARYDGALAAI 98
Query: 67 TKPEQTQKQN-------IRRKLYVFNLPWSFSVAEIKNLFAPCGTV-VDVEIIKHKGGKN 118
TK + QN L+ N P S++ I++L V + + + + +
Sbjct: 99 TKTHKVVGQNEIIVSHLTECTLWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTS 158
Query: 119 RNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLY 178
R FA++ + S E+A+ V + + ++ G + + + +K + SA+ RE +
Sbjct: 159 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGRE----IX 214
Query: 179 VSNLSWKVRSTH-LREFFSA 197
+ NLS ++ + LRE F
Sbjct: 215 IRNLSTELLDENLLRESFEG 234
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 35/167 (20%), Positives = 70/167 (41%), Gaps = 22/167 (13%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
+ V NLP S++ ++ F CG ++ V++ KN FA + A + A AA+ +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-KNFRFARIEFARYDGALAAITK-- 100
Query: 141 TQEVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFN 200
T +V G+ + + T+ L+ +N ++R+ + N
Sbjct: 101 THKVVGQ-----------------NEIIVSHLTECTLWXTNFPPSYTQRNIRDLLQ-DIN 142
Query: 201 PVSSKVVFESNE-GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPL 246
V+ + S S + ++ +KE+A + L+G ++ G L
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL 189
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
K+YV NL + + E++ F G + V + ++ G FAFV P +A AV +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVREL 130
Query: 140 DTQEVSGRIIRVEFAKKFKK 159
D + + G +RVE + K+
Sbjct: 131 DGRTLCGCRVRVELSNGEKR 150
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 73 QKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEE 131
+K+ +R +YV N+ + + +++ F+ CG++ + I+ K G + +A++ A
Sbjct: 31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS 90
Query: 132 AQAAVNQFDTQEVSGRIIRV 151
AAV D GR I+V
Sbjct: 91 VDAAV-AMDETVFRGRTIKV 109
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+YV N+ + + L FS+ + ++ + G GY ++ FA + +AA+ ++
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97
Query: 237 DGKELMGRPLRL 248
D GR +++
Sbjct: 98 DETVFRGRTIKV 109
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.0 bits (84), Expect = 0.014, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 175 HKLYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAI 233
HKL++ L + ++E ++ F P+ + +V +S G S GY F + + AI
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 234 SSLDGKELMGRPL---RLKFGQKN 254
+ L+G +L + L R G KN
Sbjct: 61 AGLNGMQLGDKKLLVQRASVGAKN 84
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
K+YV NL + + E++ F G + V + ++ G FAFV P +A AV
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDL 130
Query: 140 DTQEVSGRIIRVEFAKKFKK 159
D + + G +RVE + K+
Sbjct: 131 DGRTLCGCRVRVELSNGEKR 150
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 85 NLPWSFSVAEIKNLFAPCGTVVD----VEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
LPWS SV +++N + C T+ D V I + G+ AFV + S ++ + A+ + D
Sbjct: 51 GLPWSCSVEDVQNFLSDC-TIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK-D 108
Query: 141 TQEVSGRIIRV 151
+ + R I V
Sbjct: 109 RESMGHRYIEV 119
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 165 SASAPARETQHK--LYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFV 221
+S P R + V+NLS R T L+E F F +S + + G+S G+ F+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRP-FGSISRIYLAKDKTTGQSKGFAFI 62
Query: 222 SFATKEEAEAAISSLDG 238
SF +E+A AI+ + G
Sbjct: 63 SFHRREDAARAIAGVSG 79
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG-GKNRNFAFVTMASPEEAQAAVNQF 139
+ V NL +++ LF P G++ + + K K G+++ FAF++ E+A A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 140 DTQEVSGRIIRVEFAK 155
I+ VE+AK
Sbjct: 78 SGFGYDHLILNVEWAK 93
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVF-ESNEGRSAGYGFVSFATKEEAEAAIS 234
K+++ LSW+ LRE+F F V +V + RS G+GFV+F + + ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
>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 = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L+V+ +++ + LR F + P+ +V+ G+ GY F+ + + + +A
Sbjct: 105 LFVARVNYDTTESKLRREFEV-YGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 236 LDGKELMGR 244
DGK++ GR
Sbjct: 164 ADGKKIDGR 172
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVN 137
