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= 015091
(413 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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 56/170 (32%), Positives = 83/170 (48%), Gaps = 6/170 (3%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
R L++G+L + E L F G + +K++ +K + Y F+E+ A LQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQ 59
Query: 142 TFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPST 201
T NG + N ++NWA DDT +FVGDL +V D L+ F+ +PS
Sbjct: 60 TLNGKQIENNI--VKINWAFQSQQSSSDDT--FNLFVGDLNVNVDDETLRNAFK-DFPSY 114
Query: 202 KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPA 251
V+ D TG ++GYGFV F + + AM M G + RP+RI A
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 48/185 (25%), Positives = 85/185 (45%), Gaps = 28/185 (15%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
++VG+L +T+ +L++ F+ P K++ID+ + Y FV + + A+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGP-IANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 235 EMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIV 294
+NG ++I A +Q SQ + SDD N +FVG+L+ V
Sbjct: 60 TLNGKQIENNIVKINWA----------------FQ-SQQSSSDDTFN---LFVGDLNVNV 99
Query: 295 TDEHLRELFSQYGQLV--HV----KIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNI 348
DE LR F + + HV + + + GFV F + A+ A+ + G L G+ +
Sbjct: 100 DDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 159
Query: 349 RLSWG 353
R++W
Sbjct: 160 RINWA 164
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 82.0 bits (201), Expect = 6e-16, Method: Composition-based stats.
Identities = 45/93 (48%), Positives = 60/93 (64%), Gaps = 2/93 (2%)
Query: 165 GEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG 224
G P++++FVGDL DV D ML E F YPS +G KVV+D+ TG +KGYGFV+F
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFT 59
Query: 225 DESEQLRAMTEMNG-VFCSTRPMRIGPATNKKT 256
DE EQ RA+TE G V ++P+R+ A K +
Sbjct: 60 DELEQKRALTECQGAVGLGSKPVRLSVAIPKAS 92
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 78.2 bits (191), Expect = 7e-15, Method: Composition-based stats.
Identities = 37/83 (44%), Positives = 56/83 (67%), Gaps = 3/83 (3%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGE-VVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+LW+GDL+ +MDE +++ FA GE V++VK+IRN+ TG GY F+EF A AE+ L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 142 TFNGTPMPNG--EQNFRLNWASF 162
NG P+P + F+LN+A++
Sbjct: 71 KINGKPLPGATPAKRFKLNYATY 93
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
++++GDL + + + F + K++ +RLTG GY FV F D + + +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 235 EMNG 238
++NG
Sbjct: 71 KING 74
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 7/69 (10%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLV-HVKIPAGKRCG------FVQFADRSCAEEALR 336
++++G+L+ + + + F+ G+ V VKI + G FV+FAD + AE+ L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 337 MLNGTQLGG 345
+NG L G
Sbjct: 71 KINGKPLPG 79
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 82/155 (52%), Gaps = 7/155 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + L + F+ GEV + K+IR+K G GYGF+ +++ AER + T
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
NG + + + ++++A + + D +++ L +T +++ F +R+
Sbjct: 65 NGLRLQS--KTIKVSYARPSS----EVIKDANLYISGLPRTMTQKDVEDMF-SRFGRIIN 117
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
++V++D+ TG ++G F+RF SE A+T NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 39/161 (24%), Positives = 81/161 (50%), Gaps = 31/161 (19%)
Query: 189 MLQETFRARYPS---TKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M Q+ R+ + S + AK++ D++ G + GYGFV + + RA+ +NG+ ++
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 246 MRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQ 305
+++ Y + S S+V + D N +++ L +T + + ++FS+
Sbjct: 74 IKVS-------------YARPS---SEVIK---DAN---LYISGLPRTMTQKDVEDMFSR 111
Query: 306 YGQLVHVKIPAGKRCG------FVQFADRSCAEEALRMLNG 340
+G++++ ++ + G F++F RS AEEA+ NG
Sbjct: 112 FGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 8/95 (8%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALR 336
T + V L +T + LR LFS G++ K+ K G FV + AE A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 337 MLNGTQLGGQNIRLSWGRSPSNKQAQPDPNQWNAG 371
LNG +L + I++S+ R PS++ + D N + +G
Sbjct: 63 TLNGLRLQSKTIKVSYAR-PSSEVIK-DANLYISG 95
>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 = 75.1 bits (183), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 82/155 (52%), Gaps = 7/155 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + L + F+ GEV + K+IR+K G GYGF+ +++ AER + T
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
NG + + + ++++A + + D +++ L +T +++ F +R+
Sbjct: 65 NGLRLQS--KTIKVSYARPSS----EVIKDANLYISGLPRTMTQKDVEDMF-SRFGRIIN 117
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
++V++D+ TG ++G F+RF SE A+T NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 39/161 (24%), Positives = 81/161 (50%), Gaps = 31/161 (19%)
Query: 189 MLQETFRARYPS---TKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M Q+ R+ + S + AK++ D++ G + GYGFV + + RA+ +NG+ ++
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 246 MRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQ 305
+++ Y + S S+V + D N +++ L +T + + ++FS+
Sbjct: 74 IKVS-------------YARPS---SEVIK---DAN---LYISGLPRTMTQKDVEDMFSR 111
Query: 306 YGQLVHVKIPAGKRCG------FVQFADRSCAEEALRMLNG 340
+G++++ ++ + G F++F RS AEEA+ NG
Sbjct: 112 FGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 8/95 (8%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALR 336
T + V L +T + LR LFS G++ K+ K G FV + AE A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 337 MLNGTQLGGQNIRLSWGRSPSNKQAQPDPNQWNAG 371
LNG +L + I++S+ R PS++ + D N + +G
Sbjct: 63 TLNGLRLQSKTIKVSYAR-PSSEVIK-DANLYISG 95
>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 = 74.7 bits (182), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 81/155 (52%), Gaps = 7/155 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + + F GE+ + K++R+K TGQ GYGF+ +I AE+ + T
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
NG + + ++++A + R D ++V L +T L++ F ++Y
Sbjct: 65 NGLRLQT--KTIKVSYARPSSASIR----DANLYVSGLPKTMTQKELEQLF-SQYGRIIT 117
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
+++++D++TG ++G GF+RF E A+ +NG
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/166 (29%), Positives = 84/166 (50%), Gaps = 31/166 (18%)
Query: 189 MLQETFRARYPST---KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M QE FR+ + S + K+V D++TG++ GYGFV + D + +A+ +NG+ T+
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 246 MRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQ 305
+++ Y + S + S D N ++V L +T + L +LFSQ
Sbjct: 74 IKVS-------------YARPS------SASIRDAN---LYVSGLPKTMTQKELEQLFSQ 111
Query: 306 YGQLVHVKIP------AGKRCGFVQFADRSCAEEALRMLNGTQLGG 345
YG+++ +I + GF++F R AEEA++ LNG + G
Sbjct: 112 YGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 8/97 (8%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEA 334
+ T + V L +T E R LF G++ K+ K G FV + D AE+A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 335 LRMLNGTQLGGQNIRLSWGRSPSNKQAQPDPNQWNAG 371
+ LNG +L + I++S+ R PS+ + D N + +G
Sbjct: 61 INTLNGLRLQTKTIKVSYAR-PSSASIR-DANLYVSG 95
>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 = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 59/208 (28%), Positives = 94/208 (45%), Gaps = 27/208 (12%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P +++VGDL DVT+ ML E F P +V D +T R+ GY +V F ++ R
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 232 AMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLD 291
A+ MN +P+RI Q+ P S + S V +F+ NLD
Sbjct: 73 ALDTMNFDVIKGKPVRI---------MWSQRDP--SLRKSGVGN---------IFIKNLD 112
Query: 292 SIVTDEHLRELFSQYGQLVHVKIPA----GKRCGFVQFADRSCAEEALRMLNGTQLGGQN 347
+ ++ L + FS +G ++ K+ K GFV F + AE A+ +NG L +
Sbjct: 113 KSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRK 172
Query: 348 IRLSWGRSPSNKQAQPDPNQWNAGYYGY 375
+ + GR S K+ + + +Y Y
Sbjct: 173 VFV--GRFKSRKEREAELGARAKEFYPY 198
Score = 72.4 bits (176), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 51/178 (28%), Positives = 87/178 (48%), Gaps = 17/178 (9%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
+L++GDL + E L F+ G +++++V R+ T + GY ++ F A AER L T
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 143 FN-----GTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRAR 197
N G P+ R+ W+ ++ IF+ +L + + L +TF A
Sbjct: 77 MNFDVIKGKPV-------RIMWSQRDPSLRKSGV--GNIFIKNLDKSIDNKALYDTFSA- 126
Query: 198 YPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
+ + KVV D +KGYGFV F + RA+ +MNG+ + R + +G ++K
Sbjct: 127 FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 182
>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 = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 55/195 (28%), Positives = 90/195 (46%), Gaps = 25/195 (12%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P +++VGDL DVT+ ML E F P +V D +T R+ GY +V F ++ R
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 232 AMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLD 291
A+ MN +P+RI Q+ P S + S V +F+ NLD
Sbjct: 68 ALDTMNFDVIKGKPVRI---------MWSQRDP--SLRKSGVG---------NIFIKNLD 107
Query: 292 SIVTDEHLRELFSQYGQLVHVKIPA----GKRCGFVQFADRSCAEEALRMLNGTQLGGQN 347
+ ++ L + FS +G ++ K+ K GFV F + AE A+ +NG L +
Sbjct: 108 KSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRK 167
Query: 348 IRLSWGRSPSNKQAQ 362
+ + +S ++A+
Sbjct: 168 VFVGRFKSRKEREAE 182
Score = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 51/178 (28%), Positives = 88/178 (49%), Gaps = 17/178 (9%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
+L++GDL + E L F+ G +++++V R+ T + GY ++ F A AER L T
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 143 FN-----GTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRAR 197
N G P+ R+ W+ ++ + IF+ +L + + L +TF A
Sbjct: 72 MNFDVIKGKPV-------RIMWSQRDPSLRKSGVGN--IFIKNLDKSIDNKALYDTFSA- 121
Query: 198 YPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
+ + KVV D +KGYGFV F + RA+ +MNG+ + R + +G ++K
Sbjct: 122 FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 177
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 45/157 (28%), Positives = 78/157 (49%), Gaps = 7/157 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + L F G + +++R+ +TG GY F++F S ++R ++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
NG + N + ++++A G GE DT ++V +L +TD L F +Y S
Sbjct: 66 NGITVRN--KRLKVSYARPG-GESIKDT---NLYVTNLPRTITDDQLDTIF-GKYGSIVQ 118
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVF 240
++ D+LTGR +G FVR+ E A++ +N V
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 73/170 (42%), Gaps = 29/170 (17%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V L D+TD L FRA P +++ D TG + GY FV F E + RA+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+NG+ + +++ S + +T ++V NL +T
Sbjct: 65 LNGITVRNKRLKV----------------------SYARPGGESIKDTNLYVTNLPRTIT 102
Query: 296 DEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRMLN 339
D+ L +F +YG +V I K G FV++ R A+EA+ LN
Sbjct: 103 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++ +L + + L+T F G +V ++R+K TG+ G F+ + R A+ +
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 144 NGTPMPNGEQNFRLNWA 160
N G Q + A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEA 334
+NT + V L +TD L LF G + +I + G FV F ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 335 LRMLNGTQLGGQNIRLSWGR 354
+++LNG + + +++S+ R
Sbjct: 62 IKVLNGITVRNKRLKVSYAR 81
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 68.2 bits (165), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 48/180 (26%), Positives = 90/180 (50%), Gaps = 33/180 (18%)
Query: 189 MLQETFRARYPST---KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M Q+ F++ + S + K+V D++TG++ GYGFV + D ++ +A+ +NG+ T+
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKT 75
Query: 246 MRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQ 305
+++ SY A D ++V L ++ + + +LFSQ
Sbjct: 76 IKV------------------SYARPSSASIRD----ANLYVSGLPKTMSQKEMEQLFSQ 113
Query: 306 YGQLVHVKIP------AGKRCGFVQFADRSCAEEALRMLNGTQ-LG-GQNIRLSWGRSPS 357
YG+++ +I + GF++F R AEEA++ LNG + LG + I + + +PS
Sbjct: 114 YGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNPS 173
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 38/155 (24%), Positives = 79/155 (50%), Gaps = 7/155 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + + F G++ + K++R+K TGQ GYGF+ + A++ + T
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
NG + + ++++A + R D ++V L ++ +++ F ++Y
Sbjct: 67 NGLKLQT--KTIKVSYARPSSASIR----DANLYVSGLPKTMSQKEMEQLF-SQYGRIIT 119
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
+++++D+ TG ++G GF+RF E A+ +NG
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
>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 = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 72/143 (50%), Gaps = 7/143 (4%)
Query: 98 LNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRL 157
L F G + ++ R+ +TG GY F++F S ++R ++ NG + N + ++
Sbjct: 31 LYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRN--KRLKV 88
Query: 158 NWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKG 217
++A G GE DT ++V +L +TD L F +Y S ++ D+LTGR +G
Sbjct: 89 SYARPG-GESIKDT---NLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPRG 143
Query: 218 YGFVRFGDESEQLRAMTEMNGVF 240
FVR+ E A++ +N V
Sbjct: 144 VAFVRYNKREEAQEAISALNNVI 166
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 71/170 (41%), Gaps = 29/170 (17%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V L D TD L FRA P ++ D TG + GY FV F E + RA+
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+NG+ + +++ S + +T ++V NL +T
Sbjct: 76 LNGITVRNKRLKV----------------------SYARPGGESIKDTNLYVTNLPRTIT 113
Query: 296 DEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRMLN 339
D+ L +F +YG +V I K G FV++ R A+EA+ LN
Sbjct: 114 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++ +L + + L+T F G +V ++R+K TG+ G F+ + R A+ +
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 144 NGTPMPNGEQNFRLNWA 160
N G Q + A
Sbjct: 163 NNVIPEGGSQPLSVRLA 179
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 275 QSDD---DP--NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FV 323
+SDD DP +NT + V L TD L LF G + +I + G FV
Sbjct: 2 ESDDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFV 61
Query: 324 QFADRSCAEEALRMLNGTQLGGQNIRLSWGR 354
F ++ A+++LNG + + +++S+ R
Sbjct: 62 DFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 48/87 (55%)
Query: 278 DDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRM 337
P N TV+ G + S +TD+ +R+ FS +GQ++ +++ K FV+F+ A A+
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVS 80
Query: 338 LNGTQLGGQNIRLSWGRSPSNKQAQPD 364
+NGT + G ++ WG+ + + P
Sbjct: 81 VNGTTIEGHVVKCYWGKESPDMTSGPS 107
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
T++ G +A+ +TD ++++TF S G + I KGY FVRF A+
Sbjct: 27 TVYCGGIASGLTDQLMRQTF-----SPFGQIMEIRVFP--EKGYSFVRFSTHESAAHAIV 79
Query: 235 EMNG 238
+NG
Sbjct: 80 SVNG 83
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T++ G + + + + F+ G+++ ++V K GY F+ F + A + +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVS 80
Query: 143 FNGTPM 148
NGT +
Sbjct: 81 VNGTTI 86
>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 = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 62/111 (55%), Gaps = 7/111 (6%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G+K+D + +FVGDL+ ++T ++ F A + A+VV D TG++KGYG
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAF-APFGRISDARVVKDMATGKSKGYG 60
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQN 270
FV F ++ + A+ +M G + R +R AT K PK++Y++
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA------PKSTYES 105
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 6/84 (7%)
Query: 275 QSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI------PAGKRCGFVQFADR 328
Q D N+ VFVG+L +T E ++ F+ +G++ ++ K GFV F ++
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 329 SCAEEALRMLNGTQLGGQNIRLSW 352
AE A++ + G LGG+ IR +W
Sbjct: 68 WDAENAIQQMGGQWLGGRQIRTNW 91
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++GDL + + FA G + +V+++ TG+ +GYGF+ F ++ AE +Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 144 NGTPMPNGEQNFRLNWAS 161
G + G + R NWA+
Sbjct: 78 GGQWL--GGRQIRTNWAT 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 54/95 (56%), Gaps = 1/95 (1%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G+K+D + +FVGDL+ ++T ++ F A + A+VV D TG++KGYG
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAF-APFGKISDARVVKDMATGKSKGYG 60
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNK 254
FV F ++ + A+ M G + R +R AT K
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 275 QSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI------PAGKRCGFVQFADR 328
