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= 011718
(479 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 68.9 bits (167), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 85/169 (50%), Gaps = 15/169 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSG--ESKGFAFVAFRSKEVAKRAI 162
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV F +++ A A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 163 DELCS-KDFKGKTIRCSM----SETNN-----RLFIGNVPKSWTEKEFRKVIEDVGPGVD 212
+ L + K G M SE NN +LFIG + K TE + R + G ++
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG-QIE 135
Query: 213 TIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTV 261
+++ P S RG AFV + A A + + M A ++P V
Sbjct: 136 ECRILRGPDGLS--RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 182
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 38/156 (24%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKD-PQAPSRNRGFAFVLYYNNACADYS 243
++F+G VP++W+EK+ R++ E G V I +++D Q P +++G FV +Y A +
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 244 RQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQR 303
+ + N K+ P + D A + + L++ + + T ++ +F
Sbjct: 76 QNAL--HNMKV---LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS 130
Query: 304 HGEVTKVVTPPGKSG-KRDFGFIHYAERSSALKAIK 338
G++ + G G R F+ + R+ A AIK
Sbjct: 131 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 269 TPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKV-------VTPPGKSGKRD 321
T DH ++V +P + K L+ELF+++G V ++ PP G
Sbjct: 4 TLDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG--- 60
Query: 322 FGFIHYAERSSALKA 336
F+ + R +AL+A
Sbjct: 61 CCFVTFYTRKAALEA 75
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 68.6 bits (166), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 85/169 (50%), Gaps = 15/169 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSG--ESKGFAFVAFRSKEVAKRAI 162
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV F +++ A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 163 DELCS-KDFKGKTIRCSM----SETNN-----RLFIGNVPKSWTEKEFRKVIEDVGPGVD 212
+ L + K G M SE NN +LFIG + K TE + R + G ++
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ-IE 123
Query: 213 TIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTV 261
+++ P S RG AFV + A A + + M A ++P V
Sbjct: 124 ECRILRGPDGLS--RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 38/156 (24%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKD-PQAPSRNRGFAFVLYYNNACADYS 243
++F+G VP++W+EK+ R++ E G V I +++D Q P +++G FV +Y A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 244 RQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQR 303
+ + N K+ P + D A + + L++ + + T ++ +F
Sbjct: 64 QNAL--HNMKV---LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS 118
Query: 304 HGEVTKVVTPPGKSG-KRDFGFIHYAERSSALKAIK 338
G++ + G G R F+ + R+ A AIK
Sbjct: 119 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
>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 = 68.6 bits (166), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 75/137 (54%), Gaps = 8/137 (5%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP++ ++++LR L IGEV L++DK +G S G+ FV + + + A+RAI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 164 ELCSKDFKGKTIRCSMSETNN------RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELI 217
L + KTI+ S + ++ L+I +P++ T+K+ + G +++ L+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 218 KDPQAPSRNRGFAFVLY 234
Q +RG AF+ +
Sbjct: 123 D--QTTGLSRGVAFIRF 137
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 44/154 (28%), Positives = 71/154 (46%), Gaps = 13/154 (8%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
L + +P++ T+ E R + +G V++ +LI+D A + G+ FV Y D R
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRDKVA-GHSLGYGFVNYV--TAKDAERA 60
Query: 246 KMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRHG 305
T +L T VS+A P S A LY+ LP T K ++++F R G
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDAN-------LYISGLPRTMTQKDVEDMFSRFG 113
Query: 306 EV--TKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
+ ++V+ R FI + +RS A +AI
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T +L+ LF GEV K++ +GF++Y A +AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 341 EKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLPH 380
+ + ++V+ ARP + + A ++ SGLP
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKD------ANLYISGLPR 98
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 68.2 bits (165), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 75/137 (54%), Gaps = 8/137 (5%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP++ ++++LR L IGEV L++DK +G S G+ FV + + + A+RAI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 164 ELCSKDFKGKTIRCSMSETNN------RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELI 217
L + KTI+ S + ++ L+I +P++ T+K+ + G +++ L+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 218 KDPQAPSRNRGFAFVLY 234
Q +RG AF+ +
Sbjct: 123 D--QTTGLSRGVAFIRF 137
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 44/154 (28%), Positives = 71/154 (46%), Gaps = 13/154 (8%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
L + +P++ T+ E R + +G V++ +LI+D A + G+ FV Y D R
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRDKVA-GHSLGYGFVNYV--TAKDAERA 60
Query: 246 KMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRHG 305
T +L T VS+A P S A LY+ LP T K ++++F R G
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDAN-------LYISGLPRTMTQKDVEDMFSRFG 113
Query: 306 EV--TKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
+ ++V+ R FI + +RS A +AI
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T +L+ LF GEV K++ +GF++Y A +AI
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 341 EKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLPH 380
+ + ++V+ ARP + + A ++ SGLP
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKD------ANLYISGLPR 98
>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 = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 37/132 (28%), Positives = 70/132 (53%), Gaps = 6/132 (4%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP++ ++E+ R L IGE+ LV+DK +G+S G+ FV + + A++AI+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 164 ELCSKDFKGKTIRCSMSETNN------RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELI 217
L + KTI+ S + ++ L++ +PK+ T+KE ++ G + + L+
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 218 KDPQAPSRNRGF 229
SR GF
Sbjct: 123 DQVTGVSRGVGF 134
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 46/161 (28%), Positives = 83/161 (51%), Gaps = 15/161 (9%)
Query: 180 SETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNAC 239
S+TN L + +P++ T++EFR + +G +++ +L++D + ++ G+ FV Y +
Sbjct: 1 SKTN--LIVNYLPQNMTQEEFRSLFGSIGE-IESCKLVRD-KITGQSLGYGFVNYID--P 54
Query: 240 ADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKE 299
D + T +L T VS+A P S A LYV LP+ T K+L++
Sbjct: 55 KDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDAN-------LYVSGLPKTMTQKELEQ 107
Query: 300 LFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIK 338
LF ++G + ++++ R GFI + +R A +AIK
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 8/99 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T ++ + LF GE+ K+V +GF++Y + A KAI
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 341 EKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLP 379
+ + ++V+ ARP + + A ++ SGLP
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRD------ANLYVSGLP 97
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ GLPK ++++L L G + ++ D+ +G S+G F+ F + A+ AI
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 164 ELCSKDFKGKT 174
L + G T
Sbjct: 149 GLNGQKPSGAT 159
>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 = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 50/167 (29%), Positives = 82/167 (49%), Gaps = 15/167 (8%)
Query: 107 FIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSG--ESKGFAFVAFRSKEVAKRAIDE 164