+ L+V + + + ++++ F G + + ++ K GK R +AF+ + +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 138 QFDTQEVSGRIIRVEFAK 155
D +++ GR + V+ +
Sbjct: 163 HADGKKIDGRRVLVDVER 180
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 69/173 (39%), Gaps = 35/173 (20%)
Query: 96 KNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAK 155
++LF G DV+ +K K N A V MA +AQ A++ + ++ G+ IR+ +K
Sbjct: 19 QSLFILFGVYGDVQRVKILFNKKEN-ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 77
Query: 156 --------------------------KFKKPRPQRSASA-PARETQHKLYVSNLSWKVRS 188
+FKKP + + P T L++SN+ V
Sbjct: 78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT---LHLSNIPPSVSE 134
Query: 189 THLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKEL 241
L+ FS+N V F+ + + + + EEA A+ L +L
Sbjct: 135 EDLKVLFSSNGGVVKGFKFFQKDRKMA----LIQMGSVEEAVQALIDLHNHDL 183
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 45/96 (46%), Gaps = 15/96 (15%)
Query: 68 KPEQTQKQNI---RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG----GKNRN 120
KP QNI L++ N+P S S ++K LF+ G VV KG K+R
Sbjct: 107 KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV-------KGFKFFQKDRK 159
Query: 121 FAFVTMASPEEA-QAAVNQFDTQEVSGRIIRVEFAK 155
A + M S EEA QA ++ + +RV F+K
Sbjct: 160 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 177 LYVSNLS-WKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L VSNL+ +V L F + K++F E V A +A+ A+S
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 60
Query: 236 LDGKELMGRPLRLKFGQ-KNDDVSESNKEEEDVSED 270
L+G +L G+P+R+ + +N + +E++ +++D
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 96
>pdb|1X4D|A Chain A, Solution Structure Of Rrm Domain In Matrin 3
Length = 102
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 29/42 (69%), Gaps = 2/42 (4%)
Query: 120 NFAFVTMASPEEAQAAVNQFDTQE--VSGRIIRVEFAKKFKK 159
N AF+ MA+ E+AQAAV+ + T V G+ +RV ++K+K+
Sbjct: 53 NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR 94
>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 = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNR-NFAFVTMASPEEAQAAVNQF 139
LYV NL + + +I LF+ G + + + K K F FV S +A+ A+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 140 DTQEVSGRIIRVEFAKKFKKPRP 162
+ + RIIR ++ FK+ R
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQ 124
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYV NLS+ + E FS + + + + + + G+ FV + ++ +AE A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 237 DGKELMGRPLR 247
+G L R +R
Sbjct: 102 NGTRLDDRIIR 112
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
L NLS+ + L+E F + + ++V S +G+S G ++ F ++ +AE +
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 237 DGKELMGRPLRLKF-GQKN 254
G E+ GR + L + G+K
Sbjct: 74 QGAEIDGRSVSLYYTGEKG 92
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 69 PEQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMAS 128
P ++K R L NL ++ + E+K +F +++ ++ G K++ A++ S
Sbjct: 7 PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA---LEIRLVSQDG-KSKGIAYIEFKS 62
Query: 129 PEEAQAAVNQFDTQEVSGRIIRVEF 153
+A+ + + E+ GR + + +
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYY 87
>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 = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSA-GYGFVSFATKEEAEAAISS 235
LYV NLS+ + E FS + + K++ ++ ++A G+ FV + ++ +AE A+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDI--KKIIMGLDKMKTACGFCFVEYYSRADAENAMRY 78
Query: 236 LDGKELMGRPLR 247
++G L R +R
Sbjct: 79 INGTRLDDRIIR 90
Score = 34.7 bits (78), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
LYV NL + + +I LF+ G + + + K F FV S +A+ A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 141 TQEVSGRIIRVEFAKKFK 158
+ RIIR ++ FK
Sbjct: 81 GTRLDDRIIRTDWDAGFK 98
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 69/173 (39%), Gaps = 35/173 (20%)
Query: 96 KNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAK 155
++LF G DV+ +K K N A V MA +AQ A++ + ++ G+ IR+ +K
Sbjct: 50 QSLFILFGVYGDVQRVKILFNKKEN-ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 108
Query: 156 --------------------------KFKKPRPQRSASA-PARETQHKLYVSNLSWKVRS 188