Q D N+ VFVG+L +T E ++ F+ +G++ ++ K GFV F ++
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 329 SCAEEALRMLNGTQLGGQNIRLSW 352
AE A+ + G LGG+ IR +W
Sbjct: 68 LDAENAIVHMGGQWLGGRQIRTNW 91
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++GDL + + + FA G++ +V+++ TG+ +GYGF+ F ++ AE +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 144 NGTPMPNGEQNFRLNWAS 161
G + G + R NWA+
Sbjct: 78 GGQWL--GGRQIRTNWAT 93
>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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/137 (30%), Positives = 66/137 (48%), Gaps = 17/137 (12%)
Query: 262 QYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR-- 319
QY ++ Q + T++VGNL T+E + ELFS+ G + + + K
Sbjct: 19 QYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78
Query: 320 --CGF--VQFADRSCAEEALRMLNGTQLGGQNIRLSW----------GRSPSNKQAQPDP 365
CGF V++ R+ AE A+R +NGT+L + IR W GR S Q + +
Sbjct: 79 TACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138
Query: 366 NQ-WNAGYYGYAQGYEN 381
Q ++AG GY + +N
Sbjct: 139 RQDYDAGRGGYGKLAQN 155
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 47/86 (54%), Gaps = 3/86 (3%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
TL++G+L ++ E + F+ +G++ + + +K G+ F+E+ SRA AE ++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 143 FNGTPMPNGEQNFRLNW-ASFGAGEK 167
NGT + + + R +W A F G +
Sbjct: 101 INGTRLDD--RIIRTDWDAGFKEGRQ 124
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 56/204 (27%), Positives = 88/204 (43%), Gaps = 32/204 (15%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++G+L + E F GE V + R++ G+GFI SR AE
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKG 203
+GT + + + R+ +A+ GA + V +L+ V++ +L++ F P K
Sbjct: 79 DGTILKS--RPLRIRFATHGAA----------LTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 204 AKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEM-NGVFCST---RPMRIGPATN------ 253
VV DR GR G GFV F + +A+ +G F T RP+ + P
Sbjct: 127 VVVVDDR--GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDG 184
Query: 254 --KKTVSGQQQYPKASYQNSQVAQ 275
+K + QQY K Q + AQ
Sbjct: 185 LPEKLMQKTQQYHKEREQPPRFAQ 208
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 48/186 (25%), Positives = 82/186 (44%), Gaps = 40/186 (21%)
Query: 155 FRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGR 214
F ++ SF ++ T +FVG+L D+T+ + F RY + ++V I+R
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFE-RY--GEPSEVFINR---- 56
Query: 215 TKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVA 274
+G+GF+R + A E++G +RP+RI AT+ ++
Sbjct: 57 DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALT---------------- 100
Query: 275 QSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR-----CGFVQFADRS 329
V NL +V++E L + FSQ+G + + R GFV+FA +
Sbjct: 101 ------------VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKP 148
Query: 330 CAEEAL 335
A +AL
Sbjct: 149 PARKAL 154
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 40/69 (57%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLG 344
+FVGNL + +T+E + LF +YG+ V I + GF++ R+ AE A L+GT L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 345 GQNIRLSWG 353
+ +R+ +
Sbjct: 85 SRPLRIRFA 93
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 276 SDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEAL 335
S +D TT++VG L +T+ LR F Q+G++ + + ++C F+QFA R AE A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65
Query: 336 -RMLNGTQLGGQNIRLSWGR 354
+ N + G+ + + WGR
Sbjct: 66 EKSFNKLIVNGRRLNVKWGR 85
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
I TL++G L + ET L F GE+ + V++ +Q FI+F +R AE
Sbjct: 12 ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAA 65
Query: 141 QTFNGTPMPNGEQNFRLN 158
+ + NG RLN
Sbjct: 66 EKSFNKLIVNGR---RLN 80
>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 = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVGDL +V D L+ F+ +PS V+ D TG ++GYGFV F + + AM
Sbjct: 4 LFVGDLNVNVDDETLRNAFK-DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 236 MNGVFCSTRPMRIGPA 251
M G + RP+RI A
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++GDL +D+ L F ++ V+ + QTG GYGF+ F S+ A+ + +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 144 NGTPMPNGEQNFRLNWAS 161
G + NG R+NWA+
Sbjct: 64 QGQDL-NGRP-LRINWAA 79
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLV--HV----KIPAGKRCGFVQFADRSCAEEALRML 338
+FVG+L+ V DE LR F + + HV + + + GFV F + A+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 339 NGTQLGGQNIRLSWG 353
G L G+ +R++W
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 55.5 bits (132), Expect = 5e-08, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 48/79 (60%), Gaps = 1/79 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
++VG L ++T+ ML+ F + + ++++D TGR+KGYGF+ F D +A+ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEP-FGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 236 MNGVFCSTRPMRIGPATNK 254
+NG + RPM++G T +
Sbjct: 88 LNGFELAGRPMKVGHVTER 106
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 44/72 (61%), Gaps = 6/72 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA------GKRCGFVQFADRSCAEEALRML 338
++VG+L +T++ LR +F +G++ +++ K GF+ F+D CA++AL L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 339 NGTQLGGQNIRL 350
NG +L G+ +++
Sbjct: 89 NGFELAGRPMKV 100
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 36/62 (58%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++G L + + E L F G + +++++ + +TG+ +GYGFI F A++ L+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 144 NG 145
NG
Sbjct: 89 NG 90
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 55.1 bits (131), Expect = 7e-08, Method: Composition-based stats.
Identities = 31/81 (38%), Positives = 47/81 (58%), Gaps = 5/81 (6%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVI--DRLTGRTKGYGFVRFGDESEQLRAM 233
++VG L ++T+ ML+ F P K +V+ D TGR+KGYGF+ F D RA+
Sbjct: 8 LYVGSLHFNITEDMLRGIFE---PFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 234 TEMNGVFCSTRPMRIGPATNK 254
++NG + RPMR+G T +
Sbjct: 65 EQLNGFELAGRPMRVGHVTER 85
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA------GKRCGFVQFADRSCAEEAL 335
++ ++VG+L +T++ LR +F +G++ ++ + K GF+ F+D CA AL
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 336 RMLNGTQLGGQNIRL 350
LNG +L G+ +R+
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++G L + + E L F G++ + ++++ TG+ +GYGFI F A R L+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 144 N-----GTPMPNGEQNFRLNWAS 161
N G PM G RL+ S
Sbjct: 68 NGFELAGRPMRVGHVTERLDGGS 90
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLG 344
+F+GNL T++ +R LF QYG+++ I K GFV D++ AE+A+R L+ +L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 345 GQNIRLSWGRSPSNKQAQP 363
G NI + ++ S + P
Sbjct: 69 GVNINVEASKNKSKASSGP 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 1/86 (1%)
Query: 170 DTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQ 229
D ++FVG++ + T+ L++ F P ++V DR TG+ KGYGF + D+
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVV-SFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 230 LRAMTEMNGVFCSTRPMRIGPATNKK 255
L AM +NG S R +R+ A ++K
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEK 89
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 47/85 (55%), Gaps = 10/85 (11%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLVHVKI--------PAGKRCGFVQFADRSCAEEAL 335
+VFVGN+ T+E L+++FS+ G +V ++ P G GF ++ D+ A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG--YGFCEYQDQETALSAM 67
Query: 336 RMLNGTQLGGQNIRLSWGRSPSNKQ 360
R LNG + G+ +R+ S NK+
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKE 92
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 40/65 (61%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
+R++++G++ Y E L F+ G VV+ +++ +++TG+ +GYGF E+ + A +
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 141 QTFNG 145
+ NG
Sbjct: 68 RNLNG 72
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLG 344
+FV NL + VT+E L + FSQ+G+L VK K F+ F +R A +A+ +NG L
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--KLKDYAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 345 GQNIRLSWGRSPSNKQAQ 362
G+NI + + + P K+ +
Sbjct: 72 GENIEIVFAKPPDQKRKE 89
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV +LA VT+ +L++ F S G + +L K Y F+ F + ++AM E
Sbjct: 14 LFVRNLANTVTEEILEKAF-----SQFGKLERVKKL----KDYAFIHFDERDGAVKAMEE 64
Query: 236 MNG 238
MNG
Sbjct: 65 MNG 67
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 79 GEIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAER 138
+++ L++ +L + E L F+ G++ VK +++ Y FI F R GA +
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVK 60
Query: 139 VLQTFNG 145
++ NG
Sbjct: 61 AMEEMNG 67
>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 = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 40/177 (22%), Positives = 80/177 (45%), Gaps = 10/177 (5%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++G + Y + E + FA G + ++ + + T + +G+ F+E+ A+ L+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 144 NGTPMPNGEQNFRLNWAS-FGAGEKRDDTPD------HTIFVGDLAADVTDYMLQETFRA 196
N + G +N ++ S G + D + I+V + D++D ++ F A
Sbjct: 91 NSVML--GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 197 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATN 253
+ K A + D TG+ KGYGF+ + A++ MN + +R+G A
Sbjct: 149 -FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 43/188 (22%), Positives = 92/188 (48%), Gaps = 20/188 (10%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K + D +T + KG+ FV + E+ QL A+
Sbjct: 31 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 88
Query: 235 EMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIV 294
+MN V R +++G +N GQ Q P Q+A+ N ++V ++ +
Sbjct: 89 QMNSVMLGGRNIKVGRPSN----IGQAQ-PII----DQLAEEARAFNR--IYVASVHQDL 137
Query: 295 TDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRMLNGTQLGGQNI 348
+D+ ++ +F +G++ + K GF+++ +++A+ +N LGGQ +
Sbjct: 138 SDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Query: 349 RLSWGRSP 356
R+ +P
Sbjct: 198 RVGKAVTP 205
>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 = 51.6 bits (122), Expect = 9e-07, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 5/74 (6%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR---CGF--VQFADRSCAEEALRML 338
T++VGNL T+E + ELFS+ G + + + K CGF V++ R+ AE A+R +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 339 NGTQLGGQNIRLSW 352
NGT+L + IR W
Sbjct: 80 NGTRLDDRIIRTDW 93
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
TL++G+L ++ E + F+ +G++ + + +K G+ F+E+ SRA AE ++
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAMRY 78
Query: 143 FNGTPMPNGEQNFRLNW 159
NGT + ++ R +W
Sbjct: 79 INGTRL--DDRIIRTDW 93
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 69
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 70 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 126
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 127 -EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 179
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 17 LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 73
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 74 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 118
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 119 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 39/177 (22%), Positives = 79/177 (44%), Gaps = 10/177 (5%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++G + Y + E + FA G + ++ + + T + +G+ F+E+ A+ L+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 144 NGTPMPNGEQNFRLNWAS-FGAGEKRDDTPD------HTIFVGDLAADVTDYMLQETFRA 196
N + G +N ++ S G + D + I+V + D++D ++ F A
Sbjct: 76 NSVML--GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 133
Query: 197 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATN 253
+ K + D TG+ KGYGF+ + A++ MN + +R+G A
Sbjct: 134 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 189
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 43/188 (22%), Positives = 92/188 (48%), Gaps = 20/188 (10%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K + D +T + KG+ FV + E+ QL A+
Sbjct: 16 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 73
Query: 235 EMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIV 294
+MN V R +++G +N GQ Q P Q+A+ N ++V ++ +
Sbjct: 74 QMNSVMLGGRNIKVGRPSN----IGQAQ-PII----DQLAEEARAFNR--IYVASVHQDL 122
Query: 295 TDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRMLNGTQLGGQNI 348
+D+ ++ +F +G++ + K GF+++ +++A+ +N LGGQ +
Sbjct: 123 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 182
Query: 349 RLSWGRSP 356
R+ +P
Sbjct: 183 RVGKAVTP 190
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 68
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 69 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 126 -EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 16 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 72
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 73 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 117
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 67
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 68 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 124
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 125 -EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 177
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 15 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 71
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 72 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 116
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 117 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 71/149 (47%), Gaps = 27/149 (18%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT- 142
++IG L + E L F G V +K++++ TG+ G+GF+ F + + V++T
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 143 --FNGT------PMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETF 194
+G +P EQ+ IFVG + DV +E F
Sbjct: 66 HILDGKVIDPKRAIPRDEQD-----------------KTGKIFVGGIGPDVRPKEFEEFF 108
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRF 223
+++ + A++++D+ TG+++G+GFV +
Sbjct: 109 -SQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 66/146 (45%), Gaps = 25/146 (17%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L D T+ L+E F +Y + K++ D TGR++G+GF+ F E+ ++ E
Sbjct: 6 MFIGGLNWDTTEDNLREYF-GKYGTVTDLKIMKDPATGRSRGFGFLSF----EKPSSVDE 60
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ ++ + K + ++ P+ D+ +FVG + V
Sbjct: 61 V---------VKTQHILDGKVIDPKRAIPR-----------DEQDKTGKIFVGGIGPDVR 100
Query: 296 DEHLRELFSQYGQLVHVKIPAGKRCG 321
+ E FSQ+G ++ ++ K G
Sbjct: 101 PKEFEEFFSQWGTIIDAQLMLDKDTG 126
Score = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRC---GFVQFADRSCAEEA 334
+ +F+G L+ T+++LRE F +YG + +KI PA R GF+ F S +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 335 LR---MLNG 340
++ +L+G
Sbjct: 62 VKTQHILDG 70
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 102 FAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
F+ G ++ +++ +K TGQ G+GF+ + S +RV Q
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 68
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 69 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 126 -EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 16 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 72
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 73 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 117
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 66
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 67 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 123
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 124 -EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 176
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 14 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 70
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 71 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 115
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 116 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 76/174 (43%), Gaps = 16/174 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++R L+IG L + + L + F G + V+R+ T + G+GF+ + A E V
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY---ATVEEV 61
Query: 140 LQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD-----HTIFVGDLAADVTDYMLQETF 194
N P + + R+ + P IFVG + D ++ L++ F
Sbjct: 62 DAAMNARPH---KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 118
Query: 195 RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE----MNGVFCSTR 244
+Y + +++ DR +G+ +G+ FV F D + + + +NG C R
Sbjct: 119 E-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 171