F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV F +++ A A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 165 LCS-KDFKGK----TIRCSMSETNN-----RLFIGNVPKSWTEKEFRKVIEDVGPGVDTI 214
L + K G + + SE NN +LFIG + K TE + R G ++
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ-IEEC 125
Query: 215 ELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTV 261
+++ P S RG AFV + A A + + A ++P V
Sbjct: 126 RILRGPDGLS--RGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXV 170
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 36/156 (23%), Positives = 74/156 (47%), Gaps = 8/156 (5%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKD-PQAPSRNRGFAFVLYYNNACADYS 243
+ F+G VP++W+EK+ R++ E G V I +++D Q P +++G FV +Y A +
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 244 RQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQR 303
+ + + + P +P + ++A + + L++ + + T ++ F
Sbjct: 64 QNALHNXKVLPGXHHPI--QXKPADSEKNNAV---EDRKLFIGXISKKCTENDIRVXFSS 118
Query: 304 HGEVTKVVTPPGKSG-KRDFGFIHYAERSSALKAIK 338
G++ + G G R F+ + R+ A AIK
Sbjct: 119 FGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
++FIG + K +E D+R G++ E +++ D G S+G AFV F ++ A+ AI
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAI 153
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 62.0 bits (149), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 44/161 (27%), Positives = 83/161 (51%), Gaps = 15/161 (9%)
Query: 180 SETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNAC 239
S+TN L + +P++ T+ EF+ + +G +++ +L++D + ++ G+ FV Y +
Sbjct: 3 SKTN--LIVNYLPQNMTQDEFKSLFGSIGD-IESCKLVRD-KITGQSLGYGFVNYSDPND 58
Query: 240 ADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKE 299
AD + + KL T VS+A P S A LYV LP+ + K++++
Sbjct: 59 ADKAINTLNG--LKLQTKTIKVSYARPSSASIRDAN-------LYVSGLPKTMSQKEMEQ 109
Query: 300 LFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIK 338
LF ++G + ++++ R GFI + +R A +AIK
Sbjct: 110 LFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 73/137 (53%), Gaps = 8/137 (5%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP++ ++++ + L IG++ LV+DK +G+S G+ FV + A +AI+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 164 ELCSKDFKGKTIRCSMSETNN------RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELI 217
L + KTI+ S + ++ L++ +PK+ ++KE ++ G + T ++
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGR-IITSRIL 123
Query: 218 KDPQAPSRNRGFAFVLY 234
D QA +RG F+ +
Sbjct: 124 LD-QATGVSRGVGFIRF 139
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 49/99 (49%), Gaps = 8/99 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T + K LF G++ K+V +GF++Y++ + A KAI
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 341 EKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLP 379
++ + ++V+ ARP + + A ++ SGLP
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRD------ANLYVSGLP 99
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ GLPK S++++ L G + ++ D+ +G S+G F+ F + A+ AI
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 164 EL 165
L
Sbjct: 151 GL 152
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y
Sbjct: 12 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTYATVEEV 69
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
D + M + K+DG EPK + A VK ++V + E+T
Sbjct: 70 DAA---MNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 121
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 122 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 179
Query: 354 LA 355
A
Sbjct: 180 KA 181
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 11 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 71 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 130 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 161
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y A
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTY---ATV 58
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
+ M + K+DG EPK + A VK ++V + E+T
Sbjct: 59 EEVDAAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 113
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 171
Query: 354 LA 355
A
Sbjct: 172 KA 173
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 63 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 122 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 153
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y A
Sbjct: 9 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTY---ATV 63
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
+ M + K+DG EPK + A VK ++V + E+T
Sbjct: 64 EEVDAAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 118
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 119 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 176
Query: 354 LA 355
A
Sbjct: 177 KA 178
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 8 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 68 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 127 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 158
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y
Sbjct: 10 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTYATVEEV 67
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
D + M + K+DG EPK + A VK ++V + E+T
Sbjct: 68 DAA---MNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 119
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 120 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 177
Query: 354 LA 355
A
Sbjct: 178 KA 179
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 9 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 69 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 128 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 159
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTYATVEEV 68
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
D + M + K+DG EPK + A VK ++V + E+T
Sbjct: 69 DAA---MNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 178
Query: 354 LA 355
A
Sbjct: 179 KA 180
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 70 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 129 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 160
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 84/182 (46%), Gaps = 19/182 (10%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + T++ R E G D + +++DP R+RGF FV Y A
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNT-KRSRGFGFVTY---ATV 65
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA----AASQVKALYVKNLPENTTTKQ 296
+ M + K+DG EPK + A VK ++V + E+T
Sbjct: 66 EEVDAAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 297 LKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYE-IDGQVLEVA 353
L++ F+++G EV +++T G KR F F+ + + S K + +KY ++G EV
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGHNCEVR 178
Query: 354 LA 355
A
Sbjct: 179 KA 180
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 39/154 (25%), Positives = 72/154 (46%), Gaps = 15/154 (9%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P ++FIGGL + ++E LR E G + + +++D ++ S+GF FV + + E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 160 RAIDELCSKDFKGKTI------------RCSMSETNNRLFIGNVPKSWTEKEFRKVIEDV 207
A++ K G+ + R T ++F+G + + E R E
Sbjct: 70 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
G ++ IE++ D + + RGFAFV + ++ D
Sbjct: 129 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 160
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 48/94 (51%)
Query: 178 SMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNN 237
S S N RLFIG +PK +E + I V GV + + +NRGFAFV Y ++
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 238 ACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPD 271
A +R+K+ +L G+ V WAEP+ D
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD 96
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 106 VFIGGLPK-DASEEDLRDLCEPIGEVFEVGLVKDK-DSGESKGFAFVAFRSKEVAKRA 161
+FIGG+PK EE L ++ + V +V + D +++GFAFV + S A A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 60.1 bits (144), Expect = 3e-09, Method: Composition-based stats.