+FKKP + + P T L++SN+ V
Sbjct: 109 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT---LHLSNIPPSVSE 165
Query: 189 THLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKEL 241
L+ FS+N V F+ + + + + EEA A+ L +L
Sbjct: 166 EDLKVLFSSNGGVVKGFKFFQKDRKMA----LIQMGSVEEAVQALIDLHNHDL 214
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 45/96 (46%), Gaps = 15/96 (15%)
Query: 68 KPEQTQKQNI---RRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKG----GKNRN 120
KP QNI L++ N+P S S ++K LF+ G VV KG K+R
Sbjct: 138 KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV-------KGFKFFQKDRK 190
Query: 121 FAFVTMASPEEA-QAAVNQFDTQEVSGRIIRVEFAK 155
A + M S EEA QA ++ + +RV F+K
Sbjct: 191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 226
Score = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 177 LYVSNLS-WKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L VSNL+ +V L F + K++F E V A +A+ A+S
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 91
Query: 236 LDGKELMGRPLRLKFGQ-KNDDVSESNKEEEDVSED 270
L+G +L G+P+R+ + +N + +E++ +++D
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 127
>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 = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS- 235
++V + ++ T +R FF A + V + G S GYGFVSF + + + S
Sbjct: 12 VFVGGIDVRMDETEIRSFF-ARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 236 --LDGKEL-MGRPLR 247
GK+L +G +R
Sbjct: 71 INFHGKKLKLGPAIR 85
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
++V + EI++ FA G+V +V+II + G ++ + FV+ + + Q V
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 172 ETQHKLYVSNLSWKVRSTHLREFFS--ANFNPVSSKVVFE---SNEGRSAGYGFVSFATK 226
E ++YV NL+ V+ L+ F +F+ + +++F+ EGR G F+ +
Sbjct: 43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102
Query: 227 EEAEAAISSLDGKELMGRPLRLKFGQ 252
+ A A+ +G L G+P+ ++F +
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQFAR 128
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 34.7 bits (78), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 179 VSNLSWKVRSTHLREFFSANFNPVSSKVVFESNE-GRSAGYGFVSFATKEEAEAAISSLD 237
V N+ + V + +FF + + V + NE G G V+F +++EA AA+ L+
Sbjct: 20 VQNMPFTVSIDEILDFFYG-YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN 78
Query: 238 GKELMGRPLRLKFG 251
+ + R ++L G
Sbjct: 79 DRPIGSRKVKLVLG 92
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 34.7 bits (78), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
+Y ++ + +R+ FS F + VF GY FV F+T E A AI S+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSP-FGQIMEIRVFPEK-----GYSFVRFSTHESAAHAIVSV 81
Query: 237 DGKELMGRPLRLKFGQKNDDVS 258
+G + G ++ +G+++ D++
Sbjct: 82 NGTTIEGHVVKCYWGKESPDMT 103
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/76 (17%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
+Y + + ++ F+P G ++++ + KG ++FV ++ E A A+ +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFVRFSTHESAAHAIVSVN 82
Query: 141 TQEVSGRIIRVEFAKK 156
+ G +++ + K+
Sbjct: 83 GTTIEGHVVKCYWGKE 98
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 34.7 bits (78), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
R +++ LP + E+ +L P G V ++ ++K GKN+ AF+ M + E A VN
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK---GKNQ--AFIEMNTEEAANTMVNY 86
Query: 139 FD--TQEVSGRIIRVEFA 154
+ T + G+ I ++F+
Sbjct: 87 YTSVTPVLRGQPIYIQFS 104
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
R +++ LP + E+ +L P G V ++ ++K GKN+ AF+ M + E A VN
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK---GKNQ--AFIEMNTEEAANTMVNY 71
Query: 139 FD--TQEVSGRIIRVEFA 154
+ T + G+ I ++F+
Sbjct: 72 YTSVTPVLRGQPIYIQFS 89
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 3/83 (3%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVN 137
R +YV N+ + + E++ F CG+V V I+ K G + FA++ + E + ++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 64
Query: 138 QFDTQEVSGRIIRVEFAKKFKKP 160
D GR I+V K+ +P
Sbjct: 65 ALDESLFRGRQIKV-IPKRTNRP 86
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
T H +++ L +K + FFS NPV + +GR G V FAT EEA AA
Sbjct: 45 TGHCVHMRGLPYKATENDIYNFFSP-LNPVRVHIEI-GPDGRVTGEADVEFATHEEAVAA 102