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 24/166 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+G L+ + TD L+ F ++ + V+ D T R++G+GFV + E AM
Sbjct: 9 LFIGGLSFETTDESLRSHFE-QWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-- 65
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ RP + V G+ PK + + +FVG +
Sbjct: 66 ------NARPHK---------VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 110
Query: 296 DEHLRELFSQYGQLVHVKIP----AGKRCG--FVQFADRSCAEEAL 335
+ HLR+ F QYG++ ++I +GK+ G FV F D ++ +
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQ 342
+ +FVGNL +T+E +R+LF +YG+ V I K GF++ R+ AE A L+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 82
Query: 343 LGGQNIRLSWG 353
L G+ +R+ +
Sbjct: 83 LRGKQLRVRFA 93
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 75/167 (44%), Gaps = 44/167 (26%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVG+L D+T+ +++ F +Y K +V I + KG+GF+R + R + E
Sbjct: 25 LFVGNLPPDITEEEMRKLF-EKY--GKAGEVFIH----KDKGFGFIRL-----ETRTLAE 72
Query: 236 MNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVT 295
+ V P+R G+Q + + ++ + V NL V+
Sbjct: 73 IAKVELDNMPLR-----------GKQLRVRFACHSASLT------------VRNLPQYVS 109
Query: 296 DEHLRELFSQYGQLVHVKI-------PAGKRCGFVQFADRSCAEEAL 335
+E L E FS +GQ+ + P+GK G V+F+ + A +AL
Sbjct: 110 NELLEEAFSVFGQVERAVVIVDDRGRPSGK--GIVEFSGKPAARKAL 154
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.9 bits (115), Expect = 6e-06, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI------PAGKRCGFVQFADRSCAEE 333
P+ +TV+V NL +T+ L +FS+YG++V V I K F+ F D+ A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 334 ALRMLNGTQLGGQNIRLS 351
R +N QL G+ I+ S
Sbjct: 74 CTRAINNKQLFGRVIKAS 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
++V +L + D L++ F + + + AKV+++ GR+KG+GFV F E +A+TE
Sbjct: 18 LYVKNLDDGIDDERLRKAF-SPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 236 MNGVFCSTRPMRIGPATNKK 255
MNG +T+P+ + A K+
Sbjct: 75 MNGRIVATKPLYVALAQRKE 94
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA----GKRCGFVQFADRSCAEEALRMLNG 340
++V NLD + DE LR+ FS +G + K+ K GFV F+ A +A+ +NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 341 TQLGGQNIRLSWGRSPSNKQAQP 363
+ + + ++ + +Q+ P
Sbjct: 78 RIVATKPLYVALAQRKEERQSGP 100
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
++ L++ +L +D+ L F+ G + + KV+ + G+ +G+GF+ F S A +
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKA 71
Query: 140 LQTFNG 145
+ NG
Sbjct: 72 VTEMNG 77
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 38/177 (21%), Positives = 77/177 (43%), Gaps = 10/177 (5%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++G + Y + E + FA G + ++ + T + +G+ F+E+ A+ L+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 144 NGTPMPNGEQNFRLNWAS-FGAGEKRDDTPD------HTIFVGDLAADVTDYMLQETFRA 196
N + G +N ++ S G + D + I+V + D++D ++ F A
Sbjct: 75 NSVXL--GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 132
Query: 197 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATN 253
+ K + D TG+ KGYGF+ + A++ N + +R+G A
Sbjct: 133 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVT 188
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/195 (22%), Positives = 90/195 (46%), Gaps = 20/195 (10%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K D +T + KG+ FV + E+ QL A+
Sbjct: 15 VYVGSIYYELGEDTIRQAF-APFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQL-ALE 72
Query: 235 EMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIV 294
+ N V R +++G +N GQ Q P Q+A+ N ++V ++ +
Sbjct: 73 QXNSVXLGGRNIKVGRPSN----IGQAQ-PII----DQLAEEARAFNR--IYVASVHQDL 121
Query: 295 TDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRMLNGTQLGGQNI 348
+D+ ++ +F +G++ + K GF+++ +++A+ N LGGQ +
Sbjct: 122 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Query: 349 RLSWGRSPSNKQAQP 363
R+ +P P
Sbjct: 182 RVGKAVTPPXPLLTP 196
>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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 8/94 (8%)
Query: 174 HTIFVG--DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
+T+FVG D+ D T+ +F ARY S K K++ DR TG +KGYGFV F ++ + ++
Sbjct: 10 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD-VQ 64
Query: 232 AMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPK 265
+ E F + +++GPA K+ +S P+
Sbjct: 65 KIVESQINF-HGKKLKLGPAIRKQNLSTYHVQPR 97
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T+++G + MDET + + FA G V VK+I ++ TG +GYGF+ F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 143 ---FNGTPMPNGEQNFRLNWASF 162
F+G + G + N +++
Sbjct: 70 QINFHGKKLKLGPAIRKQNLSTY 92
Score = 32.7 bits (73), Expect = 0.36, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI-----PAGKRCGFVQF 325
PN TVFVG +D + + +R F++YG + VKI K GFV F
Sbjct: 9 PN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 7/73 (9%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA-------GKRCGFVQFADRSCAEEAL 335
T V +G L VT +H+ E+FS YG++ + +P K +V+F + AE+AL
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 336 RMLNGTQLGGQNI 348
+ ++G Q+ GQ I
Sbjct: 65 KHMDGGQIDGQEI 77
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGR-TKGYGFVRFGDESEQLRAMT 234
+ +G L +VT + E F + Y K + ++R+ +KGY +V F + E +A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIF-STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 235 EMNG 238
M+G
Sbjct: 66 HMDG 69
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 173 DHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRA 232
D T++VG L V++ +L E F P + DR+TG+ +GYGFV F E + A
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVN-THMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 233 MTEMNGVFCSTRPMRIGPAT-NKKTVSG 259
+ M+ + +P+R+ A+ + K +SG
Sbjct: 74 IKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 6/76 (7%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEAL 335
+ TV+VG LD V++ L ELF Q G +V+ +P + GFV+F A+ A+
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 336 RMLNGTQLGGQNIRLS 351
++++ +L G+ IR++
Sbjct: 75 KIMDMIKLYGKPIRVN 90
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T+++G L + E L F G VV + +++ TGQ +GYGF+EF+S A+ ++
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 143 FN 144
+
Sbjct: 77 MD 78
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVG L+ D + L++ F ++Y VV DR T R++G+GFV F + + AM
Sbjct: 15 LFVGGLSFDTNEQSLEQVF-SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 236 MNGVFCSTRPMRIGPA 251
MNG R +R+ A
Sbjct: 74 MNGKSVDGRQIRVDQA 89
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 6/85 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALRML 338
+FVG L ++ L ++FS+YGQ+ V + + GFV F + A++A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 339 NGTQLGGQNIRLSWGRSPSNKQAQP 363
NG + G+ IR+ S+ ++ P
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRSGP 99
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 36/65 (55%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++G L + +E L F+ G++ V V+++++T + G+GF+ F + A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 144 NGTPM 148
NG +
Sbjct: 75 NGKSV 79
>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 = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 32/53 (60%)
Query: 93 MDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
M + L + F+ GEV + K+IR+K G GYGF+ +++ AER + T NG
Sbjct: 16 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEE 333
P T + V L +T + LR LFS G++ K+ K G FV + AE
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 334 ALRMLNGTQLGGQNIRLSWGR 354
A+ LNG +L + I++S+ R
Sbjct: 62 AINTLNGLRLQSKTIKVSYAR 82
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 189 MLQETFRARYPS---TKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M Q+ R+ + S + AK++ D++ G + GYGFV + + RA+ +NG+ ++
Sbjct: 16 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 75
Query: 246 MRIGPA 251
+++ A
Sbjct: 76 IKVSYA 81
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 45/81 (55%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQ 342
+ +FVGNL +T+E +R+LF +YG+ V I K GF++ R+ AE A L+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 343 LGGQNIRLSWGRSPSNKQAQP 363
L G+ +R+ + ++ + P
Sbjct: 76 LRGKQLRVRFACHSASLTSGP 96
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVG+L D+T+ +++ F +Y K +V I + KG+GF+R + R + E
Sbjct: 18 LFVGNLPPDITEEEMRKLFE-KY--GKAGEVFIH----KDKGFGFIRL-----ETRTLAE 65
Query: 236 MNGVFCSTRPMR 247
+ V P+R
Sbjct: 66 IAKVELDNMPLR 77
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 4/88 (4%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
+R L + + +DE L F G + +VK++ +++T Q GYGF++F S + A++ +
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 141 QTFNGTPMPNGEQNFRLNWASFGAGEKR 168
NG + N RL A +G +R
Sbjct: 102 AGLNGFNI----LNKRLKVALAASGHQR 125
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V + V + L++ F RY + K+V DR T +++GYGFV+F S +A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFE-RYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 236 MNGVFCSTRPMRIGPATN 253
+NG + +++ A +
Sbjct: 104 LNGFNILNKRLKVALAAS 121
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALRML 338
+ V + + V + LR+LF +YG + VKI + GFV+F S A++A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 339 NGTQLGGQNIRLSWGRS 355
NG + + ++++ S
Sbjct: 105 NGFNILNKRLKVALAAS 121
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
+++G L Y + L F G++ VI ++QTG+ GYGF+ RA AER +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 144 NGTPMPNGEQNFRLNWASFGA 164
N P+ +G + +N A GA
Sbjct: 80 N--PIIDGRKA-NVNLAYLGA 97
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 170 DTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQ 229
DT IFVG L TD L++ F + + A V+ DR TG+++GYGFV D +
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEG-FGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 230 LRAMTEMNGVF 240
RA + N +
Sbjct: 73 ERACKDPNPII 83
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 279 DPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAE 332
D T +FVG L TD LR+ F +G + + ++ GFV ADR+ AE
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 333 EALRMLNGTQLGGQ-NIRLSW-GRSPSNKQ 360
A + N G + N+ L++ G P + Q
Sbjct: 74 RACKDPNPIIDGRKANVNLAYLGAKPRSLQ 103
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 42/81 (51%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
IF+G+L ++ + +L +TF A + K++ D TG +KGY F+ F A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 236 MNGVFCSTRPMRIGPATNKKT 256
MNG + RP+ + A K +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDS 88
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAV-KVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
++IG+L +DE L F+ G ++ K++R+ TG +GY FI F S ++ ++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 143 FNGTPMPN 150
NG + N
Sbjct: 68 MNGQYLCN 75
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHV-KIPAGKRCG------FVQFADRSCAEEA 334
++ +F+GNLD + ++ L + FS +G ++ KI G F+ FA ++ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 335 LRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
+ +NG L + I +S+ +K + P
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDSKGSGP 93
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 79/183 (43%), Gaps = 29/183 (15%)
Query: 170 DTPDH---TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTG--RTKGYGFVRFG 224
D PD +FVG + ++ L+E F +Y + V+ DR ++KG FV F
Sbjct: 9 DQPDLDAIKMFVGQVPRTWSEKDLRELFE-QYGAVYEINVLRDRSQNPPQSKGCCFVTFY 67
Query: 225 DESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTT 284
L A ++ M++ P + Q P S +N+ V +
Sbjct: 68 TRKAALEAQNALHN-------MKVLPGMHHPI----QMKPADSEKNNAV-------EDRK 109
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEALRMLN 339
+F+G + T+ +R +FS +GQ+ +I G + C FV F R+ A+ A++ ++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Query: 340 GTQ 342
Q
Sbjct: 170 QAQ 172
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 279 DPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI--------PAGKRCGFVQFADRSC 330
D + +FVG + +++ LRELF QYG + + + P K C FV F R
Sbjct: 12 DLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 71
Query: 331 AEEALRMLNGTQL 343
A EA L+ ++
Sbjct: 72 ALEAQNALHNMKV 84
>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 = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 30/48 (62%)
Query: 98 LNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
L + F+ GEV + K+IR+K G GYGF+ +++ AER + T NG
Sbjct: 36 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALR 336
T + V L T + LR LFS G++ K+ K G FV + AE A+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 337 MLNGTQLGGQNIRLSWGR 354
LNG +L + I++S+ R
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
Score = 35.8 bits (81), Expect = 0.051, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 191 QETFRARYPS---TKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMR 247
Q+ R+ + S + AK++ D++ G + GYGFV + + RA+ +NG+ ++ ++
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 92
Query: 248 IGPA 251
+ A
Sbjct: 93 VSYA 96
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 9/88 (10%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALR 336
T++ V NL + + LR +F +YG++ V IP + FV+F D+ AE+A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 337 MLNGTQLGGQNIRLS---WGRSPSNKQA 361
++G L G+ +R+ +GR P + +
Sbjct: 131 AMDGAVLDGRELRVQMARYGRPPDSHHS 158
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 61/144 (42%), Gaps = 10/144 (6%)
Query: 112 KVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGE-------QNFRLNWASFGA 164
K+I N +T ++G E + A AE+V + + +GE + F + S
Sbjct: 4 KLILNGKT--LKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHH 61
Query: 165 GEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG 224
D ++ V +L + L+ F +Y + DR T ++G+ FVRF
Sbjct: 62 HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFE-KYGRVGDVYIPRDRYTKESRGFAFVRFH 120
Query: 225 DESEQLRAMTEMNGVFCSTRPMRI 248
D+ + AM M+G R +R+
Sbjct: 121 DKRDAEDAMDAMDGAVLDGRELRV 144
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 34/83 (40%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 274 AQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADR 328
AQ + D TVFVGNL++ V +E L ELF Q G L V I K GFV F
Sbjct: 11 AQEEAD---RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 329 SCAEEALRMLNGTQLGGQNIRLS 351
A+ +LNG +L G+ I +S
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 173 DHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRA 232
D T+FVG+L A V + +L E F P TK + DR G+ K +GFV F A
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTK-VTICKDR-EGKPKSFGFVCFKHPESVSYA 73
Query: 233 MTEMNGVFCSTRPMRI-GPAT 252
+ +NG+ RP+ + GP++
Sbjct: 74 IALLNGIRLYGRPINVSGPSS 94
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
RT+++G+L+ + E L F G + V + ++++ G+ + +GF+ F +
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 142 TFNG 145
NG
Sbjct: 76 LLNG 79
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 76/174 (43%), Gaps = 26/174 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTG--RTKGYGFVRFGDESEQLRAM 233
+FVG + ++ L+E F +Y + V+ DR ++KG FV F L A
Sbjct: 6 MFVGQVPRTWSEKDLRELFE-QYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 234 TEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSI 293
++ M++ P + Q P S +N+ V + +F+G +
Sbjct: 65 NALHN-------MKVLPGMHHPI----QMKPADSEKNNAV-------EDRKLFIGMISKK 106
Query: 294 VTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEALRMLNGTQ 342
T+ +R +FS +GQ+ +I G + C FV F R+ A+ A++ ++ Q
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI--------PAGKRCGFVQFADRSCAEEALR 336
+FVG + +++ LRELF QYG + + + P K C FV F R A EA
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 337 MLNGTQL 343
L+ ++
Sbjct: 66 ALHNMKV 72
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 9/88 (10%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALR 336
T++ V NL + + LR +F +YG++ V IP + FV+F D+ AE+A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 337 MLNGTQLGGQNIRLS---WGRSPSNKQA 361
++G L G+ +R+ +GR P + +
Sbjct: 108 AMDGAVLDGRELRVQMARYGRPPDSHHS 135
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 209 DRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRI 248
DR T ++G+ FVRF D+ + AM M+G R +R+
Sbjct: 82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G P T+FV L+ D T+ L+E+F + A++V DR TG +KG+G
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG----SVRARIVTDRETGSSKGFG 57
Query: 220 FVRFGDESEQLRAMTEM 236
FV F E + A M
Sbjct: 58 FVDFNSEEDAKAAKEAM 74
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 4/91 (4%)
Query: 277 DDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG----FVQFADRSCAE 332
+DD T++VGNL VT+ + +LFSQ G K+ FV+F + A
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 69
Query: 333 EALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
AL +NG ++ G+ ++++W +PS++++ P
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKSGP 100
Score = 35.0 bits (79), Expect = 0.072, Method: Composition-based stats.