Identities = 31/91 (34%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S +++G L + +E+ LR + EP G++ + L+KD D+G SKG+ F+ F E A+RA++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 164 ELCSKDFKGKTIRCSMSETNNRLFIGNVPKS 194
+L + G+ +R + RL G+ P S
Sbjct: 66 QLNGFELAGRPMR--VGHVTERLDGGSGPSS 94
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 2/80 (2%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
VF+G +P +A+EE L+D+ +G V LV D+++G+ KG+ F ++ +E A A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 166 CSKDFKGKTIRC--SMSETN 183
++F G+ +R + SE N
Sbjct: 71 NGREFSGRALRVDNAASEKN 90
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 275 AAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKV-VTPPGKSGK-RDFGFIHYAERSS 332
A +++++V N+P T +QLK++F G V + ++GK + +GF Y ++ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 333 ALKAIKDTEKYEIDGQVLEVALARPQTNK 361
AL A+++ E G+ L V A + NK
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNK 91
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
+F+GN+P TE++ + + +VGP V + L+ D + + +G+ F Y + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGP-VVSFRLVYDRET-GKPKGYGFCEYQDQETALSAMR 68
Query: 246 KMTSANF 252
+ F
Sbjct: 69 NLNGREF 75
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/139 (27%), Positives = 71/139 (51%), Gaps = 12/139 (8%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP+D ++ +L L IG + +++D +G S G+AFV F S+ ++RAI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 164 ELCSKDFKGKTIRC--------SMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIE 215
L + K ++ S+ +TN L++ N+P++ T+ + + G V
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDTN--LYVTNLPRTITDDQLDTIFGKYGSIVQK-N 120
Query: 216 LIKDPQAPSRNRGFAFVLY 234
+++D + R RG AFV Y
Sbjct: 121 ILRD-KLTGRPRGVAFVRY 138
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 80/180 (44%), Gaps = 19/180 (10%)
Query: 182 TNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
+N L + +P+ T++E + +GP ++T +++D + + G+AFV + + D
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKT-GYSYGYAFVDF--TSEMD 57
Query: 242 YSRQKMTSANFKLDGNTPTVSWAEP--KSTPDHSAAAASQVKALYVKNLPENTTTKQLKE 299
R + VS+A P +S D + LYV NLP T QL
Sbjct: 58 SQRAIKVLNGITVRNKRLKVSYARPGGESIKDTN---------LYVTNLPRTITDDQLDT 108
Query: 300 LFQRHGEVT-KVVTPPGKSGK-RDFGFIHYAERSSALKAIKDTEKYEIDG--QVLEVALA 355
+F ++G + K + +G+ R F+ Y +R A +AI +G Q L V LA
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A+ AI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 164 EL 165
L
Sbjct: 150 AL 151
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV-TKVVTPPGKSG-KRDFGFIHYAERSSALKAIKDT 340
L V LP++ T ++L LF+ G + T + K+G + F+ + + +AIK
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 341 EKYEIDGQVLEVALARP 357
+ + L+V+ ARP
Sbjct: 66 NGITVRNKRLKVSYARP 82
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 58.2 bits (139), Expect = 1e-08, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 44/79 (55%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V++G +P D +EE + DLC +G V + ++ D +G SKG+AF+ FR E + A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 166 CSKDFKGKTIRCSMSETNN 184
+ ++C S ++
Sbjct: 65 NGYQLGSRFLKCGYSSNSD 83
Score = 33.9 bits (76), Expect = 0.23, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
+++G++P TE++ + +VGP ++ ++++ DPQ R++G+AF+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQT-GRSKGYAFIEF 51
>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 = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 44/83 (53%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P V++G +P D +EE + DLC +G V + ++ D +G SKG+AF+ FR E +
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 161 AIDELCSKDFKGKTIRCSMSETN 183
A+ L + ++C S +
Sbjct: 62 AVRNLNGYQLGSRFLKCGYSSNS 84
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
+++G++P TE++ + +VGP ++ ++++ DPQ R++G+AF+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQT-GRSKGYAFIEF 53
>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 = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 44/79 (55%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V++G +P D +EE + DLC +G V + ++ D +G SKG+AF+ FR E + A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 166 CSKDFKGKTIRCSMSETNN 184
+ ++C S ++
Sbjct: 66 NGYQLGSRFLKCGYSSNSD 84
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
+++G++P TE++ + +VGP ++ ++++ DPQ R++G+AF+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQT-GRSKGYAFIEF 52
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 57/103 (55%), Gaps = 6/103 (5%)
Query: 274 AAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSA 333
++ ++VK L+V+NL T + L++ F + G++ +V +D+ FIH+ ER A
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------KDYAFIHFDERDGA 58
Query: 334 LKAIKDTEKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPS 376
+KA+++ +++G+ +E+ A+P KR E A PS
Sbjct: 59 VKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPS 101
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+ L +EE L G++ V +KD +AF+ F ++ A +A++E+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 166 CSKDFKGKTI 175
KD +G+ I
Sbjct: 66 NGKDLEGENI 75
>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 = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 13/150 (8%)
Query: 94 DQLLALP-PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAF 152
D L+ P + + + LP+D ++ +L L IG + + +D +G S G+AFV F
Sbjct: 4 DDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDF 63
Query: 153 RSKEVAKRAIDELCSKDFKGKTIRC--------SMSETNNRLFIGNVPKSWTEKEFRKVI 204
S+ ++RAI L + K ++ S+ +TN L++ N+P++ T+ + +
Sbjct: 64 TSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTN--LYVTNLPRTITDDQLDTIF 121
Query: 205 EDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
G V +++D + R RG AFV Y
Sbjct: 122 GKYGSIVQK-NILRD-KLTGRPRGVAFVRY 149
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 77/178 (43%), Gaps = 15/178 (8%)
Query: 182 TNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
+N L + +P+ T++E + +GP ++T + +D + + G+AFV + + D
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKT-GYSFGYAFVDF--TSEXD 68
Query: 242 YSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELF 301
R + VS+A P + + LYV NLP T QL +F
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYARP-------GGESIKDTNLYVTNLPRTITDDQLDTIF 121
Query: 302 QRHGEVT-KVVTPPGKSGK-RDFGFIHYAERSSALKAIKDTEKYEIDG--QVLEVALA 355
++G + K + +G+ R F+ Y +R A +AI +G Q L V LA
Sbjct: 122 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A+ AI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 164 EL 165