Query: 233 IS 234
+S
Sbjct: 103 MS 104
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 34.3 bits (77), Expect = 0.079, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESN-EGRSAGYGFVSF 223
K+++ LSW+ LRE+F F V +V RS G+GFV+F
Sbjct: 2 KMFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 213 GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQKNDD 256
G+ G VSF A+AAI DGKE G P+++ F + D
Sbjct: 54 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 57/127 (44%), Gaps = 17/127 (13%)
Query: 154 AKKFKKPR---PQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSA---NFNPVSSKVV 207
A KF++ P ++ P E + ++N++ +V L+ A + + VV
Sbjct: 6 AAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV 65
Query: 208 FESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKFGQKNDDVSESNKEEEDV 267
S++ ++G ++ FAT+E A+A + + G G PL + F S + V
Sbjct: 66 DLSDD--NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF---------SETPQSQV 114
Query: 268 SEDQSAE 274
+ED S E
Sbjct: 115 AEDGSLE 121
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.9 bits (76), Expect = 0.090, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS- 235
++V + ++ T +R FF A + V + G S GYGFVSF + + + S
Sbjct: 13 VFVGGIDVRMDETEIRSFF-ARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 236 --LDGKEL-MGRPLR 247
GK+L +G +R
Sbjct: 72 INFHGKKLKLGPAIR 86
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 94 EIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
EI++ FA G+V +V+II + G ++ + FV+ + + Q V
Sbjct: 26 EIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 68
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 33.9 bits (76), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 50/97 (51%), Gaps = 11/97 (11%)
Query: 71 QTQKQNIRRKLYVFNL-PWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASP 129
+T +++ ++++ NL ++++ +F+ G +V + HKG FAFV +
Sbjct: 8 KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--HKG-----FAFVQYVNE 60
Query: 130 EEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSA 166
A+AAV D + ++G+++ + A +P+ RS
Sbjct: 61 RNARAAVAGEDGRMIAGQVLDINLA---AEPKVNRSG 94
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 171 RETQHKLYVSNL-SWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEA 229
R ++++ NL + V+ + + FS V V G+ FV + + A
Sbjct: 12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNA 63
Query: 230 EAAISSLDGKELMGRPLRLKF 250
AA++ DG+ + G+ L +
Sbjct: 64 RAAVAGEDGRMIAGQVLDINL 84
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS- 235
L V L WK L+E+FS + +V + G S G+GFV F T+ E + + S
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF-TEYETQVKVMSQ 76
Query: 236 ---LDGK 239
+DG+
Sbjct: 77 RHMIDGR 83
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 35/165 (21%), Positives = 70/165 (42%), Gaps = 22/165 (13%)
Query: 83 VFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFDTQ 142
V NLP S++ ++ F CG ++ V+ + KN FA + A + A AA+ + T
Sbjct: 9 VKNLPKSYNQNKVYKYFKHCGPIIHVD-VADSLKKNFRFARIEFARYDGALAAITK--TH 65
Query: 143 EVSGRIIRVEFAKKFKKPRPQRSASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPV 202
+V G ++ + T+ L+++N ++R+ + N V
Sbjct: 66 KVVG-----------------QNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQ-DINVV 107
Query: 203 SSKVVFESNE-GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPL 246
+ + S S + ++ +KE+A + L+G ++ G L
Sbjct: 108 ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL 152
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
LYV NL E FN + V + R Y FV F+ +E+A A+ +L
Sbjct: 18 LYVRNLMLSTS----EEMIEKEFNNIKPGAVERVKKIRD--YAFVHFSNREDAVEAMKAL 71
Query: 237 DGKELMGRPLRLKFGQKND 255
+GK L G P+ + + D
Sbjct: 72 NGKVLDGSPIEVTLAKPVD 90
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 86 LPWSFSVAEIKNLFAPC---GTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
LPWS ++ ++ N F+ C + + ++ GK R A + M S ++ Q A+
Sbjct: 19 LPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
>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 = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 3/83 (3%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHK-GGKNRNFAFVTMASPEEAQAAVN 137