Identities = 29/107 (27%), Positives = 52/107 (48%), Gaps = 6/107 (5%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G DD T++VG+L+ DVT+ ++ + F P K K++ + + Y
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGP-CKSCKMITEHTS--NDPYC 58
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKA 266
FV F + + A+ MNG + +++ AT T S Q+ P +
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT---TPSSQKSGPSS 102
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 79 GEIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAER 138
G+ RTL++G+L + E + F+ G + K+I + + Y F+EF A
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAA 70
Query: 139 VLQTFNGTPMPNGEQNFRLNWASFGAGEK 167
L NG + E ++NWA+ + +K
Sbjct: 71 ALAAMNGRKILGKE--VKVNWATTPSSQK 97
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 8/84 (9%)
Query: 174 HTIFVG--DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
+T+FVG D+ D T+ +F ARY S K K++ DR TG +KGYGFV F ++ + ++
Sbjct: 10 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD-VQ 64
Query: 232 AMTEMNGVFCSTRPMRIGPATNKK 255
+ E F + +++GPA K+
Sbjct: 65 KIVESQINF-HGKKLKLGPAIRKQ 87
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T+++G + MDET + + FA G V VK+I ++ TG +GYGF+ F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 143 ---FNGTPMPNG 151
F+G + G
Sbjct: 70 QINFHGKKLKLG 81
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI-----PAGKRCGFVQF 325
PN TVFVG +D + + +R F++YG + VKI K GFV F
Sbjct: 9 PN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLG 344
+FV NL + VT+E L + FS++G+L VK K FV F DR A +A+ +NG ++
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK--KLKDYAFVHFEDRGAAVKAMDEMNGKEIE 75
Query: 345 GQNIRLSWGRSPSNKQAQP 363
G+ I + + P K++ P
Sbjct: 76 GEEIEIVLAKPPDKKRSGP 94
Score = 35.8 bits (81), Expect = 0.051, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV +LA VT+ +L+++F S G + +L K Y FV F D ++AM E
Sbjct: 18 LFVRNLATTVTEEILEKSF-----SEFGKLERVKKL----KDYAFVHFEDRGAAVKAMDE 68
Query: 236 MNG 238
MNG
Sbjct: 69 MNG 71
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVH--VKIPAGKR--CGFVQFADRSCAEEALRM 337
++ +FV NL T + L++ F++ G +++ +K+ GK CG V+F AE A RM
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 64
Query: 338 LNGTQLGGQNIRLSWGRSPS 357
+NG +L G+ I + R+ S
Sbjct: 65 MNGMKLSGREIDVRIDRNAS 84
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI------PAGKRCGFVQFADRSCAEEALRML 338
++VGNL T E ++ELFSQ+G++ +VK+ K GFV+ + S + EA+ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAKL 62
Query: 339 NGTQLGGQNIRLS 351
+ T G+ IR++
Sbjct: 63 DNTDFMGRTIRVT 75
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 2/82 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
I+VG+L T ++E F +++ K++ DR T + KG+GFV +ES A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELF-SQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAK 61
Query: 236 MNGVFCSTRPMRIGPATNKKTV 257
++ R +R+ A KK++
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSL 83
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 37/64 (57%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
+R +++G+L Y + F+ G+V VK+I +++T + +G+GF+E + +E +
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 141 QTFN 144
+ N
Sbjct: 61 KLDN 64
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVH--VKIPAGKR--CGFVQFADRSCAEEALRMLNG 340
+FV NL T + L++ F++ G +++ +K+ GK CG V+F AE A RM+NG
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 341 TQLGGQNIRLSWGRSPS 357
+L G+ I + R+ S
Sbjct: 71 MKLSGREIDVRIDRNAS 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 8/84 (9%)
Query: 174 HTIFVG--DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
+T+FVG D+ D T+ +F ARY S K K++ DR TG +KGYGFV F ++ + ++
Sbjct: 11 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD-VQ 65
Query: 232 AMTEMNGVFCSTRPMRIGPATNKK 255
+ E F + +++GPA K+
Sbjct: 66 KIVESQINF-HGKKLKLGPAIRKQ 88
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T+++G + MDET + + FA G V VK+I ++ TG +GYGF+ F + ++++++
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 70
Query: 143 ---FNGTPMPNG 151
F+G + G
Sbjct: 71 QINFHGKKLKLG 82
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI-----PAGKRCGFVQF 325
PN TVFVG +D + + +R F++YG + VKI K GFV F
Sbjct: 10 PN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/184 (20%), Positives = 83/184 (45%), Gaps = 15/184 (8%)
Query: 176 IFVGDLAADVTDYMLQETFRAR-----YPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
++VG++ +T+ + + F A+ G V+ ++ + K + F+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 65
Query: 231 RAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNL 290
+AM +G+ + ++I + + + G + P Y V+ D + +F+G L
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSV-YVPGVVSTVVPDSAHK-LFIGGL 122
Query: 291 DSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRMLNGTQLG 344
+ + D+ ++EL + +G L + G F ++ D + ++A+ LNG QLG
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182
Query: 345 GQNI 348
+ +
Sbjct: 183 DKKL 186
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 76/180 (42%), Gaps = 27/180 (15%)
Query: 82 RTLWIGDLQYWMDETYLNTCF-----------AHTGEVVAVKVIRNKQTGQIE------- 123
R L++G++ + + E + F A V+AV++ ++K +E
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 124 --GYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPD--HTIFVG 179
F I + + ++ + + P+P +N + + G PD H +F+G
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSEN----PSVYVPGVVSTVVPDSAHKLFIG 120
Query: 180 DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGV 239
L + D ++E + P K +V D TG +KGY F + D + +A+ +NG+
Sbjct: 121 GLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L+IG L ++++ + G + A ++++ TG +GY F E++ ++ +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 144 NGTPMPNGEQNFRLNWASFGA 164
NG M G++ + AS GA
Sbjct: 177 NG--MQLGDKKLLVQRASVGA 195
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 269 QNSQVAQSDDDPN-NTTVFVGNLDS-IVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFA 326
Q S V +D + N+ VF+GNL++ +V + +FS+YG++ + G FVQ++
Sbjct: 13 QASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGY--AFVQYS 70
Query: 327 DRSCAEEALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
+ A A+ NG L GQ + ++ P ++ P
Sbjct: 71 NERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGP 107
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVGDL+ ++T + F + A+VV D TG++KGYGFV F ++ + A+ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAP-FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 236 MNGVFCSTRPMRIGPATNK 254
M G + R +R AT K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 106 GEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWAS 161
G + +V+++ TG+ +GYGF+ F ++ AE +Q G + G + R NWA+
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL--GGRQIRTNWAT 84
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA------GKRCGFVQFADRSCAEEALRML 338
VFVG+L +T + F+ +G++ ++ K GFV F ++ AE A++ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 339 NGTQLGGQNIRLSWG-RSP 356
G LGG+ IR +W R P
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 173 DHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRA 232
D ++V +L +TD L F +Y S ++ D+LTGR +G FVR+ E A
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 233 MTEMNGVF 240
++ +N V
Sbjct: 72 ISALNNVI 79
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEAL 335
+T ++V NL +TD+ L +F +YG +V I K G FV++ R A+EA+
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 336 RMLN 339
LN
Sbjct: 73 SALN 76
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++ +L + + L+T F G +V ++R+K TG+ G F+ + R A+ +
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 144 NGTPMPNGEQNFRLNWA 160
N G Q + A
Sbjct: 76 NNVIPEGGSQPLSVRLA 92
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 47/84 (55%), Gaps = 8/84 (9%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEAL 335
+ ++V L ++ + + +LFSQYG+++ +I + GF++F R AEEA+
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 336 RMLNGTQ-LG-GQNIRLSWGRSPS 357
+ LNG + LG + I + + +PS
Sbjct: 61 KGLNGQKPLGAAEPITVKFANNPS 84
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++ L M + + F+ G ++ +++ ++ TG G GFI F R AE ++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 144 NG 145
NG
Sbjct: 64 NG 65
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 173 DHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRA 232
D ++V L ++ +++ F ++Y +++++D+ TG ++G GF+RF E A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 59
Query: 233 MTEMNG 238
+ +NG
Sbjct: 60 IKGLNG 65
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 189 MLQETFRARYPST---KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M Q+ F++ + S + K+V D++TG++ GYGFV + D ++ +A+ +NG+ T+
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKT 75
Query: 246 MRIGPA 251
+++ A
Sbjct: 76 IKVSYA 81
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 30/53 (56%)
Query: 93 MDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
M + + F G++ + K++R+K TGQ GYGF+ + A++ + T NG
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEA 334
+ T + V L +T + + LF G + K+ K G FV ++D + A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 335 LRMLNGTQLGGQNIRLSWGRSPS 357
+ LNG +L + I++S+ R S
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSS 85
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V +L V+D +QE F A + + K A V DR +GR+ G V F +++ L+AM +
Sbjct: 31 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 236 MNGVFCSTRPMRIGPATN 253
NGV RPM I T+
Sbjct: 89 YNGVPLDGRPMNIQLVTS 106
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 7/73 (9%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRCGF--VQFADRSCAEEALRMLN 339
+ V NLD V+D ++ELF+++G L + +G+ G V F ++ A +A++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 340 GTQLGGQ--NIRL 350
G L G+ NI+L
Sbjct: 91 GVPLDGRPMNIQL 103
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALRML 338
+FVG LD T E LR FSQYG++V I K GFV+F D +C L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 339 NGTQLGGQNI 348
T L G+NI
Sbjct: 79 PHT-LDGRNI 87
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 31/51 (60%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
EI L++G L + + L + F+ GEVV ++++K T Q G+GF++F
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGD 225
+FVG L T L+ F ++Y ++ D+ T +++G+GFV+F D
Sbjct: 19 LFVGGLDWSTTQETLRSYF-SQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 282 NTTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKR-CGFVQFADRSCAEEALRMLN 339
N+ + V NL+ VT + L LF YG + VKI K+ VQ AD + A+ A+ LN
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 340 GTQLGGQNIRLSWGR 354
G +L G+ IR++ +
Sbjct: 63 GHKLHGKPIRITLSK 77
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 39/163 (23%), Positives = 68/163 (41%), Gaps = 30/163 (18%)
Query: 216 KGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQ--QYPK-------- 265
K V+ D ++ AM+ +NG +P+RI T+S Q Q P+
Sbjct: 41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI-------TLSKHQNVQLPREGQEDQGL 93
Query: 266 -ASYQNSQVAQSDDD---------PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVH--VK 313
Y NS + + P + T+ + N+ V++E L+ LFS G +V
Sbjct: 94 TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 153
Query: 314 IPAGKRCGFVQFADRSCAEEALRMLNGTQLG-GQNIRLSWGRS 355
++ +Q A +AL L+ LG ++R+S+ +S
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196
>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 = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 282 NTTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKR-CGFVQFADRSCAEEALRMLN 339
N+ + V NL+ VT + L LF YG + VKI K+ VQ AD + A+ A+ LN
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93
Query: 340 GTQLGGQNIRLSWGR 354
G +L G+ IR++ +
Sbjct: 94 GHKLHGKPIRITLSK 108
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 39/163 (23%), Positives = 68/163 (41%), Gaps = 30/163 (18%)
Query: 216 KGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQ--QYPK-------- 265
K V+ D ++ AM+ +NG +P+RI T+S Q Q P+
Sbjct: 72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI-------TLSKHQNVQLPREGQEDQGL 124
Query: 266 -ASYQNSQVAQSDDD---------PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVH--VK 313
Y NS + + P + T+ + N+ V++E L+ LFS G +V
Sbjct: 125 TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 184
Query: 314 IPAGKRCGFVQFADRSCAEEALRMLNGTQLG-GQNIRLSWGRS 355
++ +Q A +AL L+ LG ++R+S+ +S
Sbjct: 185 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
IF+ +L + + L +TF A + + KVV D +KGYGFV F + RA+ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSA-FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 236 MNGVFCSTRPMRIGPATNKK 255
MNG+ + R + +G ++K
Sbjct: 71 MNGMLLNDRKVFVGRFKSRK 90
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI----PAGKRCGFVQFADRSCAEEALRMLNG 340
+F+ NLD + ++ L + FS +G ++ K+ K GFV F + AE A+ +NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 341 TQLGGQNIRLSWGRSPSNKQAQ 362
L + + + +S ++A+
Sbjct: 74 MLLNDRKVFVGRFKSRKEREAE 95
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
+ ++I +L +D L F+ G +++ KV+ ++ + GYGF+ F ++ AER +
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAI 68
Query: 141 QTFNG 145
+ NG
Sbjct: 69 EKMNG 73
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 274 AQSDDDPNNTTVFVGNLDSIVTDEH-LRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAE 332
++D N+ VF+GNL+++V + + +FS+YG++V + G FVQ+ + A
Sbjct: 7 GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--FAFVQYVNERNAR 64
Query: 333 EALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
A+ +G + GQ + ++ P ++ P
Sbjct: 65 AAVAGEDGRMIAGQVLDINLAAEPKVNRSGP 95
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC-GFVQFADRSCAE 332
++ VFVG +T++ LRE FSQYG ++ V IP R FV FAD A+
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56
>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 = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
IF+ +L + + L +TF A + + KVV D +KGYGFV F + RA+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSA-FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64
Query: 236 MNGVFCSTRPMRIGPATNKK 255
MNG+ + R + +G ++K
Sbjct: 65 MNGMLLNDRKVFVGRFKSRK 84
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI----PAGKRCGFVQFADRSCAEEALRMLNG 340
+F+ NLD + ++ L + FS +G ++ K+ K GFV F + AE A+ +NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 341 TQLGGQNIRLSWGRSPSNKQAQ 362
L + + + +S ++A+
Sbjct: 68 MLLNDRKVFVGRFKSRKEREAE 89
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
++I +L +D L F+ G +++ KV+ ++ + GYGF+ F ++ AER ++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKM 65
Query: 144 NG 145
NG
Sbjct: 66 NG 67
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 285 VFVGNLDSIVTDEHL-RELFSQYGQLVHVKIPAGKR-------CGFVQFADRSCAEEALR 336
+ + NL + + DE+L RE F +G + + IPAG++ C F F ++ AE AL+
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERALQ 272
Query: 337 MLNGTQLGGQNIRLSWG 353
N + LG + I +S
Sbjct: 273 X-NRSLLGNREISVSLA 288
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 35/75 (46%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLN 339
P TT ++GN+ T+ L LF +G ++ K K C F+++ A + L