L
Sbjct: 161 AL 162
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFG--FIHYAERSSALKAIKDT 340
L V LP++ T ++L LF+ G + FG F+ + + +AIK
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 341 EKYEIDGQVLEVALARP 357
+ + L+V+ ARP
Sbjct: 77 NGITVRNKRLKVSYARP 93
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 37/57 (64%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
+ + L +D E DL++L P G + + L KDK +G+SKGFAF++F +E A RAI
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSG--KRDFGFIHYAERSSALKAIKDT 340
+ V NL E+T L+ELF+ G ++++ K+ + F FI + R A +AI
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 341 EKYEIDGQVLEVALARPQTN 360
+ D +L V A+P TN
Sbjct: 78 SGFGYDHLILNVEWAKPSTN 97
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++G L A+ E +++L G+VF V L+ D+++ + KGF FV + + V++ AI +L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 166 CSKDFKGKTIRCS 178
+ DF G+TIR +
Sbjct: 63 DNTDFMGRTIRVT 75
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 280 VKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAI 337
++ +YV NL + T++Q+KELF + G+V V + K + FGF+ E S + +AI
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAI 59
Query: 338 KDTEKYEIDGQVLEVALARPQ 358
+ + G+ + V A P+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPK 80
>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 = 54.7 bits (130), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 48/79 (60%)
Query: 102 HGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRA 161
G+ + + LP++ ++++LR L IGEV L++DK +G S G+ FV + + + A+RA
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 162 IDELCSKDFKGKTIRCSMS 180
I+ L + KTI+ S +
Sbjct: 78 INTLNGLRLQSKTIKVSYA 96
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T +L+ LF GEV K++ +GF++Y A +AI
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 341 EKYEIDGQVLEVALARP 357
+ + ++V+ ARP
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>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 = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 39/172 (22%), Positives = 79/172 (45%), Gaps = 23/172 (13%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S V++G + + E+ +R P G + + + D + + KGFAFV + E A+ A++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 164 ELCSKDFKGKTIRCSM-----------------SETNNRLFIGNVPKSWTEKEFRKVIED 206
++ S G+ I+ + NR+++ +V + ++ + + V E
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 207 VGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKLDGN 257
G + + L +DP +++G+ F+ Y A S+ ++S N F L G
Sbjct: 149 FGK-IKSATLARDPTT-GKHKGYGFIEYEK---AQSSQDAVSSMNLFDLGGQ 195
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/179 (23%), Positives = 82/179 (45%), Gaps = 12/179 (6%)
Query: 184 NRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYS 243
+R+++G++ E R+ GP + +I++ D +++GFAFV Y A +
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWD-SVTMKHKGFAFVEYEVPEAAQLA 86
Query: 244 RQKMTSA-----NFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLK 298
++M S N K+ G + A+P D A A +YV ++ ++ + +K
Sbjct: 87 LEQMNSVMLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 299 ELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVLEVALA 355
+F+ G++ + P + +GFI Y + S+ A+ +++ GQ L V A
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
VF+G L + + ED++ P G + + +VKD +G+SKG+ FV+F +K A+ AI +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 165 LCSKDFKGKTIRCSMS 180
+ + G+ IR + +
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 46/82 (56%)
Query: 99 LPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVA 158
L P S V++ LP + DL + G+V +V ++KDKD+ +SKG AF+ F K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 159 KRAIDELCSKDFKGKTIRCSMS 180
+ + +K G+ I+ S++
Sbjct: 72 QNCTRAINNKQLFGRVIKASIA 93
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 277 ASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFG--FIHYAERSSAL 334
A +YV NLP + T L +F ++G+V KV K ++ G FI + ++ SA
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 335 KAIKDTEKYEIDGQVLEVALA 355
+ ++ G+V++ ++A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+GGL D +E+ L + G++ EV +VKD+++ S+GF FV F + + AK A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 165 LCSKDFKGKTIRC 177
+ K G+ IR
Sbjct: 74 MNGKSVDGRQIRV 86
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 2/89 (2%)
Query: 277 ASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSAL 334
AS L+V L +T + L+++F ++G++++VV + +R FGF+ + A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 335 KAIKDTEKYEIDGQVLEVALARPQTNKRT 363
A+ +DG+ + V A ++ R+
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97
>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 = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 48/80 (60%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P + + + LP++ ++++LR L IGEV L++DK +G S G+ FV + + + A+R
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 161 AIDELCSKDFKGKTIRCSMS 180
AI+ L + KTI+ S +
Sbjct: 62 AINTLNGLRLQSKTIKVSYA 81
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T +L+ LF GEV K++ +GF++Y A +AI
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 341 EKYEIDGQVLEVALARP 357
+ + ++V+ ARP
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
VF+G L + + ED++ P G++ + +VKD +G+SKG+ FV+F +K A+ AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 165 LCSKDFKGKTIRCSMS 180
+ + G+ IR + +
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 60/121 (49%), Gaps = 6/121 (4%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S +F+G LP D +EE++R L E G+ EV + KD KGF F+ ++ +A+ A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 164 ELCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAP 223
EL + +GK +R + + L + N+P+ + + + G + ++ D P
Sbjct: 77 ELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRP 136
Query: 224 S 224
S
Sbjct: 137 S 137
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
+Q L+V NLP + T +++++LF+++G+ +V K FGFI R+ A A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLAEIAK 75
Query: 338 KDTEKYEIDGQVLEVALA 355
+ + + G+ L V A
Sbjct: 76 VELDNMPLRGKQLRVRFA 93
>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 = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 81/178 (45%), Gaps = 12/178 (6%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
R+++G++ E R+ GP + +I++ D +++GFAFV Y A +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWD-SVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 245 QKMTSA-----NFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKE 299
