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= 021950
(305 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 91.7 bits (226), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 56/171 (32%), Positives = 83/171 (48%), Gaps = 6/171 (3%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
R L++G+L + E L F G + +K++ +K + Y F+E+ A LQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQ 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 KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPAT 252
V+ D TG ++GYGFV F + + AM M G + RP+RI A
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 83.2 bits (204), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 44/86 (51%), Positives = 59/86 (68%), Gaps = 2/86 (2%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P++++FVGDL DV D ML E F YPS +G KVV+D+ TG +KGYGFV+F DE EQ R
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66
Query: 232 AMTEMNG-VFCSTRPMRIGPATNKKT 256
A+TE G V ++P+R+ A K +
Sbjct: 67 ALTECQGAVGLGSKPVRLSVAIPKAS 92
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
+L++GDL +D+ L F + QTG +GYGF++F +R L
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 143 FNGTPMPNGEQNFRLNWA 160
G + G + RL+ A
Sbjct: 71 CQGA-VGLGSKPVRLSVA 87
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 78.6 bits (192), Expect = 4e-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 = 0.023, 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
>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 = 5e-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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
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: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 246 MRIGPA 251
+++ A
Sbjct: 74 IKVSYA 79
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 75.1 bits (183), Expect = 5e-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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 189 MLQETFRARYPST---KGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRP 245
M QE FR+ + S + K+V D++TG++ GYGFV + D + +A+ +NG+ T+
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 246 MRIGPA 251
+++ A
Sbjct: 74 IKVSYA 79
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 74.7 bits (182), Expect = 5e-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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
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: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 246 MRIGPA 251
+++ A
Sbjct: 74 IKVSYA 79
>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 = 72.4 bits (176), Expect = 3e-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: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 143 FN-----GTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRAR 197
N G P+ R+ W+ ++ IF+ +L + + L +TF A
Sbjct: 72 MNFDVIKGKPV-------RIMWSQRDPSLRKSGV--GNIFIKNLDKSIDNKALYDTFSA- 121
Query: 198 YPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKK 255
+ + KVV D +KGYGFV F + RA+ +MNG+ + R + +G ++K
Sbjct: 122 FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 177
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
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 AMTEMNGVFCSTRPMRI 248
A+ MN +P+RI
Sbjct: 68 ALDTMNFDVIKGKPVRI 84
>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 = 72.4 bits (176), Expect = 3e-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
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
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 AMTEMNGVFCSTRPMRI 248
A+ MN +P+RI
Sbjct: 73 ALDTMNFDVIKGKPVRI 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 70.9 bits (172), 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 = 39.7 bits (91), Expect = 0.002, 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 = 39.7 bits (91), Expect = 0.002, 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
>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 = 67.0 bits (162), 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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 35/78 (44%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
L++ +L + + L+T F G +V ++R+K TG+ G F+ + R A+ +
Sbjct: 102 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 143 FNGTPMPNGEQNFRLNWA 160
N G Q + A
Sbjct: 162 LNNVIPEGGSQPLSVRLA 179
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
+ V L D TD L FRA P ++ D TG + GY FV F E + RA+
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 235 EMNGVFCSTRPMRIGPA 251
+NG+ + +++ A
Sbjct: 75 VLNGITVRNKRLKVSYA 91
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 66.2 bits (160), Expect = 2e-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
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
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
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/109 (33%), Positives = 59/109 (54%), Gaps = 7/109 (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 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKGTF 268
FV F ++ + A+ +M G + R +R AT K PK T+
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA------PKSTY 103
Score = 47.4 bits (111), Expect = 9e-06, 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 = 57.0 bits (136), 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 = 45.8 bits (107), 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|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
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|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 = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FVGDL +V D L+ F+ +PS V+ D TG ++GYGFV F + + AM
Sbjct: 4 LFVGDLNVNVDDETLRNAFK-DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 236 MNGVFCSTRPMRI 248
M G + RP+RI
Sbjct: 63 MQGQDLNGRPLRI 75
Score = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 42/78 (53%), 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-NG-RPLRINWAA 79
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.3 bits (129), Expect = 8e-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 = 42.7 bits (99), 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|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 53/194 (27%), Positives = 84/194 (43%), Gaps = 32/194 (16%)
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 --KKTVSGQQQYPK 265
+K + QQY K
Sbjct: 185 LPEKLMQKTQQYHK 198
>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 = 2e-07, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 174 HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAM 233
++FVG++ + T+ L++ F P ++V DR TG+ KGYGF + D+ L AM
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVV-SFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 234 TEMNGVFCSTRPMRIGPATNKKT 256
+NG S R +R+ A ++K
Sbjct: 68 RNLNGREFSGRALRVDNAASEKN 90
Score = 48.9 bits (115), Expect = 4e-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|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 = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 80/176 (45%), Gaps = 10/176 (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 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPAT 252
+ K A + D TG+ KGYGF+ + A++ MN + +R+G A
Sbjct: 149 -FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K + D +T + KG+ FV + E+ QL A+
Sbjct: 31 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 88
Query: 235 EMNGVFCSTRPMRIGPATN 253
+MN V R +++G +N
Sbjct: 89 QMNSVMLGGRNIKVGRPSN 107
>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 = 1e-06, Method: Compositional matrix adjust.