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALA 84
Query: 340 GTQLGGQNIRLSWGR 354
G+N+R WG+
Sbjct: 85 NFPFQGRNLRTGWGK 99
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 30/88 (34%), Positives = 43/88 (48%), Gaps = 11/88 (12%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC-GFVQFADRSCAEEALRMLNGT 341
+ VFVG +T E L++ F QYG++V V IP R FV FAD A+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ--------- 62
Query: 342 QLGGQNIRLSWGRSPSNKQAQPDPNQWN 369
L G+++ + G S A+P N+ N
Sbjct: 63 SLCGEDLIIK-GISVHISNAEPKHNKLN 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 9/108 (8%)
Query: 251 ATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLV 310
++ +++G QQ + S A D N + V L T+ LRE+FS+YG +
Sbjct: 18 GSHMASMTGGQQMGRGSRHVGNRANPDP---NCCLGVFGLSLYTTERDLREVFSKYGPIA 74
Query: 311 HVKIPAGKRC------GFVQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
V I ++ FV F + A+EA NG +L G+ IR+ +
Sbjct: 75 DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 4/108 (3%)
Query: 148 MPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVV 207
M G+Q + S G + + P+ + V L+ T+ L+E F ++Y +V
Sbjct: 24 MTGGQQ---MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIV 79
Query: 208 IDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
D+ + R++G+ FV F + + A NG+ R +R+ + K+
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 42/177 (23%), Positives = 71/177 (40%), Gaps = 34/177 (19%)
Query: 177 FVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTG--RTKGYGFVRFGDESEQLRAMT 234
FVG + ++ L+E F +Y + V+ DR ++KG FV F L A
Sbjct: 7 FVGQVPRTWSEKDLRELFE-QYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 235 EMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTT----VFVGNL 290
++ N K + G + Q +D + NN +F+G +
Sbjct: 66 ALH---------------NXKVLPG-------XHHPIQXKPADSEKNNAVEDRKLFIGXI 103
Query: 291 DSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEALRMLNGTQ 342
T+ +R FS +GQ+ +I G + C FV F R+ A+ A++ + Q
Sbjct: 104 SKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQ 160
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 286 FVGNLDSIVTDEHLRELFSQYGQLVHVKI--------PAGKRCGFVQFADRSCAEEALRM 337
FVG + +++ LRELF QYG + + + P K C FV F R A EA
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 338 LNGTQL 343
L+ ++
Sbjct: 67 LHNXKV 72
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
E R L+IG + E + F+ G++ +++R G G F+ F +RA A+
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTA 152
Query: 140 L------QTFNGTPMP 149
+ QT G P
Sbjct: 153 IKAXHQAQTXEGCSSP 168
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/118 (31%), Positives = 56/118 (47%), Gaps = 5/118 (4%)
Query: 131 ISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYML 190
I+R G R P+P+ Q+ + + G GE + + V +L V+D +
Sbjct: 49 IARGGRNRPAPYSRPKPLPDKWQHDLFD-SGCGGGEGVETG--AKLLVSNLDFGVSDADI 105
Query: 191 QETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRI 248
QE F A + + K A V DR +GR+ G V F ++ L+AM + GV RPM I
Sbjct: 106 QELF-AEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIP---AGKRCGF--VQFADRSCAEEALRM 337
+ V NLD V+D ++ELF+++G L + +G+ G V F R+ A +A++
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 338 LNGTQLGGQ 346
G L G+
Sbjct: 149 YKGVPLDGR 157
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 64/151 (42%), Gaps = 22/151 (14%)
Query: 207 VIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKA 266
V+D G T+ +G+V F + +E L E+ G+ +++ + PK
Sbjct: 39 VVDVRIGMTRKFGYVDF-ESAEDLEKALELTGLKVFGNEIKL-------------EKPKG 84
Query: 267 SYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHV-KIPAGKRCGFVQF 325
S + + T+ NL VT + L+E+F ++ V K K +++F
Sbjct: 85 K-------DSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEF 137
Query: 326 ADRSCAEEALRMLNGTQLGGQNIRLSWGRSP 356
+ AE+ GT++ G++I L + P
Sbjct: 138 KTEADAEKTFEEKQGTEIDGRSISLYYTGEP 168
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
RTL +L Y + + L F E+ V + G+ +G +IEF + A AE+ +
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFEDAAEIRLVS-----KDGKSKGIAYIEFKTEADAEKTFE 148
Query: 142 TFNGTPM 148
GT +
Sbjct: 149 EKQGTEI 155
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIP-------AGKRCGFVQFADRSCAEEAL 335
+ + V N+ +RELFS +G+L V++P A + GFV F + A++A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 336 RML-NGTQLGGQNIRLSWGRSPSNKQAQP 363
L + T L G+ + L W S Q+ P
Sbjct: 76 NALCHSTHLYGRRLVLEWADSEVTVQSGP 104
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 275 QSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADR 328
+++ DPN + V L T+ LRE+FS+YG + V I ++ FV F +
Sbjct: 9 RANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 329 SCAEEALRMLNGTQLGGQNIRLS 351
A+EA NG +L G+ IR+S
Sbjct: 68 DDAKEAKERANGMELDGRRIRVS 90
Score = 34.7 bits (78), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G + + P+ + V L+ T+ L+E F ++Y +V D+ + R++G+
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFA 60
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRI-GPAT 252
FV F + + A NG+ R +R+ GP++
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 12/92 (13%)
Query: 273 VAQSDDDP------NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF---- 322
V Q D+P +FV + T+E + + F++YG++ ++ + +R G+
Sbjct: 8 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67
Query: 323 --VQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
V++ A+ A+ LNG L GQ I + W
Sbjct: 68 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 26 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 85 LNGQDLMGQPISV 97
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 95 ETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQN 154
E ++ FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q
Sbjct: 37 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 94
Query: 155 FRLNWA 160
++W
Sbjct: 95 ISVDWC 100
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 49/232 (21%), Positives = 92/232 (39%), Gaps = 30/232 (12%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 102
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCS 242
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 103 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG---- 157
Query: 243 TRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDP--NNTTVFVGNLDSIVTDEHLR 300
+P+ GP T + Q A + + P N+ L ++ + +
Sbjct: 158 -KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 214
Query: 301 ELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
Q GQL K +++ AEEA + +G LGG ++R+S+
Sbjct: 215 LACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 258
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 113 VIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFG 163
++ +++TGQ +GYGF E++ + A R G P+ G + ++W G
Sbjct: 125 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTDAG 173
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 274 AQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFAD 327
++++ DPN + V L T+ LRE+FS+YG + V I ++ FV F +
Sbjct: 5 SRANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 328 RSCAEEALRMLNGTQLGGQNIRLSW 352
A+EA NG +L G+ IR+ +
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVDF 88
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 1/91 (1%)
Query: 165 GEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG 224
G + + P+ + V L+ T+ L+E F ++Y +V D+ + R++G+ FV F
Sbjct: 4 GSRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Query: 225 DESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
+ + A NG+ R +R+ + K+
Sbjct: 63 NVDDAKEAKERANGMELDGRRIRVDFSITKR 93
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 49/232 (21%), Positives = 92/232 (39%), Gaps = 30/232 (12%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 104
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCS 242
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 105 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG---- 159
Query: 243 TRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDP--NNTTVFVGNLDSIVTDEHLR 300
+P+ GP T + Q A + + P N+ L ++ + +
Sbjct: 160 -KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 301 ELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
Q GQL K +++ AEEA + +G LGG ++R+S+
Sbjct: 217 LACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 113 VIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFG 163
++ +++TGQ +GYGF E++ + A R G P+ G + ++W G
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTDAG 175
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 49/232 (21%), Positives = 92/232 (39%), Gaps = 30/232 (12%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 104
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCS 242
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 105 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG---- 159
Query: 243 TRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDP--NNTTVFVGNLDSIVTDEHLR 300
+P+ GP T + Q A + + P N+ L ++ + +
Sbjct: 160 -KPL--GPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 301 ELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
Q GQL K +++ AEEA + +G LGG ++R+S+
Sbjct: 217 LACGQDGQL--------KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 113 VIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFG 163
++ +++TGQ +GYGF E++ + A R G P+ G + ++W G
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTDAG 175
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 26/106 (24%), Positives = 52/106 (49%), Gaps = 4/106 (3%)
Query: 173 DH--TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
DH +F+G L + + ML+ F P ++ ++I T +++G+ F+ F + ++
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISE--VLLIKDRTSKSRGFAFITFENPADAK 62
Query: 231 RAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQS 276
A +MNG + +++ A SG ++ P AS +N + S
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHV-----KIPAGKRCGFVQFADRSCAEEALRMLN 339
+F+G L+ ++ L+ +F ++G + V + + F+ F + + A+ A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 340 GTQLGGQNIRLSWGRSPS 357
G L G+ I++ + PS
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P +++G + D T+ + + P K++ D TGR+KGY F+ F D
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 232 AMTEMNGVFCSTRPMRIGPATN 253
A+ +NG +R ++ G ++N
Sbjct: 60 AVRNLNGYQLGSRFLKCGYSSN 81
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 82 RTLWIGDLQY-WMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
R +++G + Y +E L+ C ++ G V+ +K++ + QTG+ +GY FIEF + +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLC-SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 141 QTFNG 145
+ NG
Sbjct: 62 RNLNG 66
Score = 35.4 bits (80), Expect = 0.052, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRML 338
V++G++ T+E + +L S G ++++K+ + G F++F D + A+R L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 339 NGTQLGGQNIRLSW 352
NG QLG + ++ +
Sbjct: 65 NGYQLGSRFLKCGY 78
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V L D+TD L FRA P +++ D TG + GY FV F E + RA+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 236 MNGVFCSTRPMRIGPA 251
+NG+ + +++ A
Sbjct: 65 LNGITVRNKRLKVSYA 80
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L + L M + L F G + +++R+ +TG GY F++F S ++R ++
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 144 NGTPMPNGEQNFRLNWASFG 163
NG + N + ++++A G
Sbjct: 66 NGITVRN--KRLKVSYARPG 83
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEA 334
+NT + V L +TD L LF G + +I + G FV F ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 335 LRMLNGTQLGGQNIRLSWGR 354
+++LNG + + +++S+ R
Sbjct: 62 IKVLNGITVRNKRLKVSYAR 81
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 275 QSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADR 328
+++ DPN + V L T+ LRE+FS+YG + V I ++ FV F +
Sbjct: 9 RANPDPN-CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 329 SCAEEALRMLNGTQLGGQNIRLSW 352
A+EA NG +L G+ IR+ +
Sbjct: 68 DDAKEAKERANGMELDGRRIRVDF 91
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G + + P+ + V L+ T+ L+E F ++Y +V D+ + R++G+
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFA 60
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
FV F + + A NG+ R +R+ + K+
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 96
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 12/92 (13%)
Query: 273 VAQSDDDP------NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF---- 322
V Q D+P +FV + T+E + + F++YG++ ++ + +R G+
Sbjct: 7 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 323 --VQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
V++ A+ A+ LNG L GQ I + W
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 25 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 84 LNGQDLMGQPISV 96
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 95 ETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQN 154
E ++ FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q
Sbjct: 36 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 93
Query: 155 FRLNWA 160
++W
Sbjct: 94 ISVDWC 99
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 48/92 (52%), Gaps = 6/92 (6%)
Query: 278 DDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCA 331
+ P +F+ +L D+ L ++F +G +V K+ K+ GFV + + A
Sbjct: 21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 332 EEALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
+ A++ +NG Q+G + +++ RS ++ ++ P
Sbjct: 81 QAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGP 112
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 163 GAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVR 222
AG +++ +F+ L + D L + F + + AKV ID+ T +K +GFV
Sbjct: 15 AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLSKCFGFVS 73
Query: 223 FGDESEQLRAMTEMNGVFCSTRPMRI 248
+ + A+ MNG + +++
Sbjct: 74 YDNPVSAQAAIQSMNGFQIGMKRLKV 99
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 102 FAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
F G VV+ KV +KQT + +GF+ + + A+ +Q+ NG
Sbjct: 46 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 170 DTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQ 229
+ P +++G + D T+ + + P K++ D TGR+KGY F+ F D
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESS 59
Query: 230 LRAMTEMNGVFCSTRPMRIGPATN 253
A+ +NG +R ++ G ++N
Sbjct: 60 ASAVRNLNGYQLGSRFLKCGYSSN 83
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 82 RTLWIGDLQY-WMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
R +++G + Y +E L+ C ++ G V+ +K++ + QTG+ +GY FIEF + +
Sbjct: 5 RVVYLGSIPYDQTEEQILDLC-SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 141 QTFNG 145
+ NG
Sbjct: 64 RNLNG 68
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 279 DPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAE 332
+P + V++G++ T+E + +L S G ++++K+ + G F++F D +
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 333 EALRMLNGTQLGGQNIRLSW 352
A+R LNG QLG + ++ +
Sbjct: 61 SAVRNLNGYQLGSRFLKCGY 80
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 294 VTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNIRLSWG 353
+T LR FS +G ++ + + + C FV + A++A+ LNGTQ+ ++++
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
Query: 354 R 354
R
Sbjct: 85 R 85