++M S N K+ G + A+P D A A +YV ++ ++ + +K
Sbjct: 73 EQMNSVMLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 129
Query: 300 LFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVLEVALA 355
+F+ G++ + P + +GFI Y + S+ A+ +++ GQ L V A
Sbjct: 130 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 41/183 (22%), Positives = 81/183 (44%), Gaps = 23/183 (12%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V++G + + E+ +R P G + + + D + + KGFAFV + E A+ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 166 CSKDFKGKTIRCSM-----------------SETNNRLFIGNVPKSWTEKEFRKVIEDVG 208
S G+ I+ + NR+++ +V + ++ + + V E G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 209 PGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKLDGNTPTVSWAEPK 267
+ + L +DP +++G+ F+ Y A S+ ++S N F L G V A
Sbjct: 136 K-IKSCTLARDPTT-GKHKGYGFIEYEK---AQSSQDAVSSMNLFDLGGQYLRVGKAVTP 190
Query: 268 STP 270
P
Sbjct: 191 PMP 193
>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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 68/138 (49%), Gaps = 14/138 (10%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++FIGGL D +E++LR+ G V ++ ++KD +G S+GF F++F ++DE
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPS----SVDE 60
Query: 165 LCSKD--FKGKTIRCSMS------ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIEL 216
+ GK I + + ++F+G + KEF + G +D +L
Sbjct: 61 VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA-QL 119
Query: 217 IKDPQAPSRNRGFAFVLY 234
+ D ++RGF FV Y
Sbjct: 120 MLDKDT-GQSRGFGFVTY 136
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+GG+ D ++ + G + + L+ DKD+G+S+GF FV + S + A+D
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----AVDR 144
Query: 165 LCSK---DFKGKTIRCSMSE 181
+C DFK + I +E
Sbjct: 145 VCQNKFIDFKDRKIEIKRAE 164
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 50/99 (50%), Gaps = 5/99 (5%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVT--KVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
+++ L +TT L+E F ++G VT K++ P R FGF+ + + SS + +K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63
Query: 341 EKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLP 379
++ +DG+V++ A P+ + G G+ P P
Sbjct: 64 TQHILDGKVIDPKRAIPRDEQDKTGKI-FVGGIGPDVRP 101
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 44/71 (61%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++G L + +E+ LR + EP G + + L+ D ++G SKG+ F+ F E AK+A+++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 166 CSKDFKGKTIR 176
+ G+ ++
Sbjct: 89 NGFELAGRPMK 99
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKV-VTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
LYV +L N T L+ +F+ G + + + ++G+ + +GFI +++ A KA++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 341 EKYEIDGQVLEVALARPQTN 360
+E+ G+ ++V +T+
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>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 = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 45/195 (23%), Positives = 84/195 (43%), Gaps = 16/195 (8%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++G L D +E L + P G + + + +D + S G+A+V F+ A+RA+D
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 164 ELCSKDFKGKTIRCSMSETNNRL--------FIGNVPKSWTEKEFRKVIEDVGPGVDTIE 215
+ KGK +R S+ + L FI N+ KS K G + + +
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCK 134
Query: 216 LIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAA 275
++ D ++G+ FV + A+ + +KM N V KS + A
Sbjct: 135 VVCDENG---SKGYGFVHFETQEAAERAIEKMNGMLL----NDRKVFVGRFKSRKEREAE 187
Query: 276 AASQVKALYVKNLPE 290
++ K Y ++P+
Sbjct: 188 LGARAKEFYPYDVPD 202
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/184 (21%), Positives = 87/184 (47%), Gaps = 19/184 (10%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
L++G++ TE + GP + +I + +D R+ G+A+V + A A+ +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAE---R 72
Query: 246 KMTSANFKLDGNTPT-VSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRH 304
+ + NF + P + W++ + S V +++KNL ++ K L + F
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSG-----VGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 305 GEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVL---EVALARPQTNK 361
G + ++G + +GF+H+ + +A +AI+ +++G +L +V + R ++ K
Sbjct: 128 GNILSCKVVCDENGSKGYGFVHFETQEAAERAIE-----KMNGMLLNDRKVFVGRFKSRK 182
Query: 362 RTEG 365
E
Sbjct: 183 EREA 186
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 102 HGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRA 161
H ++FIGGL ++ +E+ L+ + G + EV L+KD+ S +S+GFAF+ F + AK A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNA 64
Query: 162 IDELCSKDFKGKTIRC 177
++ K GK I+
Sbjct: 65 AKDMNGKSLHGKAIKV 80
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
+LFIG + + EK + V GP + + LIKD S++RGFAF+ + N A A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGP-ISEVLLIKD--RTSKSRGFAFITFENPADAKNAA 65
Query: 245 QKMT 248
+ M
Sbjct: 66 KDMN 69
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 60/246 (24%), Positives = 98/246 (39%), Gaps = 30/246 (12%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+G LP D +EED + L E GE EV + +D +GF F+ S+ +A+ A EL
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 166 CSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSR 225
K + +R + L + N+ + + + GP + ++ D R
Sbjct: 79 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD---RGR 135
Query: 226 NRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYV 285
G FV + A + ++ F L TP EP D
Sbjct: 136 ATGKGFVEFAAKPPARKALERCGDGAFLLT-TTPRPVIVEPMEQFDDE------------ 182
Query: 286 KNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEI 345
LPE K +++ Q H E + PP + F F YA R AL ++ ++ ++
Sbjct: 183 DGLPE----KLMQKTQQYHKEREQ---PPRFAQPGTFEF-EYASRWKALDEMEKQQREQV 234
Query: 346 DGQVLE 351
D + E
Sbjct: 235 DRNIRE 240
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 52/188 (27%), Positives = 80/188 (42%), Gaps = 35/188 (18%)
Query: 171 KGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFA 230
K T RC RLF+GN+P TE++F+++ E G + +R+RGF
Sbjct: 17 KTYTQRC-------RLFVGNLPTDITEEDFKRLFERYGEPSEVF--------INRDRGFG 61
Query: 231 FVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPE 290
F+ + A+ ++ +LDG KS P A+ AL VKNL
Sbjct: 62 FIRLESRTLAEIAKA-------ELDGTI-------LKSRP-LRIRFATHGAALTVKNLSP 106
Query: 291 NTTTKQLKELFQRHGEVTKVVTPPGKSGKRD-FGFIHYAERSSALKAIKDTEKYEIDGQV 349
+ + L++ F + G V K V G+ GF+ +A + A KA++ DG