R +YV N+ + + E++ F CG+V V I+ K G + FA++ + E + ++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65
Query: 138 QFDTQEVSGRIIRVEFAKKFKKP 160
D GR I+V K+ +P
Sbjct: 66 ALDESLFRGRQIKV-IPKRTNRP 87
>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 = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS- 235
++V + ++ T +R FF A + V + G S GYGFVSF + + + S
Sbjct: 12 VFVGGIDVRMDETEIRSFF-ARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 236 --LDGKEL-MGRPLR 247
GK+L +G +R
Sbjct: 71 INFHGKKLKLGPAIR 85
Score = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 94 EIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
EI++ FA G+V +V+II + G ++ + FV+ + + Q V
Sbjct: 25 EIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFN-PVSSKVVFESNEGRSAGYGFVSFATKEEAEAAIS 234
K+++ L+ V H+ E FS + V + S GY +V F +EAE A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 235 SLDGKELMGRPL 246
+DG ++ G+ +
Sbjct: 66 HMDGGQIDGQEI 77
Score = 28.9 bits (63), Expect = 3.2, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTV--VDVEIIKHKGGKNRNFAFVTMASPEEAQAAVN 137
K+++ L + + I +F+ G + +D+ + + ++ +A+V +P+EA+ A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 138 QFDTQEVSGRII 149
D ++ G+ I
Sbjct: 66 HMDGGQIDGQEI 77
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
LYV+ + ++ ++ F+P G ++D+ + RN AFVT E A AV + +
Sbjct: 18 LYVYGEDMTPTL--LRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELN 70
Query: 141 TQEVSGRIIRVEFAKK 156
+V ++V A+K
Sbjct: 71 GTQVESVQLKVNIARK 86
>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 = 0.16, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
+ R LY+ NLP+ + E+ ++F G + + + + R A+V +A+ AV
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAV 64
Query: 137 NQFDTQEVSGRIIRVEF 153
+ VS R + V +
Sbjct: 65 DHLSGFNVSNRYLVVLY 81
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 213 GRSAGYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
G+ G VSF A+AAI DGKE G P+++ F
Sbjct: 60 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 179 VSNLSWKVRSTHLREFFSANFNPVSSKVVFESNE-GRSAGYGFVSFATKEEAEAAISSLD 237
V N+ + V + +FF + + V + NE G G V+F +++EA AA+ L+
Sbjct: 20 VQNMPFTVSIDEILDFFYG-YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN 78
Query: 238 GKELMGRPLRL 248
+ + R ++L
Sbjct: 79 DRPIGSRKVKL 89
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
LYV+ + ++ ++ F+P G ++D+ + RN AFVT E A AV + +
Sbjct: 42 LYVYGEDMTPTL--LRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELN 94
Query: 141 TQEVSGRIIRVEFAKK 156
+V ++V A+K
Sbjct: 95 GTQVESVQLKVNIARK 110
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
L++ NL + SVAE+K + D+ ++ + G NR F +V S E+ + A+ +
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 78
Query: 141 TQEVSGRIIRVE 152
+V G I++E
Sbjct: 79 GLKVFGNEIKLE 90
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
R L++ LP + E+ L P G V ++ ++K GKN+ AF+ +A+ E A VN
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK---GKNQ--AFLELATEEAAITMVNY 70
Query: 139 F 139
+
Sbjct: 71 Y 71
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 55/108 (50%), Gaps = 14/108 (12%)
Query: 60 LQDTTVETKPEQTQKQNIRRKLYVFNLPWSF-SVAEIKNLFAPCGTVVDVEIIKHKGGKN 118
LQ + V K + ++I ++++ NL + ++++ +F+ G V + HKG
Sbjct: 12 LQASNVTNKND---PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKG--- 63
Query: 119 RNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEFAKKFKKPRPQRSA 166
+AFV ++ A+AAV + + ++G+ + + A +P+P RS
Sbjct: 64 --YAFVQYSNERHARAAVLGENGRVLAGQTLDINMA---GEPKPDRSG 106
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 217 GYGFVSFATKEEAEAAISSLDGKELMGRPLRLKF 250
GY FV ++ + A AA+ +G+ L G+ L +
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 79 RKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQ 138
RK+ + LP + E+ +L + D E+ K + AFVT+ + E+A+AA+N
Sbjct: 3 RKILIRGLPGDVTNQEVHDLLS------DYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 56
Query: 139 FDTQEVSGRIIRVEF 153
F + R + V+
Sbjct: 57 FHQSRLRERELSVQL 71
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 83 VFNLPWSFSVAEIKNLFAPC---GTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
V LPWS S E++ F+ C + I + G+ AFV + S +E + A+ +