Identities = 39/176 (22%), Positives = 79/176 (44%), Gaps = 10/176 (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 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPAT 252
+ K + D TG+ KGYGF+ + A++ MN + +R+G A
Sbjct: 134 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K + D +T + KG+ FV + E+ QL A+
Sbjct: 16 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL-ALE 73
Query: 235 EMNGVFCSTRPMRIGPATN 253
+MN V R +++G +N
Sbjct: 74 QMNSVMLGGRNIKVGRPSN 92
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 50.1 bits (118), Expect = 1e-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 E-QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 179
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 50.1 bits (118), Expect = 1e-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
>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 = 50.1 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
>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
>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
>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 = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 102 FAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
F+ G ++ +++ +K TGQ G+GF+ + S +RV Q
Sbjct: 108 FSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
>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 = 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: 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
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.1 bits (113), Expect = 6e-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 = 33.1 bits (74), Expect = 0.19, 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|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 = 47.8 bits (112), Expect = 7e-06, 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 = 37.7 bits (86), Expect = 0.008, 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|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 = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 38/176 (21%), Positives = 77/176 (43%), Gaps = 10/176 (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 RYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPAT 252
+ K + D TG+ KGYGF+ + A++ N + +R+G A
Sbjct: 133 -FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFG-DESEQLRAMT 234
++VG + ++ + +++ F A + K D +T + KG+ FV + E+ QL A+
Sbjct: 15 VYVGSIYYELGEDTIRQAF-APFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQL-ALE 72
Query: 235 EMNGVFCSTRPMRIGPATN 253
+ N V R +++G +N
Sbjct: 73 QXNSVXLGGRNIKVGRPSN 91
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 47.4 bits (111), Expect = 9e-06, 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 = 43.9 bits (102), Expect = 1e-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|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 47.4 bits (111), Expect = 1e-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 = 43.1 bits (100), 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
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 171 TPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
+ + +FVG L+ D + L++ F ++Y VV DR T R++G+GFV F + +
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVF-SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 231 RAMTEMNGVFCSTRPMRIGPA 251
AM MNG R +R+ A
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQA 89
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L++G L + +E L F+ G++ V V+++++T + G+GF+ F + A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 144 NGTPMPNGEQNFRLNWA 160
NG + +G Q R++ A
Sbjct: 75 NGKSV-DGRQ-IRVDQA 89
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 47.0 bits (110), Expect = 1e-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 = 38.5 bits (88), Expect = 0.005, 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
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 172 PDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
P T+FV L+ D T+ L+E+F A++V DR TG +KG+GFV F E +
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFDGSVR----ARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 232 AMTEM 236
A M
Sbjct: 70 AKEAM 74
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 11/82 (13%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
+TL++ L E L F + V +++ +++TG +G+GF++F S A+ +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 142 TFNGTPMPNGE---QNFRLNWA 160
M +GE L+WA
Sbjct: 73 A-----MEDGEIDGNKVTLDWA 89
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
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 KIVESQINFHGKK-LKLGPAIRKQNLSTYHVQPR 97
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
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
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 46.6 bits (109), 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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 169 DDTPD--HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDE 226
+ PD + V + V + L++ F RY + K+V DR T +++GYGFV+F
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFE-RYGPIESVKIVCDRETRQSRGYGFVKFQSG 94
Query: 227 SEQLRAMTEMNGVFCSTRPMRIGPATN 253
S +A+ +NG + +++ A +
Sbjct: 95 SSAQQAIAGLNGFNILNKRLKVALAAS 121
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 46.6 bits (109), Expect = 2e-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 = 36.2 bits (82), Expect = 0.025, 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|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 = 44.7 bits (104), Expect = 7e-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|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
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
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 48/85 (56%), Gaps = 10/85 (11%)
Query: 174 HTIFVG--DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRF-GDESEQL 230
+T+FVG D+ D T+ +F ARY S K K++ DR TG +KGYGFV F D Q
Sbjct: 10 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQK 65
Query: 231 RAMTEMNGVFCSTRPMRIGPATNKK 255
+++N + +++GPA K+
Sbjct: 66 IVESQIN---FHGKKLKLGPAIRKQ 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 = 1e-04, Method: Compositional matrix adjust.