Sbjct: 107 VVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG----DGAF 162
Query: 350 LEVALARP 357
L RP
Sbjct: 163 LLTTTPRP 170
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 2/63 (3%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSG--ESKGFAFVAFRSKEVAKRAI 162
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV F +++ A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 163 DEL 165
+ L
Sbjct: 65 NAL 67
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKD-PQAPSRNRGFAFVLYYNNACA 240
++F+G VP++W+EK+ R++ E G V I +++D Q P +++G FV +Y A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/170 (22%), Positives = 76/170 (44%), Gaps = 23/170 (13%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V++G + + E+ +R P G + + D + + KGFAFV + E A+ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 166 CSKDFKGKTIRCSM-----------------SETNNRLFIGNVPKSWTEKEFRKVIEDVG 208
S G+ I+ + NR+++ +V + ++ + + V E G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 209 PGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKLDGN 257
+ + L +DP +++G+ F+ Y A S+ ++S N F L G
Sbjct: 135 K-IKSCTLARDPTT-GKHKGYGFIEYEK---AQSSQDAVSSXNLFDLGGQ 179
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 41/178 (23%), Positives = 79/178 (44%), Gaps = 12/178 (6%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
R+++G++ E R+ GP + +I+ D +++GFAFV Y A +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDXSWD-SVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 245 QKMTSA-----NFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKE 299
++ S N K+ G + A+P D A A +YV ++ ++ + +K
Sbjct: 72 EQXNSVXLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 300 LFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVLEVALA 355
+F+ G++ + P + +GFI Y + S+ A+ +++ GQ L V A
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 40/57 (70%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRA 161
++FIG +P++ E+DL+ L E G+++E+ ++KD+ +G KG AF+ + +E A +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGK--SGKRDFGFIHYAERSSALKA 336
L++ +P N K LK LF+ G++ ++ + + F+ Y ER SALKA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
+LFIG +P++ EK+ + + E+ G + + ++KD + ++G AF+ Y C S
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGK-IYELTVLKD-RFTGMHKGCAFLTY----CERESA 68
Query: 245 QKMTSA 250
K SA
Sbjct: 69 LKAQSA 74
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 8/82 (9%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQ--RHGEVTKVVTPPGKSGKRDFGFIHYAERSSALK 335
S VK LYV+NL +T+ + +++ F + G V +V RD+ F+H++ R A++
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVE 66
Query: 336 AIKDTEKYEIDGQVLEVALARP 357
A+K +DG +EV LA+P
Sbjct: 67 AMKALNGKVLDGSPIEVTLAKP 88
>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 = 48.9 bits (115), Expect = 6e-06, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+FIGGL D +++DL+D GEV + L D +G S+GF FV F+ E + +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 166 CSKDFKGKTI 175
K GK I
Sbjct: 62 EHK-LNGKVI 70
Score = 37.4 bits (85), Expect = 0.020, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTP--PGKSGKRDFGFIHYAERSSALKAIKDT 340
+++ L +TT K LK+ F + GEV P R FGF+ + E S ++ + D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE-SESVDKVMDQ 60
Query: 341 EKYEIDGQVLE 351
++++++G+V++
Sbjct: 61 KEHKLNGKVID 71
Score = 29.6 bits (65), Expect = 3.4, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVD-TIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
+FIG + T+K+ + G VD T++L DP R+RGF FVL+ + D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKL--DP-ITGRSRGFGFVLFKESESVD--- 55
Query: 245 QKMTSANFKLDG 256
+ M KL+G
Sbjct: 56 KVMDQKEHKLNG 67
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 37/153 (24%), Positives = 70/153 (45%), Gaps = 12/153 (7%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++G L D +E L + P G + + + +D + S G+A+V F+ A+RA+D
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 164 ELCSKDFKGKTIRCSMSETNNRL--------FIGNVPKSWTEKEFRKVIEDVGPGVDTIE 215
+ KGK +R S+ + L FI N+ KS K G + + +
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCK 129
Query: 216 LIKDPQAPSRNRGFAFVLYYNNACADYSRQKMT 248
++ D ++G+ FV + A+ + +KM
Sbjct: 130 VVCDENG---SKGYGFVHFETQEAAERAIEKMN 159
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 40/184 (21%), Positives = 87/184 (47%), Gaps = 19/184 (10%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
L++G++ TE + GP + +I + +D R+ G+A+V + A A+ +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAE---R 67
Query: 246 KMTSANFKLDGNTPT-VSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRH 304
+ + NF + P + W++ + S V +++KNL ++ K L + F
Sbjct: 68 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSG-----VGNIFIKNLDKSIDNKALYDTFSAF 122
Query: 305 GEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVL---EVALARPQTNK 361
G + ++G + +GF+H+ + +A +AI+ +++G +L +V + R ++ K
Sbjct: 123 GNILSCKVVCDENGSKGYGFVHFETQEAAERAIE-----KMNGMLLNDRKVFVGRFKSRK 177
Query: 362 RTEG 365
E
Sbjct: 178 EREA 181
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 96 LLALPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSK 155
L PP ++F+G L K SE+D+R L E G + E +++ D G SKG AFV + S
Sbjct: 8 CLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSH 66
Query: 156 EVAKRAIDEL 165
A+ AI+ L
Sbjct: 67 AEAQAAINAL 76
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 44/84 (52%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V++GGL + SE L +L G V + KD+ +G+ +G+ FV F S+E A AI +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 166 CSKDFKGKTIRCSMSETNNRLFIG 189
GK IR + + +N+ G
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGK-SGKRD-FGFIHYAERSSALK 335
+Q +YV L E + L ELF + G V P + +G+ +GF+ + A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 336 AIKDTEKYEIDGQVLEVALARPQTNKRTEG 365
AIK + ++ G+ + V A NK G
Sbjct: 73 AIKIMDMIKLYGKPIRVNKASAH-NKNLSG 101
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRA 161
+++F+GGLP ++ LR E G++ E ++ D+ +G+S+G+ FV + A+RA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 3/75 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTK-VVTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
++V LP +TT L++ F+ G++ + VV ++GK R +GF+ A+R++A +A KD
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 341 EKYEIDGQVLEVALA 355
IDG+ V LA
Sbjct: 80 NPI-IDGRKANVNLA 93
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S +F+G LP D +EE++R L E G+ EV + KD KGF F+ ++ +A+ A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 164 ELCSKDFKGKTIRCSMS 180