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P +++G + D T+ + + P K++ D TGR+KGY F+ F D
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 232 AMTEMNGVFCSTRPMRIGPATN 253
A+ +NG +R ++ G ++N
Sbjct: 61 AVRNLNGYQLGSRFLKCGYSSN 82
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 79 GEIRTLWIGDLQY-WMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAE 137
G R +++G + Y +E L+ C ++ G V+ +K++ + QTG+ +GY FIEF +
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLC-SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 59
Query: 138 RVLQTFNG 145
++ NG
Sbjct: 60 SAVRNLNG 67
Score = 35.0 bits (79), Expect = 0.070, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRML 338
V++G++ T+E + +L S G ++++K+ + G F++F D + A+R L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 339 NGTQLGGQNIRLSW 352
NG QLG + ++ +
Sbjct: 66 NGYQLGSRFLKCGY 79
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI--------PAGKRCGFVQFADRSCAEEALR 336
+FVG + +++ LRELF QYG + + + P K C FV F R A EA
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 337 MLNGTQL 343
L+ ++
Sbjct: 66 ALHNMKV 72
>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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 294 VTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQLGGQNIRLSWG 353
+T LR FS +G ++ + + + C FV + A++A+ LNGTQ+ ++++
Sbjct: 49 MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
Query: 354 R 354
R
Sbjct: 109 R 109
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNG 340
N +FVGN+ + T + LR LF + G+++ + K FV + A+ A+ LNG
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNG 65
Query: 341 TQLGGQNIRL 350
++ G+ I +
Sbjct: 66 KEVKGKRINV 75
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF------VQFADRSCAEEALRML 338
+FV + T+E + + F++YG++ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 339 NGTQLGGQNIRLSW 352
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISV 81
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 95 ETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQN 154
E ++ FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 78
Query: 155 FRLNWA 160
++W
Sbjct: 79 ISVDWC 84
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF------VQFADRSCAEEALRML 338
+FV + T+E + + F++YG++ ++ + +R G+ V++ A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 339 NGTQLGGQNIRLSW 352
NG L GQ I + W
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 12 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 71 LNGQDLMGQPISV 83
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 95 ETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQN 154
E ++ FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q
Sbjct: 23 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 80
Query: 155 FRLNWA 160
++W
Sbjct: 81 ISVDWC 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF------VQFADRSCAEEALRML 338
+FV + T+E + + F++YG++ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 339 NGTQLGGQNIRLSW 352
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISV 81
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 102 FAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWA 160
FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q ++W
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QPISVDWC 84
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
++IG L + + L F GEV V+R+ T + G+GF+ F+ +AG ++VL
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
Score = 35.4 bits (80), Expect = 0.064, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDES 227
+F+G L+ T L+E F ++ K V+ D LT R++G+GFV F D++
Sbjct: 3 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 53
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQL---VHVKIPAGKRC---GFVQFADRSCAEEAL 335
+F+G L T E LRE F Q+G++ + ++ P KR GFV F D++ ++ L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/103 (24%), Positives = 48/103 (46%), Gaps = 15/103 (14%)
Query: 265 KASYQNSQVAQSDDD-----PNNTT----VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP 315
+A + +V DDD P + +FV ++ ++ ++E F YG++ ++ +
Sbjct: 46 EAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLN 105
Query: 316 AGKRCGF------VQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
+R GF V++ A A LNG ++ GQ I++ W
Sbjct: 106 LDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + + +QE F Y K + +DR TG +KGY V + + L A
Sbjct: 75 LFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 236 MNGVFCSTRPMRI------GPATNKKT 256
+NG + +++ GP KK+
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVKKS 160
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++ + E + F GE+ + + +++TG +GY +E+ + A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKR 168
NG + Q +++W F G KR
Sbjct: 135 NGAEIMG--QTIQVDWC-FVKGPKR 156
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGF------VQFADRSCAEEALRML 338
+FV + T+E + + F++YG++ ++ + +R G+ V++ A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 339 NGTQLGGQNIRLSW 352
NG L GQ I + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + T+ + + F A Y K + +DR TG KGY V + E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 236 MNGVFCSTRPMRI 248
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISV 81
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 102 FAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWA 160
FA GE+ + + +++TG ++GY +E+ + A+ ++ NG + Q ++W
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QPISVDWC 84
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
++IG L + + L F GEV V+R+ T + G+GF+ F+ +AG ++VL
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Score = 34.7 bits (78), Expect = 0.092, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDES 227
+F+G L+ T L+E F ++ K V+ D LT R++G+GFV F D++
Sbjct: 28 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
Score = 32.3 bits (72), Expect = 0.44, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQL---VHVKIPAGKRC---GFVQFADRSCAEEAL 335
+F+G L T E LRE F Q+G++ + ++ P KR GFV F D++ ++ L
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEA 334
P++ +FVG L+ +++ +R LF +G + I G K C FV+++ + A+ A
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAA 72
Query: 335 LRMLNGTQ-LGGQNIRLSWGRSPSNKQAQP 363
+ L+G+Q + G + L + ++K++ P
Sbjct: 73 INALHGSQTMPGASSSLVVKFADTDKESGP 102
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 264 PKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR---- 319
P+ S+ N++ + + V N+ D LR++F Q+G+++ V+I +R
Sbjct: 16 PRGSHMNTE-----NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70
Query: 320 CGFVQFADRSCAEEALRMLNGTQLGGQNIRLS 351
GFV F + + A+ A L+GT + G+ I ++
Sbjct: 71 FGFVTFENSADADRAREKLHGTVVEGRKIEVN 102
Score = 31.6 bits (70), Expect = 0.95, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+ L + ++ + + L F G+++ V++I N++ + G+GF+ F + A A+R +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 87
Query: 142 TFNGT 146
+GT
Sbjct: 88 KLHGT 92
Score = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 215 TKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNK 254
+KG+GFV F + ++ RA +++G R + + AT +
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V +L V+D +QE F A + + K A V DR +GR+ G V F ++ L+AM +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 95
Query: 236 MNGVFCSTRPMRI 248
GV RPM I
Sbjct: 96 YKGVPLDGRPMDI 108
Score = 32.0 bits (71), Expect = 0.67, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP---AGKRCGF--VQFADRSCAEEALRMLN 339
+ V NLD V+D ++ELF+++G L + +G+ G V F R+ A +A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 340 GTQLGGQ 346
G L G+
Sbjct: 98 GVPLDGR 104
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V +L V+D +QE F A + + K A V DR +GR+ G V F ++ L+AM +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 95
Query: 236 MNGVFCSTRPMRI 248
GV RPM I
Sbjct: 96 YKGVPLDGRPMDI 108
Score = 32.0 bits (71), Expect = 0.70, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP---AGKRCGF--VQFADRSCAEEALRMLN 339
+ V NLD V+D ++ELF+++G L + +G+ G V F R+ A +A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 340 GTQLGGQ 346
G L G+
Sbjct: 98 GVPLDGR 104
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G R + TI V +L+ D + LQE FR + S + D+ TG++KG+
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRP-FGSISRIYLAKDKTTGQSKGFA 60
Query: 220 FVRFGDESEQLRAMTEMNG 238
F+ F + RA+ ++G
Sbjct: 61 FISFHRREDAARAIAGVSG 79
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEA 334
+N T+ V NL + L+ELF +G + + + K G F+ F R A A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 335 LRMLNGTQLGGQNIRLSWGRSPSN 358
+ ++G + + W + +N
Sbjct: 74 IAGVSGFGYDHLILNVEWAKPSTN 97
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV +L+ ++ L++ F A P ++ ID LT + KG+ FV F ++A E
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSE-LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 236 MNGVFCSTRPMRIGPATNKKTVS 258
++G R + + P+T KK S
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEAS 92
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGT 341
+T + VGN+ T++ LR F +YG ++ I K FV A EA+R L+ T
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNT 67
Query: 342 QLGGQ--NIRLSWGR 354
+ G+ +++LS R
Sbjct: 68 EFQGKRMHVQLSTSR 82
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+F+ L + TD L TF + + AKV ID+ T +K +GFV F + A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLP-FGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 236 MNGVFCSTRPMRI 248
MNG T+ +++
Sbjct: 102 MNGFQVGTKRLKV 114
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 278 DDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGK-----RC-GFVQFADRSCA 331
+ P +F+ +L TD L F +G ++ K+ K +C GFV F + A
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 332 EEALRMLNGTQLGGQNIRL 350
+ A++ +NG Q+G + +++
Sbjct: 96 QVAIKAMNGFQVGTKRLKV 114
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L+I L +T L + F G V++ KV +KQT + +GF+ F + A+ ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 144 NG 145
NG
Sbjct: 103 NG 104
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 277 DDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRCGFVQFADRSCAEE 333
D P + V+VGNL + L F YG L V + P G FV+F D A +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAAD 125
Query: 334 ALRMLNGTQLGGQNIRL 350
A+R L+G L G +R+
Sbjct: 126 AVRELDGRTLCGCRVRV 142
>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 = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEE 333
P +F+G L + + D+ ++EL + +G L + G F ++ D + ++
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 334 ALRMLNGTQLGGQNI 348
A+ LNG QLG + +
Sbjct: 154 AIAGLNGMQLGDKKL 168
Score = 35.8 bits (81), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 76/188 (40%), Gaps = 31/188 (16%)
Query: 79 GEIRTLWIGDLQYWMDETYLNTCF-----------AHTGEVVAVKVIRNKQTGQIEGYGF 127
G R L++G++ + + E + F A V+AV++ ++K + F
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAF 57
Query: 128 IEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTP---DHTIFVGDLAAD 184
+EF S + + F+G R D P H +F+G L
Sbjct: 58 LEFRSVDETTQAM-AFDGIIFQGQSLKIR---------RPHDYQPLPGAHKLFIGGLPNY 107
Query: 185 VTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTR 244
+ D ++E + P K +V D TG +KGY F + D + +A+ +NG+ +
Sbjct: 108 LNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 166
Query: 245 PMRIGPAT 252
+ + A+
Sbjct: 167 KLLVQRAS 174
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 281 NNTTVFVGNLDSIVTDEHL---------RELFSQYGQLVHVKIPAGKRCGFVQFADRSCA 331
N T++VG +D + +HL R +FS+ G + ++ K CGFV+F ++ A
Sbjct: 133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANA 192
Query: 332 EEALRMLNGTQL 343
E A ++ L
Sbjct: 193 EFAKEAMSNQTL 204
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 27/69 (39%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRCGFVQFADRSCAEEALRMLNGT 341
V+VGNL + L FS YG L V I P G FV+F D AE+A+R L+G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG--FAFVEFEDPRDAEDAVRGLDGK 60
Query: 342 QLGGQNIRL 350
+ G +R+
Sbjct: 61 VICGSRVRV 69
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 282 NTTVFVGNLDSIVTDEHL---------RELFSQYGQLVHVKIPAGKRCGFVQFADRSCAE 332
N T++VG +D + +HL R +FS+ G + ++ K CGFV+F ++ AE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 333 EALRMLNGTQL 343
A ++ L
Sbjct: 196 FAKEAMSNQTL 206
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 280 PNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEE 333
P +F+G L + + D+ ++EL + +G L + G F ++ D + ++
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 334 ALRMLNGTQLGGQNI 348
A+ LNG QLG + +
Sbjct: 152 AIAGLNGMQLGDKKL 166
Score = 35.4 bits (80), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 76/188 (40%), Gaps = 31/188 (16%)
Query: 79 GEIRTLWIGDLQYWMDETYLNTCF-----------AHTGEVVAVKVIRNKQTGQIEGYGF 127
G R L++G++ + + E + F A V+AV++ ++K + F
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAF 55
Query: 128 IEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTP---DHTIFVGDLAAD 184
+EF S + + F+G R D P H +F+G L
Sbjct: 56 LEFRSVDETTQAM-AFDGIIFQGQSLKIR---------RPHDYQPLPGAHKLFIGGLPNY 105
Query: 185 VTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTR 244
+ D ++E + P K +V D TG +KGY F + D + +A+ +NG+ +
Sbjct: 106 LNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 164
Query: 245 PMRIGPAT 252
+ + A+
Sbjct: 165 KLLVQRAS 172
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 27/100 (27%), Positives = 49/100 (49%), Gaps = 6/100 (6%)
Query: 159 WASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGY 218
++S+ GE P+ +++ +L+ VT+ L F AR+ KG + +TGR +G
Sbjct: 16 FSSYNPGE-----PNKVLYLKNLSPRVTERDLVSLF-ARFQEKKGPPIQFRMMTGRMRGQ 69
Query: 219 GFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVS 258
F+ F ++ +A+ +NG + + I NKK S
Sbjct: 70 AFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS 109
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 5/96 (5%)
Query: 264 PKASYQNSQVAQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFV 323
P+ S+ + + + + +NT +FV V + L E+F +G + VKI G FV
Sbjct: 16 PRGSHMHHR---QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFV 70
Query: 324 QFADRSCAEEALRMLNGTQLGGQNIRLSWGRSPSNK 359
+F + A +A+ ++G Q + + + + P+ +
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 277 DDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRCGFVQFADRSCAEE 333
D P + V+VGNL + L F YG L V + P G FV+F D A +
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAAD 125
Query: 334 ALRMLNGTQLGGQNIRL 350
A+R L+G L G +R+
Sbjct: 126 AVRDLDGRTLCGCRVRV 142
>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 = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+ V +L V+D +QE F A + + K A V DR +GR+ G V F +++ L+A +
Sbjct: 32 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 236 MNGVFCSTRPMRIGPATN 253
NGV RP I T+
Sbjct: 90 YNGVPLDGRPXNIQLVTS 107
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKI---PAGKRCGF--VQFADRSCAEEALRMLN 339
+ V NLD V+D ++ELF+++G L + +G+ G V F ++ A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 340 GTQLGGQ--NIRL 350
G L G+ NI+L
Sbjct: 92 GVPLDGRPXNIQL 104
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.0 bits (84), Expect = 0.021, Method: Composition-based stats.