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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 10/86 (11%)
Query: 174 HTIFVG--DLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRF-GDESEQL 230
+T+FVG D+ D T+ +F ARY S K K++ DR TG +KGYGFV F D Q
Sbjct: 11 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQK 66
Query: 231 RAMTEMNGVFCSTRPMRIGPATNKKT 256
+++N + +++GPA K+
Sbjct: 67 IVESQIN---FHGKKLKLGPAIRKQN 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.9 bits (102), Expect = 1e-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 = 2.6, 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|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 43.1 bits (100), Expect = 2e-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 = 41.2 bits (95), Expect = 7e-04, 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
>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 = 2e-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 = 39.7 bits (91), Expect = 0.002, 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
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
IF+ +L + + L +TF A + + KVV D +KGYGFV F + RA+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSA-FGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63
Query: 235 EMNGVFCSTRPMRIGPATNKK 255
+MNG+ + R + +G ++K
Sbjct: 64 KMNGMLLNDRKVFVGRFKSRK 84
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
++I +L +D L F+ G +++ KV+ ++ + GYGF+ F ++ AER ++
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 64
Query: 143 FNGTPM 148
NG +
Sbjct: 65 MNGMLL 70
>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 = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (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 MTEMNGV 239
++ +N V
Sbjct: 72 ISALNNV 78
Score = 37.0 bits (84), Expect = 0.014, Method: Composition-based stats.
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|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 41.6 bits (96), Expect = 5e-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 = 35.8 bits (81), Expect = 0.027, 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|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.8 bits (94), Expect = 0.001, 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 = 39.3 bits (90), Expect = 0.003, 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
>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 = 40.8 bits (94), Expect = 0.001, 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 = 39.3 bits (90), Expect = 0.003, 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
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 40.4 bits (93), Expect = 0.001, 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 = 39.7 bits (91), Expect = 0.002, 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
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.4 bits (93), 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 = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDES 227
+FVG L T L+ F ++Y ++ D+ T +++G+GFV+F D +
Sbjct: 19 LFVGGLDWSTTQETLRSYF-SQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
>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 = 0.001, 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
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
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
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
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
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
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 = 37.0 bits (84), Expect = 0.014, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 93 MDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTFNGTPMPN 150
M + L F G + +++R+ +TG GY F++F S ++R ++ NG + N
Sbjct: 15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 72
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
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
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 174 HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAM 233
I+VG+L T ++E F +++ K++ DR T + KG+GFV +ES A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELF-SQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAI 59
Query: 234 TEMNGVFCSTRPMRIGPATNKKTV 257
+++ R +R+ A KK++
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSL 83
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
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|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
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|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 = 39.3 bits (90), 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|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
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 = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
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|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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/73 (35%), 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+A +
Sbjct: 32 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 236 MNGVFCSTRPMRI 248
NGV RP I
Sbjct: 90 YNGVPLDGRPXNI 102
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
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 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 144 NG 145
NG
Sbjct: 87 NG 88
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
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
>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 = 38.1 bits (87), Expect = 0.007, 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 = 0.009, 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|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.7 bits (86), Expect = 0.007, 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|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
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
>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 = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 9/101 (8%)
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 QLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKGTFL 269
A+ M G +PMRI A + + KGTF+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM---KGTFV 101
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
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 = 35.4 bits (80), Expect = 0.040, Method: Composition-based stats.