EL + +GK +R +
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
+Q L+V NLP + T +++++LF+++G+ +V K FGFI R+ A A
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLAEIAK 68
Query: 338 KDTEKYEIDGQVLEVALA 355
+ + + G+ L V A
Sbjct: 69 VELDNMPLRGKQLRVRFA 86
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 16/96 (16%)
Query: 183 NNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADY 242
+RLF+GN+P TE+E RK+ E G + +++GF F+ A+
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF--------IHKDKGFGFIRLETRTLAEI 66
Query: 243 SRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAAS 278
++ ++ N L G V +A HSA+ S
Sbjct: 67 AKVELD--NMPLRGKQLRVRFA------CHSASLTS 94
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 107 FIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
F+GGL D S++DL+D GEV + + D ++G S+GF F+ F+ ++ +D+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 284 YVKNLPENTTTKQLKELFQRHGEVT--KVVTPPGKSGKRDFGFIHYAERSSALKAIKDTE 341
+V L +T+ K LK+ F + GEV + P R FGFI + + +S K + D +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQK 73
Query: 342 KYEIDGQVLE 351
++ +DG+V++
Sbjct: 74 EHRLDGRVID 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++GGL ++ ++ L P G++ ++ + D ++ + +GFAFV F E A AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 166 CSKDFKGKTIRCSMSE 181
+ G+TIR ++++
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 277 ASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSAL 334
A+ + LYV L E K L F G++T + P + R F F+ + A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 335 KAIKDTEKYEIDGQVLEVALAR 356
AI + + E+ G+ + V LA+
Sbjct: 64 AAIDNMNESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++GGL ++ ++ L P G++ ++ + D ++ + +GFAFV F E A AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 166 CSKDFKGKTIRCSMS 180
+ G+TIR +++
Sbjct: 68 NESELFGRTIRVNLA 82
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 2/78 (2%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAIK 338
+ LYV L E K L F G++T + P + R F F+ + A AI
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 339 DTEKYEIDGQVLEVALAR 356
+ + E+ G+ + V LA+
Sbjct: 66 NMNESELFGRTIRVNLAK 83
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++GGL ++ ++ L P G++ ++ + D ++ + +GFAFV F E A AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 166 CSKDFKGKTIRCSMSE 181
+ G+TIR ++++
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
Query: 273 SAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAER 330
S+ A+ + LYV L E K L F G++T + P + R F F+ +
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 331 SSALKAIKDTEKYEIDGQVLEVALARPQTNKRT 363
A AI + + E+ G+ + V LA+P K +
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 42/76 (55%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
+F+G L + +E LR+ + ++ D +G S+G+ FV+F S++ A+ A+D
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 165 LCSKDFKGKTIRCSMS 180
+ +D G+ +R + +
Sbjct: 149 MQGQDLNGRPLRINWA 164
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/167 (21%), Positives = 77/167 (46%), Gaps = 13/167 (7%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++G L K +E+ L+ + G + + ++ DK++ ++ +AFV + A A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 166 CSKDFKGKTIRC--------SMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELI 217
K + ++ S S+ LF+G++ + ++ R +D P + ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDF-PSYLSGHVM 120
Query: 218 KDPQAPSRNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWA 264
D Q S +RG+ FV + + A + M + L+G ++WA
Sbjct: 121 WDMQTGS-SRGYGFVSFTSQDDAQNAMDSMQGQD--LNGRPLRINWA 164
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 1/93 (1%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKR-DFGFIHYAERSSALKAIKD 339
+ LYV NL + T LK+ FQ G + + K+ K ++ F+ Y + A A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 340 TEKYEIDGQVLEVALARPQTNKRTEGVYSCAAG 372
+I+ ++++ A ++ ++ G
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVG 93
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 40/61 (65%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+G +P+ E+DL+ L E G ++E+ ++KD+ +G KG AF+ + +++ A +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 165 L 165
L
Sbjct: 77 L 77
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
+LF+G +P+ E++ + + E+ G + + ++KD + ++G AF+ Y CA S
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGR-IYELTVLKD-RLTGLHKGCAFLTY----CARDSA 70
Query: 245 QKMTSA 250
K SA
Sbjct: 71 LKAQSA 76
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 58/257 (22%), Positives = 103/257 (40%), Gaps = 21/257 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++ I GLP D + +++ DL +E+ K + KG AFV + E A+ AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSD----YEL---KYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 165 LCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPS 224
+ + + + T+ L + N+P S T+++F +++ G + + S
Sbjct: 77 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 136
Query: 225 RNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEP-KSTPDHSAAAASQVKAL 283
+ GFA + ++A +R K L T V W + + TP A + L
Sbjct: 137 KGYGFAEYMKKDSA----ARAKSDLLGKPLGPRTLYVHWTDAGQLTP-----ALLHSRCL 187
Query: 284 YVKNLPE--NTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
V LP N + L H T G+ G+ + F + Y A +A +
Sbjct: 188 CVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 341 EKYEIDGQVLEVALARP 357
+ + G L V+ P
Sbjct: 247 DGLSLGGSHLRVSFCAP 263
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%)
Query: 99 LPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVA 158
L P + + + LP +++ +L P G + LV + +G+SKG+ F + K+ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 159 KRAIDELCSKDFKGKTI 175
RA +L K +T+
Sbjct: 151 ARAKSDLLGKPLGPRTL 167
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 58/257 (22%), Positives = 103/257 (40%), Gaps = 21/257 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++ I GLP D + +++ DL +E+ K + KG AFV + E A+ AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSD----YEL---KYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 165 LCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPS 224
+ + + + T+ L + N+P S T+++F +++ G + + S
Sbjct: 77 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 136
Query: 225 RNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEP-KSTPDHSAAAASQVKAL 283
+ GFA + ++A +R K L T V W + + TP A + L
Sbjct: 137 KGYGFAEYMKKDSA----ARAKSDLLGKPLGPRTLYVHWTDAGQLTP-----ALLHSRCL 187
Query: 284 YVKNLPE--NTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