Identities = 25/102 (24%), Positives = 47/102 (46%), Gaps = 15/102 (14%)
Query: 266 ASYQNSQVAQSDDD-----PNNTT----VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA 316
A + +V DDD P + +FV ++ ++ ++E F YG++ ++ +
Sbjct: 1 AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60
Query: 317 GKRCGF------VQFADRSCAEEALRMLNGTQLGGQNIRLSW 352
+R GF V++ A A LNG ++ GQ I++ W
Sbjct: 61 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + + +QE F Y K + +DR TG +KGY V + + L A
Sbjct: 29 LFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 236 MNG 238
+NG
Sbjct: 88 LNG 90
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 287 VGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR----CGFVQFADRSCAEEALRMLNGTQ 342
V N+ D LR++F Q+G+++ V+I +R GFV F + + A+ A L+GT
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 79
Query: 343 LGGQNIRLS 351
+ G+ I ++
Sbjct: 80 VEGRKIEVN 88
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+ L + ++ + + L F G+++ V++I N++ + G+GF+ F + A A+R +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 73
Query: 142 TFNGT 146
+GT
Sbjct: 74 KLHGT 78
Score = 28.5 bits (62), Expect = 8.1, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 215 TKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNK 254
+KG+GFV F + ++ RA +++G R + + AT +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 93
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 3/96 (3%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G++ P +T +VG+L + + F+ S + ++V D+ T + KG+
Sbjct: 2 SSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL--SIRSVRLVRDKDTDKFKGFC 59
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
+V F DE + L+ +G R +R+ A +K
Sbjct: 60 YVEF-DEVDSLKEALTYDGALLGDRSLRVDIAEGRK 94
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRML 338
+F+G L + + D+ ++EL + +G L + G F ++ D + ++A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 339 NGTQLGGQNI 348
NG QLG + +
Sbjct: 64 NGMQLGDKKL 73
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L+IG L ++++ + G + A ++++ TG +GY F E++ ++ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 144 NGTPMPNGEQNFRLNWASFGA 164
NG M G++ + AS GA
Sbjct: 64 NG--MQLGDKKLLVQRASVGA 82
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 174 HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAM 233
H +F+G L + D ++E + P K +V D TG +KGY F + D + +A+
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 234 TEMNGV 239
+NG+
Sbjct: 61 AGLNGM 66
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
+F+G L+ D T L++ F +++ + +D +TGR++G+GFV F ESE +
Sbjct: 2 MFIGGLSWDTTKKDLKDYF-SKFGEVVDCTLKLDPITGRSRGFGFVLF-KESESV 54
Score = 29.6 bits (65), Expect = 3.4, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
++IG L + + L F+ GEVV + + TG+ G+GF+ F ++V+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>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 = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIF-SQFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 65 ATNALRSMQGFPFYDKPMRI 84
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 35.4 bits (80), Expect = 0.053, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 59
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 60 ATNALRSMQGFPFYDKPMRI 79
>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 = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 65 ATNALRSMQGFPFYDKPMRI 84
>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 = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 58
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 59 ATNALRSMQGFPFYDKPMRI 78
>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 = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 64 ATNALRSMQGFPFYDKPMRI 83
>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 = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 60
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 61 ATNALRSMQGFPFYDKPMRI 80
>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 = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 64 ATNALRSMQGFPFYDKPMRI 83
>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 = 35.4 bits (80), Expect = 0.057, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 64 ATNALRSMQGFPFYDKPMRI 83
>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 = 35.4 bits (80), Expect = 0.057, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 61
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 62 ATNALRSMQGFPFYDKPMRI 81
>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 = 35.4 bits (80), Expect = 0.060, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIF-SRFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 65 ATNALRSMQGFPFYDKPMRI 84
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.069, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIP---AGKRCGFVQFADRSCAEEALRM 337
N+ ++VGNL + + + ++F +YG + + + G FV+F D AE+A+
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 338 LNGTQLGGQNIRLSWGRSPSNKQAQP 363
+G G +R+ + RS + P
Sbjct: 81 RDGYDYDGYRLRVEFPRSGRGTGSGP 106
>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 = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
+TL++ + Y E+ L F G + + ++ +K++G+ GY FIE+
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFADRSCAEEALRM 337
T+FV ++ T+ LR F YG + + + KR G F+++ A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 338 LNGTQLGGQNI 348
+G ++ G+ +
Sbjct: 164 ADGKKIDGRRV 174
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 35.0 bits (79), Expect = 0.080, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGTQ 342
T + NL + ++E FS++G L V +P G V+F + A +A R L ++
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 343 LGGQNIRLSW------GRSPSNKQAQ 362
+ L W G +P K +Q
Sbjct: 71 FHHVPLYLEWAPIGVFGAAPQKKDSQ 96
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 34.7 bits (78), Expect = 0.092, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIF-SQFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 65 ATNALRSMQGFPFYDKPMRI 84
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G KR + V L T+ L+E F + + +V D TG +KG+G
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYF-STFGEVLMVQVKKDLKTGHSKGFG 60
Query: 220 FVRFGDESEQLRAMTE---MNGVFCSTR 244
FVRF + Q++ M++ ++G +C +
Sbjct: 61 FVRFTEYETQVKVMSQRHMIDGRWCDCK 88
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 89 LQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
L + E L F+ GEV+ V+V ++ +TG +G+GF+ F
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEALRMLN 339
+FVG L+ ++E + LF +G + + G K C FV+F+ + A+ A+ L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 340 GTQ-LGGQNIRLSWGRSPSNKQAQP 363
G+Q + G + L + ++K++ P
Sbjct: 78 GSQTMPGASSSLVVKFADTDKESGP 102
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 39/189 (20%), Positives = 81/189 (42%), Gaps = 26/189 (13%)
Query: 166 EKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGD 225
E + T +F+G+L + + L+ + A V+D TG + +G+V F +
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA--VVDVRTGTNRKFGYVDF-E 62
Query: 226 ESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKASYQNSQVAQSDDDPNNTTV 285
+E L E+ G+ K + + K ++S+ ++ T+
Sbjct: 63 SAEDLEKALELTGL---------------KVFGNEIKLEKPKGRDSKKVRA-----ARTL 102
Query: 286 FVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG--FVQFADRSCAEEALRMLNGTQL 343
NL +T++ L+E+F ++ V GK G +++F + AE+ L G ++
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Query: 344 GGQNIRLSW 352
G+++ L +
Sbjct: 162 DGRSVSLYY 170
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
RTL +L + + E L F E+ V Q G+ +G +IEF S A AE+ L+
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 154
Query: 142 TFNGTPM 148
G +
Sbjct: 155 EKQGAEI 161
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 81 IRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
+TL++ + Y E+ L F G + + ++ +K++G+ GY FIE+
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
Score = 32.0 bits (71), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 278 DDPNN-----TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFA 326
+DPN T+FV ++ T+ LR F YG + + + KR G F+++
Sbjct: 93 NDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Query: 327 DRSCAEEALRMLNGTQLGGQNIRLSWGR 354
A + +G ++ G+ + + R
Sbjct: 153 HERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 85 WIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
++G L + + L F GEVV + + TG+ G+GFI F A E+VL
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 177 FVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDES 227
FVG L+ D + L++ F ++ + D TGR++G+GF+ F D +
Sbjct: 15 FVGGLSWDTSKKDLKDYF-TKFGEVVDCTIKXDPNTGRSRGFGFILFKDAA 64
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNG 340
+NT +FV V + L E+F +G + VKI G FV+F + A +A+ ++G
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHG 60
Query: 341 TQLGGQNIRLSWGR 354
Q + + + +
Sbjct: 61 KSFANQPLEVVYSK 74
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L+I +L MDE L G+V++ +++R+ +G G GF S E V+ F
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 144 NG 145
NG
Sbjct: 87 NG 88
>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 = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 174 HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAM 233
H +F+ L T L+E +A + + K ++V +R G+ KG +V + +ES+ +A+
Sbjct: 18 HKLFISGLPFSCTKEELEEICKA-HGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAV 75
Query: 234 TEMNGV 239
+M+G+
Sbjct: 76 MKMDGM 81
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT---KGYGFVRFGDESE 228
P+HTI++ +L + L+++ A + S G ++D L R+ +G FV F + S
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIF-SQFGQ--ILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ M G +PMRI
Sbjct: 64 ATNALRSMQGFPFYDKPMRI 83
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAG-----KRCGFVQFADRSCAEEALRMLN 339
+FVG L TDE +R++F +G + + G K C FV+F + A+ A+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 340 GTQ-LGGQNIRLSWGRSPSNKQAQP 363
++ L G + L + + K++ P
Sbjct: 75 SSRTLPGASSSLVVKFADTEKESGP 99
>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 = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 36/80 (45%)
Query: 169 DDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESE 228
D P+HTI++ ++ + L+ + A + ++ T + +G FV F +
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 229 QLRAMTEMNGVFCSTRPMRI 248
A+ ++ G +PMRI
Sbjct: 62 STNALRQLQGFPFYGKPMRI 81
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 278 DDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKI------PAGKRCGFVQFADRSCA 331
D TVF+ NL +E L E+ Q+G L +V++ K C F QF + A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 332 EEAL 335
++ L
Sbjct: 71 QKCL 74
>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 = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISR 133
R++++G++ Y L F+ G + + ++ +K +G +GY +IEF R
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER 88
Score = 31.6 bits (70), Expect = 0.84, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 274 AQSDDDPNNTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCG------FVQFAD 327
A+ + + +V+VGN+D T + L FS G + + I K G +++FA+
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 328 RSCAEEALRMLNGTQLGGQNIRL 350
R+ + A+ M + T G+ I++
Sbjct: 88 RNSVDAAVAM-DETVFRGRTIKV 109
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPA---GKRCG--FVQFADRSCAEEALRML 338
T+ + NL T+E L+E+F + +K+P GK G F++FA A+EAL
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 339 NGTQLGGQNIRL 350
N ++ G+ IRL
Sbjct: 74 NKREIEGRAIRL 85
Score = 32.3 bits (72), Expect = 0.56, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
E +TL + +L Y E L F + +KV +N Q G+ +GY FIEF S A+
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFE---KATFIKVPQN-QNGKSKGYAFIEFASFEDAKEA 69
Query: 140 LQTFN 144
L + N
Sbjct: 70 LNSCN 74
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.1 bits (74), Expect = 0.28, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 26/41 (63%)
Query: 106 GEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGT 146
G++V+ K I +K T + +GYGF++F S + A++ + +
Sbjct: 30 GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS 70
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 198 YPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEM 236
Y K ++D+ T + KGYGFV F S +A+T +
Sbjct: 29 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 32/48 (66%)
Query: 98 LNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
L + F+ G+VV ++ ++ TG+ +G+ F+E S A++++++F+G
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>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 = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 32/48 (66%)
Query: 98 LNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNG 145
L + F+ G+VV ++ ++ TG+ +G+ F+E S A++++++F+G
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
IFVG L+ + T ++ F ++ A ++ D+ T R +G+GFV F ESE +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTF--ESEDI 53
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.7 bits (73), Expect = 0.33, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRML 338
++VG L V D+ L F +G + ++IP + FV+F A A+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 339 NGTQLGGQNIRLSWGRSPSNKQAQP 363
N ++L G+ IR++ + K++ P
Sbjct: 75 NESELFGRTIRVNLAKPMRIKESGP 99
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Score = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 12/93 (12%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
T ++VG LA +V D +L F + ++ +D T + +G+ FV F +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 231 RAMTEMN--GVFCST------RPMRI---GPAT 252
A+ MN +F T +PMRI GP++
Sbjct: 69 AAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 283 TTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR-----CGFVQFADRSCAEEALRM 337
+TVFV NLD V + L+E+FS G +V I K G V F A +A+ M
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 338 LNGTQL 343
NG L
Sbjct: 76 FNGQLL 81
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLT---GRTKGYGFVRFGDESEQLR 231
T+FV +L V L+E F S G V D L G+++G G V F E ++
Sbjct: 17 TVFVANLDYKVGWKKLKEVF-----SMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQ 71
Query: 232 AMTEMNGVFCSTRPMRI 248
A++ NG RPM +
Sbjct: 72 AISMFNGQLLFDRPMHV 88
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF A +
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 142 TFNGTPMPNGEQNFRLNWA 160
N + + + R+N A
Sbjct: 124 NMNESELFG--RTIRVNLA 140
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
T ++VG LA +V D +L F + ++ +D T + +G+ FV F +
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 231 RAMTEMNGVFCSTRPMRIGPA 251
A+ MN R +R+ A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 284 TVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRC------GFVQFADRSCAEEALRM 337
++VG L V D+ L F +G + ++IP FV+F A A+
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 338 LNGTQLGGQNIRLSWG 353
+N ++L G+ IR++
Sbjct: 125 MNESELFGRTIRVNLA 140
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 32.3 bits (72), Expect = 0.44, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 282 NTTVFVGNLDSIVTDE----HLRELFSQYGQL---VHVKIPAGKRCGFVQFADRSCAEEA 334
N T+++ NL+ + E L +FSQ+GQ+ V +K + FV F + A A
Sbjct: 6 NQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNA 65
Query: 335 LRMLNGTQLGGQNIRLSWGRSPSNKQAQ 362
LR + G + +++++ +S S+ A+
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAK 93
>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 = 32.3 bits (72), Expect = 0.49, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 51
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRML 338
++VG L V D+ L F +G + ++IP + FV+F A A+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 339 NGTQLGGQNIRLS 351
N ++L G+ IR++
Sbjct: 65 NESELFGRTIRVN 77
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
++VG LA +V D +L F + ++ +D T + +G+ FV F + A+
Sbjct: 5 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 236 MNGVFCSTRPMRIGPA 251
MN R +R+ A
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.3 bits (72), Expect = 0.56, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 280 PNNTTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRML 338
P + +F+GNL V+ E L +FS YG ++ + I GF+QF + +A+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--FGFIQFDNPQSVRDAIECE 65
Query: 339 NGTQLGGQNIRLSWGRSPSNKQAQPD 364
+ G+ + L S SN + Q D
Sbjct: 66 SQEMNFGKKLILE--VSSSNARPQFD 89
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTG--EVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+++G +W + L G +VV +K N+ GQ +GY + S ++L+
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 142 TFNGTPMPNGEQ 153
G + NGE+
Sbjct: 118 LLPGKVL-NGEK 128
>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 = 32.3 bits (72), Expect = 0.57, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
T ++VG LA +V D +L F + ++ +D T + +G+ FV F +
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 231 RAMTEMNGVFCSTRPMRIGPA 251
A+ MN R +R+ A
Sbjct: 64 AAIDNMNESELFGRTIRVNLA 84
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRML 338
++VG L V D+ L F +G + ++IP + FV+F A A+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 339 NGTQLGGQNIRLSWGR 354
N ++L G+ IR++ +
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.0 bits (71), Expect = 0.58, Method: Composition-based stats.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKR---------CGFVQFADRSCAE 332
++ +F+ NL+ T+E L+ +FS+ G + I K GFV++ A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 333 EALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
+AL+ L G + G + + + + P
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKPASGP 95
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.0 bits (71), Expect = 0.60, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 54
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
T ++VG LA +V D +L F + ++ +D T + +G+ FV F +
Sbjct: 3 TTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 231 RAMTEMNGVFCSTRPMRIGPA 251
A+ MN R +R+ A
Sbjct: 62 AAIDNMNESELFGRTIRVNLA 82
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP------AGKRCGFVQFADRSCAEEALRML 338
++VG L V D+ L F +G + ++IP + FV+F A A+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 339 NGTQLGGQNIRLSWGR 354
N ++L G+ IR++ +
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.6 bits (70), Expect = 0.77, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQL---VHVKIPAGKRC---GFVQFADRSCAEEAL 335
+F+G L T+E LR + Q+G+L V ++ PA KR GFV F+ + + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRA 134
+ R L+IG L + E L + G++ V+R+ + + G+GF+ F S A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80
Score = 29.3 bits (64), Expect = 4.8, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 166 EKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGD 225
+KR+ +F+G L+ + T+ L+ + ++ V+ D + R++G+GFV F
Sbjct: 20 KKREKEQFRKLFIGGLSFETTEESLRNYYE-QWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Query: 226 ESEQLRAM 233
+E AM
Sbjct: 79 MAEVDAAM 86
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 278 DDPNNTTVFVGNLDSIVTDEHLRELFSQYGQL------------VHVKIPAGKRCG--FV 323
D+ +N T+FV L VT E + + F Q G + ++ GK G V
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 324 QFADRSCAEEALRMLNGTQLGGQNIRLSWG 353
F D A+ A+ +G + G I++S+
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 7/95 (7%)
Query: 167 KRDDTPDHTIFVGDLAADVTDYMLQETFR----ARYPSTKGAKVV---IDRLTGRTKGYG 219
++D++ ++TIFV L +VT + + F+ + G ++ DR TG+ KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNK 254
V F D A+ +G S P+++ AT +
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRR 95
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 2/95 (2%)
Query: 271 SQVAQSDDDPNNTT--VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADR 328
S + D+D ++ ++V NL ++E + + F+ ++ + FV F++R
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61
Query: 329 SCAEEALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
A EA++ LNG L G I ++ + + P
Sbjct: 62 EDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGP 96
Score = 28.9 bits (63), Expect = 5.9, Method: Composition-based stats.