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|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 37.0 bits (84), Expect = 0.014, 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|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 9/101 (8%)
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 QLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKGTFL 269
A+ M G +PMRI A + + KGTF+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM---KGTFV 101
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/97 (22%), Positives = 47/97 (48%), Gaps = 4/97 (4%)
Query: 173 DHT--IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQL 230
DH +F+G L + + ML+ F P ++ ++I T +++G+ F+ F + ++
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISE--VLLIKDRTSKSRGFAFITFENPADAK 62
Query: 231 RAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKGT 267
A +MNG + +++ A SG ++ P +
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPAS 99
>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 = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
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
>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 = 0.027, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 9/101 (8%)
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 QLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYPKGTFL 269
A+ M G +PMRI A + + KGTF+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM---KGTFV 102
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 51/105 (48%), Gaps = 6/105 (5%)
Query: 160 ASFGAGEKRDDTPDHTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYG 219
+S +G DD T++VG+L+ DVT+ ++ + F P K K++ + + Y
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGP-CKSCKMITEHTSNDP--YC 58
Query: 220 FVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNKKTVSGQQQYP 264
FV F + + A+ MNG + +++ AT T S Q+ P
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT---TPSSQKSGP 100
Score = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
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|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 71/175 (40%), Gaps = 31/175 (17%)
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 VTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNGV 239
+ D ++E + P K +V D TG +KGY F + D + +A+ +NG+
Sbjct: 108 LNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 161
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 84 LWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQTF 143
L+IG L ++++ + G + A ++++ TG +GY F E++ ++ +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 144 NGTPMPNGEQNFRLNWAS 161
NG M G++ + AS
Sbjct: 159 NG--MQLGDKKLLVQRAS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.8 bits (81), Expect = 0.030, 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|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.4 bits (80), Expect = 0.035, 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 = 34.3 bits (77), Expect = 0.083, 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|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.4 bits (80), Expect = 0.037, Method: Composition-based stats.
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|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 = 0.037, 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|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 = 0.038, 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|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 = 0.039, 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|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 = 0.039, 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|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.4 bits (80), Expect = 0.043, Method: Compositional matrix adjust.
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
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 48/87 (55%), Gaps = 7/87 (8%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T ++G+L + + ++ F + +V+++R+K T + +G+ ++EF + L T
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74
Query: 143 FNGTPMPNGEQNFRLNWASFGAGEKRD 169
++G + G+++ R++ A G K+D
Sbjct: 75 YDGALL--GDRSLRVDIAE---GRKQD 96
>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 = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 2/93 (2%)
Query: 157 LNWASFGAGEKRDDTPD-HTIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRT 215
L S GA + + P+ +F+ L + D L + F + + AKV ID+ T +
Sbjct: 8 LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLS 66
Query: 216 KGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRI 248
K +GFV + + A+ MNG + +++
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV 99
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%)
Query: 80 EIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERV 139
E L+I L + L F G VV+ KV +KQT + +GF+ + + A+
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 140 LQTFNG 145
+Q+ NG
Sbjct: 84 IQSMNG 89
>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 = 0.044, 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|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.4 bits (80), Expect = 0.044, 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|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 = 0.044, 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|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 = 0.045, 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|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 = 35.0 bits (79), Expect = 0.048, 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|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.0 bits (79), Expect = 0.055, Method: Composition-based stats.