Sbjct: 12 VRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALKK- 70
Query: 140 DTQEVSGRIIRV 151
D + + R + V
Sbjct: 71 DRETMGHRYVEV 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.6 bits (70), Expect = 0.54, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSS-KVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
L V+ L + L F A P+++ +++ + G S GY FV F ++ +++ AI
Sbjct: 6 LIVNYLPQDMTDRELYALFRA-IGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 236 LDGKELMGRPLRLKFGQ 252
L+G + + L++ + +
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.8 bits (68), Expect = 0.77, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 202 VSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSL 236
VS+K + + + GYGFV F + A+ A+++L
Sbjct: 33 VSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+L+V P +E+ +F P G + +V+I+ FAFV E A A+ +
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEV 85
Query: 140 DTQEVSGRIIRVEFAK 155
+ + + + V ++K
Sbjct: 86 HGKSFANQPLEVVYSK 101
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
+L+V V+ + L E F F P+ + G+ FV F E A AI
Sbjct: 33 RLFVRPFPLDVQESELNEIFGP-FGPMKEVKILN-------GFAFVEFEEAESAAKAIEE 84
Query: 236 LDGKELMGRPLRLKF 250
+ GK +PL + +
Sbjct: 85 VHGKSFANQPLEVVY 99
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 173 TQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAA 232
T H +++ L ++ + FFS NP+ + +GR G V FAT E+A AA
Sbjct: 14 TGHCVHMRGLPYRATENDIYNFFSP-LNPMRVHIEI-GPDGRVTGEADVEFATHEDAVAA 71
Query: 233 IS 234
++
Sbjct: 72 MA 73
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 176 KLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISS 235
+L+V V+ + L E F F P+ + G+ FV F E A AI
Sbjct: 6 RLFVRPFPLDVQESELNEIFGP-FGPMKEVKILN-------GFAFVEFEEAESAAKAIEE 57
Query: 236 LDGKELMGRPLRLKFGQ 252
+ GK +PL + + +
Sbjct: 58 VHGKSFANQPLEVVYSK 74
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 80 KLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+L+V P +E+ +F P G + +V+I+ FAFV E A A+ +
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEV 58
Query: 140 DTQEVSGRIIRVEFAK 155
+ + + + V ++K
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 10/93 (10%)
Query: 75 QNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVV--DVEIIKHKGGK-NRNFAFVTMASPEE 131
+N + + NL ++ I AP + +V +IK K + NR FAF+ +++ E
Sbjct: 20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEA 79
Query: 132 AQ-----AAVNQFDTQEVSGRIIRVEFAKKFKK 159
AQ A++ T + G+ I VEFAK K+
Sbjct: 80 AQLLQILQALHPPLT--IDGKTINVEFAKGSKR 110
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%)
Query: 192 REFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAEAAISSLDGKELMG 243
R F + +S K++ G AGY FV FA AE + ++GK L G
Sbjct: 28 RAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG 79
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTV-VDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
L++ N P S++ I++L V + + + + +R FA++ + S E+A+ V +
Sbjct: 6 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 65
Query: 140 DTQEVSG 146
+ ++ G
Sbjct: 66 NGLKIEG 72
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 177 LYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNE-GRSAGYGFVSFATKEEAEAAISS 235
+ V N + V + +FF + + V + NE G G V+F +++EA AA+
Sbjct: 18 IKVQNXPFTVSIDEILDFFYG-YQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID 76
Query: 236 LDGKELMGRPLRL 248
L+ + + R ++L
Sbjct: 77 LNDRPIGSRKVKL 89
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 165 SASAPARETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFA 224
+S + T H + + + V ++ EF A PV+ ++V ++ G GY FV F+
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFL-APLKPVAIRIVRNAH-GNKTGYIFVDFS 58
Query: 225 TKEEAEAAISSLDGKELMG 243
+EE + A+ +E MG
Sbjct: 59 NEEEVKQALKC--NREYMG 75
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 15/73 (20%)
Query: 169 PARETQHKLYVSNL----SWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFA 224
P R + ++ VS L SW+ H+RE + V G G V +
Sbjct: 10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-----------GMGMVEYL 58
Query: 225 TKEEAEAAISSLD 237
KE+ E A+ LD
Sbjct: 59 RKEDMEYALRKLD 71