Identities = 17/89 (19%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G++ + ++V +L ++ M+++ F P ++R+ + + Y
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVK-KIRDYA 54
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRI 248
FV F + + + AM +NG P+ +
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEV 83
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 286 FVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEAL---RMLNGTQ 342
F G+LD E L LFS +G++ + G + G + F ++ A+EAL + N
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEK--AKEALGKAKDANNGN 80
Query: 343 LGGQNIRLSW 352
L +N ++W
Sbjct: 81 LQLRNKEVTW 90
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 103 AHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+H + V+++RNK +GQ G+ F+EF A R ++
Sbjct: 24 SHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGA 136
L+IG + +DE L F G++ + V++++ TG +G F+ + R A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 14/101 (13%)
Query: 277 DDDPNNTTVFVGNLDSIVTDEHLRELFSQYG----------QLVHVKI--PAGKRCG--F 322
D+D +N+ ++V L+ VT + L + F Q G ++H+ + GK G
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 69
Query: 323 VQFADRSCAEEALRMLNGTQLGGQNIRLSWGRSPSNKQAQP 363
V + D A+ A+ +G G +++S R + P
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGP 110
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNG-TQL 343
+++GNL VT + LR+LF + ++ FV + D++ A A+ L+G +L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL 70
Query: 344 GGQNIRLSWGRSPSNKQAQP 363
G+ + + + S + + P
Sbjct: 71 HGKIMEVDYSVSKKLRSSGP 90
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 283 TTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEAL 335
+ +F+GNL V+ E L +FS YG ++ + I GF+QF + +A+
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--FGFIQFDNPQSVRDAI 54
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 283 TTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEAL 335
+ +F+GNL V+ E L +FS YG ++ + I GF+QF + +A+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--FGFIQFDNPQSVRDAI 74
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP----AGKRCGF 322
+FVG L +E +RE F +G++ +++P KR GF
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 45
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 111 VKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMP 149
+++I++KQT Q G+ F++ S A ++LQ P
Sbjct: 41 IRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPP 79
>pdb|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A
Structure-Based Role Of The N-Terminal Domain
Length = 369
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 33/81 (40%)
Query: 148 MPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVV 207
+P E + + G E D + + + + L +R + ++K +VV
Sbjct: 14 IPTTENLYFQGHXNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVV 73
Query: 208 IDRLTGRTKGYGFVRFGDESE 228
IDR TG K Y + +E E
Sbjct: 74 IDRNTGNIKVYQLLEVVEEVE 94
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 2.7, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 283 TTVFVGNLD-SIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEAL 335
+ +F+GNL V+ E L +FS YG ++ + I GF+QF + +A+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--FGFIQFDNPQSVRDAI 74
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 285 VFVGNLDSIVTDEHLRELFSQYGQLVHVKIP----AGKRCGF 322
+FVG L +E +RE F +G++ +++P KR GF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 43
>pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima
Length = 344
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 185 VTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESE 228
+ + L +R + ++K +VVIDR TG K Y + +E E
Sbjct: 26 ILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVE 69
>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 = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 14/86 (16%)
Query: 281 NNTTVFVGNLDSIVTDEHLRELFSQYGQL------------VHVKIPAGKRCG--FVQFA 326
+N T+FV L VT E + + F Q G + ++ GK G V F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 327 DRSCAEEALRMLNGTQLGGQNIRLSW 352
D A+ A+ +G + G I++S+
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKVSF 97
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 173 DHTIFVGDLAADVTDYMLQETFR----ARYPSTKGAKVV---IDRLTGRTKGYGFVRFGD 225
++TIFV L +VT + + F+ + G ++ DR TG+ KG V F D
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Query: 226 ESEQLRAMTEMNGVFCSTRPMRIGPAT 252
A+ +G S P+++ AT
Sbjct: 73 PPSAKAAIDWFDGKEFSGNPIKVSFAT 99
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 30/69 (43%)
Query: 282 NTTVFVGNLDSIVTDEHLRELFSQYGQLVHVKIPAGKRCGFVQFADRSCAEEALRMLNGT 341
T ++VG L + L F ++G + + G ++Q+ A+ A + G
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76
Query: 342 QLGGQNIRL 350
LGG + RL
Sbjct: 77 PLGGPDRRL 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
RTL +L + + E L F E+ V Q G+ +G +IEF S A AE+ L+
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71
Query: 142 TFNG 145
G
Sbjct: 72 EKQG 75
>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 = 29.3 bits (64), Expect = 4.2, Method: Composition-based stats.
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
+I+VG++ T L+ F S ++ D+ +G KG+ ++ F D+ E +R
Sbjct: 7 SIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSL 64
Query: 235 EMNGVFCSTRPMRIGPA-TNK 254
++ R +++ P TN+
Sbjct: 65 ALDESLFRGRQIKVIPKRTNR 85
>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 = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
+I+VG++ T L+ F S ++ D+ +G KG+ ++ F D+ E +R
Sbjct: 8 SIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSL 65
Query: 235 EMNGVFCSTRPMRIGPA-TNK 254
++ R +++ P TN+
Sbjct: 66 ALDESLFRGRQIKVIPKRTNR 86
>pdb|3LPD|A Chain A, Crystal Structure Of A Subtilisin-Like Protease
Length = 339
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 64/265 (24%), Positives = 103/265 (38%), Gaps = 43/265 (16%)
Query: 105 TGEVVAVKVI-------RNKQTGQIEGYGFIEF--ISRAGAERVLQTFNGTPMPNGEQNF 155
TG+ V V V+ R+ + GY FI IS G R F+ E ++
Sbjct: 30 TGQNVVVAVVDTGILHHRDLNANVLPGYDFISNSQISLDGDGRDADPFD-------EGDW 82
Query: 156 RLNWASFGAGEKRDDTPD---HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLT 212
NWA G + R + D H V A VT+ + A GAKVV R
Sbjct: 83 FDNWACGGYPDPRKERSDSSWHGSHVAGTIAAVTNNRIGVAGVA-----YGAKVVPVRAL 137
Query: 213 GRTKGYGFVRFGDESEQL--RAMTEMNGVFCSTRP-----MRIGPATNKKTVSGQQQYPK 265
GR+ GY D S+ L A + G+ + P M +G + + + + Q +
Sbjct: 138 GRSGGYD----SDISDGLYWAAGGRIAGIPENRNPAKVINMSLG-SDGQCSYNAQTMIDR 192
Query: 266 ASYQNSQ--VAQSDDDPNNTTVFVGNLDSIV-----TDEHLRELFSQYGQLVHVKIPAGK 318
A+ + VA +++ N + + + ++++ T +R FS YG V + P
Sbjct: 193 ATRLGALVVVAAGNENQNASNTWPTSCNNVLSVGATTSRGIRASFSNYGVDVDLAAPGQD 252
Query: 319 RCGFVQFADRSCAEEALRMLNGTQL 343
V R +A + GT +
Sbjct: 253 ILSTVDSGTRRPVSDAYSFMAGTSM 277
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.5 bits (62), Expect = 6.6, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 111 VKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRD 169
V+VI++KQT G+ FI+ +S A ++LQ P +N F G KRD
Sbjct: 55 VRVIKDKQTQLNRGFAFIQ-LSTIEAAQLLQILQALHPPLTIDGKTIN-VEFAKGSKRD 111
>pdb|3LPC|A Chain A, Crystal Structure Of A Subtilisin-Like Protease
Length = 340
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 64/265 (24%), Positives = 102/265 (38%), Gaps = 43/265 (16%)
Query: 105 TGEVVAVKVI-------RNKQTGQIEGYGFIEF--ISRAGAERVLQTFNGTPMPNGEQNF 155
TG+ V V V+ R+ + GY FI IS G R F+ E ++
Sbjct: 30 TGQNVVVAVVDTGILHHRDLNANVLPGYDFISNSQISLDGDGRDADPFD-------EGDW 82
Query: 156 RLNWASFGAGEKRDDTPD---HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLT 212
NWA G + R + D H V A VT+ + A GAKVV R
Sbjct: 83 FDNWACGGRPDPRKERSDSSWHGSHVAGTIAAVTNNRIGVAGVA-----YGAKVVPVRAL 137
Query: 213 GRTKGYGFVRFGDESEQL--RAMTEMNGVFCSTRP-----MRIGPATNKKTVSGQQQYPK 265
GR GY D S+ L A + G+ + P M +G + + + + Q +
Sbjct: 138 GRCGGYD----SDISDGLYWAAGGRIAGIPENRNPAKVINMSLG-SDGQCSYNAQTMIDR 192
Query: 266 ASYQNSQ--VAQSDDDPNNTTVFVGNLDSIV-----TDEHLRELFSQYGQLVHVKIPAGK 318
A+ + VA +++ N + + + ++++ T +R FS YG V + P
Sbjct: 193 ATRLGALVVVAAGNENQNASNTWPTSCNNVLSVGATTSRGIRASFSNYGVDVDLAAPGQD 252
Query: 319 RCGFVQFADRSCAEEALRMLNGTQL 343
V R +A + GT +
Sbjct: 253 ILSTVDSGTRRPVSDAYSFMAGTSM 277
>pdb|3LPA|A Chain A, Crystal Structure Of A Subtilisin-Like Protease
Length = 340
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 64/265 (24%), Positives = 102/265 (38%), Gaps = 43/265 (16%)
Query: 105 TGEVVAVKVI-------RNKQTGQIEGYGFIEF--ISRAGAERVLQTFNGTPMPNGEQNF 155
TG+ V V V+ R+ + GY FI IS G R F+ E ++
Sbjct: 30 TGQNVVVAVVDTGILHHRDLNANVLPGYDFISNSQISLDGDGRDADPFD-------EGDW 82
Query: 156 RLNWASFGAGEKRDDTPD---HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLT 212
NWA G + R + D H V A VT+ + A GAKVV R
Sbjct: 83 FDNWACGGYPDPRKERSDSSWHGSHVAGTIAAVTNNRIGVAGVA-----YGAKVVPVRAL 137
Query: 213 GRTKGYGFVRFGDESEQL--RAMTEMNGVFCSTRP-----MRIGPATNKKTVSGQQQYPK 265
GR GY D S+ L A + G+ + P M +G + + + + Q +
Sbjct: 138 GRCGGYD----SDISDGLYWAAGGRIAGIPENRNPAKVINMSLG-SDGQCSYNAQTMIDR 192
Query: 266 ASYQNSQ--VAQSDDDPNNTTVFVGNLDSIV-----TDEHLRELFSQYGQLVHVKIPAGK 318
A+ + VA +++ N + + + ++++ T +R FS YG V + P
Sbjct: 193 ATRLGALVVVAAGNENQNASNTWPTSCNNVLSVGATTSRGIRASFSNYGVDVDLAAPGQD 252
Query: 319 RCGFVQFADRSCAEEALRMLNGTQL 343
V R +A + GT +
Sbjct: 253 ILSTVDSGTRRPVSDAYSFMAGTSM 277
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.5 bits (62), Expect = 8.1, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 13/59 (22%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRL------TGRTKGYGFVRF 223
+P +T F+G+L DVT+ ++E FR G + RL R KG+G+ F
Sbjct: 17 SPPYTAFLGNLPYDVTEESIKEFFR-------GLNISAVRLPREPSNPERLKGFGYAEF 68
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 28.1 bits (61), Expect = 8.7, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 13/59 (22%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRL------TGRTKGYGFVRF 223
+P +T F+G+L DVT+ ++E FR G + RL R KG+G+ F
Sbjct: 13 SPPYTAFLGNLPYDVTEESIKEFFR-------GLNISAVRLPREPSNPERLKGFGYAEF 64
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
0.317 0.134 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,439,591
Number of Sequences: 62578
Number of extensions: 443901
Number of successful extensions: 1542
Number of sequences better than 100.0: 202
Number of HSP's better than 100.0 without gapping: 140
Number of HSP's successfully gapped in prelim test: 62
Number of HSP's that attempted gapping in prelim test: 1033
Number of HSP's gapped (non-prelim): 445
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)