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|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 35.0 bits (79), Expect = 0.058, 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|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 34.7 bits (78), Expect = 0.060, 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: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 142 TFNGTPMPNGEQNFRLNWA 160
N + + + R+N A
Sbjct: 73 NMNESELFG--RTIRVNLA 89
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
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|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTE 235
+FV + + + +QE F Y K + +DR TG +KGY V + + L A
Sbjct: 29 LFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 236 MNGV 239
+NG
Sbjct: 88 LNGA 91
Score = 28.9 bits (63), Expect = 4.0, 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: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 144 NGTPMPNGEQNFRLNWASFGAGEKR 168
NG + Q +++W F G KR
Sbjct: 89 NGAEIMG--QTIQVDWC-FVKGPKR 110
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 34.7 bits (78), Expect = 0.069, 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 = 30.8 bits (68), Expect = 0.91, 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|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 = 34.7 bits (78), Expect = 0.069, 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 = 30.8 bits (68), Expect = 0.97, 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|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
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 = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 95 ETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT-------FNGTP 147
E L F+ GEV+ V+V ++ +TG +G+GF+ F +V+ +
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCK 88
Query: 148 MPNGEQN 154
+PN +Q+
Sbjct: 89 LPNSKQS 95
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.071, 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 = 30.8 bits (68), Expect = 0.95, 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|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.7 bits (78), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 79 GEIRTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAER 138
+++ L++ +L + E L F+ G++ VK +++ Y FI F R GA +
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVK 60
Query: 139 VLQTFNGTPM 148
++ NG +
Sbjct: 61 AMEEMNGKDL 70
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 13/96 (13%)
Query: 175 TIFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
+FV +LA VT+ +L++ F S G + +L K Y F+ F + ++AM
Sbjct: 13 VLFVRNLANTVTEEILEKAF-----SQFGKLERVKKL----KDYAFIHFDERDGAVKAME 63
Query: 235 EMNGVFCSTRPMRI----GPATNKKTVSGQQQYPKG 266
EMNG + I P +K Q+Q G
Sbjct: 64 EMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASG 99
>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 = 34.7 bits (78), Expect = 0.073, 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 = 28.9 bits (63), Expect = 3.9, 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|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 = 34.7 bits (78), Expect = 0.075, 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 = 30.8 bits (68), Expect = 0.99, 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|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 = 34.7 bits (78), Expect = 0.077, 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|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 = 34.3 bits (77), Expect = 0.082, 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 = 31.6 bits (70), Expect = 0.58, 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|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 = 34.3 bits (77), Expect = 0.087, 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 = 29.3 bits (64), 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|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 34.3 bits (77), Expect = 0.094, 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 = 0.58, 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|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 34.3 bits (77), Expect = 0.095, Method: Composition-based stats.
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 = 34.3 bits (77), Expect = 0.098, 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
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 13/116 (11%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 104
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 105 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 34.3 bits (77), Expect = 0.098, 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
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 13/116 (11%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 104
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 105 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159
>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 = 34.3 bits (77), Expect = 0.099, 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
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 13/116 (11%)
Query: 123 EGYGFIEFISRAGAERVLQTFNGTPMPNGEQNFRLNWASFGAGEKRDDTPDHTIFVGDLA 182
+G F+ ++ AE + F+ + + E + +L D + V +L
Sbjct: 55 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT------------DALLCVANLP 102
Query: 183 ADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMTEMNG 238
+T +E R + S + +V TG++KGYGF + + RA +++ G
Sbjct: 103 PSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 157
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
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 = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 215 TKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPATNK 254
+KG+GFV F + ++ RA +++G R + + AT +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 93
>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 = 0.11, 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|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
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 = 27.7 bits (60), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 215 TKGYGFVRFGDESEQLRAMTEMNGVFCSTRPMRIGPAT 252
+KG+GFV F + ++ RA +++G R + + AT
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
>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 = 0.13, 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 = 30.4 bits (67), Expect = 1.2, 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|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 = 33.9 bits (76), Expect = 0.13, 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|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.5 bits (75), Expect = 0.13, 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 = 31.6 bits (70), Expect = 0.64, 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|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 = 0.16, 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|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
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|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
+TL++ + Y E+ L F G + + ++ +K++G+ GY FIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.1 bits (74), Expect = 0.19, 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|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 33/67 (49%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQ 141