>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 = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 77 IRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAV 136
+ R LY+ NLP+ + E+ ++F G + + + + R A+V +A+ A
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAC 74
Query: 137 NQFDTQEVSGRIIRVEF 153
+ V R + V +
Sbjct: 75 DHLSGFNVCNRYLVVLY 91
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 107 DVEIIKHKGGK-NRNFAFVTMASPEEAQAAVNQFDT----QEVSGRIIRVEFAK 155
++ +IK K + NR FAFV ++S +A + + ++ G+ I V+FAK
Sbjct: 40 NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 95 IKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+ +LF+ G VV++E I GK + F FV S +A+ + F
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSF 74
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 117 KNRNFAFVTMASPEEAQAAVNQFDTQEVSGRIIRVEF 153
K + AFVT+ + E+A+AA+N F + R + V+
Sbjct: 38 KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQL 74
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 16/86 (18%)
Query: 70 EQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASP 129
++ +K+ ++R LY LF+ G VVD I+ K K R AFV
Sbjct: 16 DKIKKEELKRSLYA--------------LFSQFGHVVD--IVALKTMKMRGQAFVIFKEL 59
Query: 130 EEAQAAVNQFDTQEVSGRIIRVEFAK 155
+ A+ Q G+ +R+++AK
Sbjct: 60 GSSTNALRQLQGFPFYGKPMRIQYAK 85
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 28.1 bits (61), Expect = 4.9, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
+ V NLP + E+ +L D ++ +N+ AFVT+ + E+AQ A+ F
Sbjct: 8 ILVKNLPQDSNCQEVHDLLK------DYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61
Query: 141 TQEVSGRIIRVEF 153
G+ + V+
Sbjct: 62 QYSFRGKDLIVQL 74
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 95 IKNLFAPCGTVVDVEI-IKHKGGKNRNFAFVTMASPEEAQAAVNQF 139
+ +LF+ G VV++E I GK + F FV S +A+ + F
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSF 74
>pdb|1RXT|A Chain A, Crystal Structure Of Human Myristoyl-Coa:protein N-
Myristoyltransferase.
pdb|1RXT|B Chain B, Crystal Structure Of Human Myristoyl-Coa:protein N-
Myristoyltransferase.
pdb|1RXT|C Chain C, Crystal Structure Of Human Myristoyl-Coa:protein N-
Myristoyltransferase.
pdb|1RXT|D Chain D, Crystal Structure Of Human Myristoyl-Coa:protein N-
Myristoyltransferase
Length = 496
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 65 VETKPEQTQKQNIRRKLYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNF-AF 123
+ETK Q + R L F+L S E+++ F P ++D ++++ G+ +F +F
Sbjct: 341 METKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSF 400
Query: 124 VTMAS 128
T+ S
Sbjct: 401 YTLPS 405
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 7/90 (7%)
Query: 81 LYVFNLPWSFSVAEIKNLFAPCGTVVDVEIIKHKGGKNRNFAFVTMASPEEAQAAVNQFD 140
L+V NL + + ++ F+ G + V+ +K ++AF+ + A A+ + +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMN 66
Query: 141 TQEVSGRIIRVEFAKKFKKPRPQRSASAPA 170
+++ G I + FAK + R +R A A
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
>pdb|3OP1|A Chain A, Crystal Structure Of Macrolide-Efflux Protein Sp_1110 From
Streptococcus Pneumoniae
pdb|3OP1|B Chain B, Crystal Structure Of Macrolide-Efflux Protein Sp_1110 From
Streptococcus Pneumoniae
pdb|3OP1|C Chain C, Crystal Structure Of Macrolide-Efflux Protein Sp_1110 From
Streptococcus Pneumoniae
Length = 308
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 171 RETQHKLYVSNLSWKVRSTHLREFFSANFNPVSSKVVFESNEGRSAGYGFVSFATKEEAE 230
RE +LY+ + S + S +EFF+ ++K++ AG+ + + K+ AE
Sbjct: 90 REGVEELYLLDFSSQFASLTAQEFFATYIKAXNAKIIV-------AGFDYTFGSDKKTAE 142
Query: 231 AAISSLDGKELMGRPL 246
+ DG+ ++ P+
Sbjct: 143 DLKNYFDGEVIIVPPV 158
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.128 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,578,941
Number of Sequences: 62578
Number of extensions: 291876
Number of successful extensions: 1017
Number of sequences better than 100.0: 208
Number of HSP's better than 100.0 without gapping: 150
Number of HSP's successfully gapped in prelim test: 58
Number of HSP's that attempted gapping in prelim test: 673
Number of HSP's gapped (non-prelim): 318
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)