R L++G L +D+ L+ F G++ +++ + +T + G+ F+EF A +
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 142 TFNGTPM 148
N + +
Sbjct: 124 NMNESEL 130
Score = 31.2 bits (69), Expect = 0.86, 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
>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 = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 82 RTLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEF 130
+TL++ + Y E+ L F G + + ++ +K++G+ GY FIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>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 = 0.22, 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 = 0.22, 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|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.1 bits (74), Expect = 0.22, 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|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
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|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.7 bits (73), Expect = 0.24, 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|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.7 bits (73), Expect = 0.26, 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 = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTGEVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVLQT 142
T++ G + + + + F+ G+++ ++V K GY F+ F + A + +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVS 80
Query: 143 FNGT 146
NGT
Sbjct: 81 VNGT 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
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
>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 = 0.33, 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 = 30.4 bits (67), Expect = 1.4, 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|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 = 32.0 bits (71), Expect = 0.44, 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 = 30.8 bits (68), Expect = 0.91, 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
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.0 bits (71), Expect = 0.45, 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 = 30.8 bits (68), Expect = 0.95, 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
>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 = 32.0 bits (71), Expect = 0.45, 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|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 32.0 bits (71), Expect = 0.46, 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|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 = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 83 TLWIGDLQYWMDETYLNTCFAHTG--EVVAVKVIRNKQTGQIEGYGFIEFISRAGAERVL 140
+++G +W + L G +VV +K N+ GQ +GY + S ++L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 141 QTFNGTPMPNGEQ 153
+ G + NGE+
Sbjct: 117 ELLPGKVL-NGEK 128
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.6 bits (70), Expect = 0.58, 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|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 7/95 (7%)
Query: 167 KRDDTPDHTIFVGDLAADVTDYMLQETFRA----RYPSTKGAKVV---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|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
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: 25 LFVGNLPPDITEEEMRKLF-EKY--GKAGEVFIH----KDKGFGFIRL-----ETRTLAE 72
Query: 236 MNGVFCSTRPMR 247
+ V P+R
Sbjct: 73 IAKVELDNMPLR 84
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
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
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.4 bits (67), Expect = 1.3, 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|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.0 bits (66), Expect = 1.7, 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|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima
Length = 344
Score = 29.6 bits (65), Expect = 1.9, 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|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A
Structure-Based Role Of The N-Terminal Domain
Length = 369
Score = 29.6 bits (65), Expect = 1.9, 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: 51 ILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVE 94
>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 = 29.6 bits (65), Expect = 2.0, 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|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 29.3 bits (64), Expect = 2.6, 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|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.3 bits (64), Expect = 2.7, 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|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.3 bits (64), Expect = 2.7, 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|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 = 29.3 bits (64), Expect = 2.9, 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|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 = 3.2, 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 = 4.0, 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|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 = 5.0, Method: Compositional matrix adjust.
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-LSTIEAAQLLQILQALHPPLTIDGKTINV-EFAKGSKRD 111
>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 = 28.5 bits (62), Expect = 5.1, 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|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 27.7 bits (60), Expect = 7.3, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 176 IFVGDLAADVTDYMLQETF----RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
IFV +L D T ML++ F Y K G++KG G V+F R
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-------NGKSKGCGVVKFESPEVAER 63
Query: 232 AMTEMNGVFCSTRPMRI 248
A MNG+ S R + +
Sbjct: 64 ACRMMNGMKLSGREIDV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 27.7 bits (60), Expect = 8.2, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 176 IFVGDLAADVTDYMLQETF----RARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLR 231
IFV +L D T ML++ F Y K G++KG G V+F R
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-------NGKSKGCGVVKFESPEVAER 60
Query: 232 AMTEMNGVFCSTRPMRI 248
A MNG+ S R + +
Sbjct: 61 ACRMMNGMKLSGREIDV 77
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 176 IFVGDLAADVTDYMLQETFRARYPSTKGAKVVIDRLTGRTKGYGFVRFGDESEQLRAMT 234
IFVG + + + L+E F+ ++ ++ D R +G+GF+ F DE +A+
Sbjct: 13 IFVGGIPHNCGETELREYFK-KFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
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
0.321 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,615,472
Number of Sequences: 62578
Number of extensions: 271236
Number of successful extensions: 954
Number of sequences better than 100.0: 158
Number of HSP's better than 100.0 without gapping: 113
Number of HSP's successfully gapped in prelim test: 45
Number of HSP's that attempted gapping in prelim test: 690
Number of HSP's gapped (non-prelim): 262
length of query: 305
length of database: 14,973,337
effective HSP length: 98
effective length of query: 207
effective length of database: 8,840,693
effective search space: 1830023451
effective search space used: 1830023451
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)