V LP N + L H T G+ G+ + F + Y A +A +
Sbjct: 188 CVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 341 EKYEIDGQVLEVALARP 357
+ + G L V+ P
Sbjct: 247 DGLSLGGSHLRVSFCAP 263
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%)
Query: 99 LPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVA 158
L P + + + LP +++ +L P G + LV + +G+SKG+ F + K+ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 159 KRAIDELCSKDFKGKTI 175
RA +L K +T+
Sbjct: 151 ARAKSDLLGKPLGPRTL 167
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 58/257 (22%), Positives = 103/257 (40%), Gaps = 21/257 (8%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++ I GLP D + +++ DL +E+ K + KG AFV + E A+ AI+
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSD----YEL---KYCFVDKYKGTAFVTLLNGEQAEAAINA 74
Query: 165 LCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPS 224
+ + + + T+ L + N+P S T+++F +++ G + + S
Sbjct: 75 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 134
Query: 225 RNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEP-KSTPDHSAAAASQVKAL 283
+ GFA + ++A +R K L T V W + + TP A + L
Sbjct: 135 KGYGFAEYMKKDSA----ARAKSDLLGKPLGPRTLYVHWTDAGQLTP-----ALLHSRCL 185
Query: 284 YVKNLPE--NTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
V LP N + L H T G+ G+ + F + Y A +A +
Sbjct: 186 CVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 244
Query: 341 EKYEIDGQVLEVALARP 357
+ + G L V+ P
Sbjct: 245 DGLSLGGSHLRVSFCAP 261
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%)
Query: 99 LPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVA 158
L P + + + LP +++ +L P G + LV + +G+SKG+ F + K+ A
Sbjct: 89 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 148
Query: 159 KRAIDELCSKDFKGKTI 175
RA +L K +T+
Sbjct: 149 ARAKSDLLGKPLGPRTL 165
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++GGL ++ ++ L P G++ ++ + D ++ + +GFAFV F E A AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 166 CSKDFKGKTIRCSMS 180
+ G+TIR +++
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 32.7 bits (73), Expect = 0.49, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAIK 338
+ LYV L E K L F G++T + P + R F F+ + A AI
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 339 DTEKYEIDGQVLEVALA 355
+ + E+ G+ + V LA
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+++F+GG+P + E +LR+ + G V EV ++ D + +GF F+ F ++ +A++
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 164 ELCSKDFKGKTIRCSMSE 181
+ D GK + +E
Sbjct: 71 -MHFHDIMGKKVEVKRAE 87
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVT--PPGKSGKRDFGFIHYAERSSALKAIKDT 340
++V +P N +L+E F++ G VT+VV K R FGFI + + S +A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 341 EKYEIDGQVLEVALARPQTNKRT 363
++I G+ +EV A P+ +K +
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSS 94
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%)
Query: 110 GLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKD 169
GL +E DLR++ G + +V +V D+ S S+GFAFV F + + AK A + +
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 170 FKGKTIRCSMSET 182
G+ IR S T
Sbjct: 113 LDGRRIRVDFSIT 125
Score = 35.4 bits (80), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 196 TEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKL 254
TE++ R+V GP D + ++ D Q+ R+RGFAFV + N D +++ AN +L
Sbjct: 59 TERDLREVFSKYGPIAD-VSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 113
Query: 255 DGNTPTVSWAEPK 267
DG V ++ K
Sbjct: 114 DGRRIRVDFSITK 126
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 282 ALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSALKAIKD 339
L V L TT + L+E+F ++G + V + +R F F+++ A +A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 340 TEKYEIDGQVLEV 352
E+DG+ + V
Sbjct: 108 ANGMELDGRRIRV 120
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++GGL ++ ++ L P G++ ++ + D ++ + +GFAFV F E A AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 166 CSKDFKGKTIRCSMS 180
+ G+TIR +++
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 277 ASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSAL 334
A+ + LYV L E K L F G++T + P + R F F+ + A
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 335 KAIKDTEKYEIDGQVLEVALA 355
AI + + E+ G+ + V LA
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 98 ALPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEV 157
+P ++FIGGLP +++ +++L G + LVKD +G SKG+AF + V
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168
Query: 158 AKRAIDELCSKDFKGKTI---RCSMSETN 183
+AI L K + R S+ N
Sbjct: 169 TDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 38/174 (21%), Positives = 72/174 (41%), Gaps = 46/174 (26%)
Query: 105 EVFIGGLPKDASEEDLRDLCE-----------PIGEVFEVGLVKDKDSGESKGFAFVAFR 153
+++G +P +EE + D P V V + +DK+ FAF+ FR
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFR 59
Query: 154 SKEVAKRAIDELCSKDFKGKTIRC----------SMSE----------------TNNRLF 187
S + +A+ F+G++++ MSE + ++LF
Sbjct: 60 SVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLF 118
Query: 188 IGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
IG +P + + ++++ GP + L+KD A ++G+AF Y + D
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGP-LKAFNLVKD-SATGLSKGYAFCEYVDINVTD 170
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 108 IGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCS 167
+ GL +E DLR++ G + +V +V D+ S S+GFAFV F + + AK A +
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 168 KDFKGKTIRCSMSET 182
+ G+ IR S T
Sbjct: 77 MELDGRRIRVDFSIT 91
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 196 TEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKL 254
TE++ R+V GP D + ++ D Q+ R+RGFAFV + N D +++ AN +L
Sbjct: 25 TERDLREVFSKYGPIAD-VSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 79
Query: 255 DGNTPTVSWAEPK 267
DG V ++ K
Sbjct: 80 DGRRIRVDFSITK 92
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 282 ALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSALKAIKD 339
L V L TT + L+E+F ++G + V + +R F F+++ A +A +
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 340 TEKYEIDGQVLEVALA---RPQT 359
E+DG+ + V + RP T
Sbjct: 74 ANGMELDGRRIRVDFSITKRPHT 96
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+G L K ++ED+R + EP G + E +++ D G SKG AFV F++ A+ AI+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 165 LCS 167
L S
Sbjct: 73 LHS 75
Score = 32.7 bits (73), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 183 NNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNA 238
+ +LF+G + K T+++ RK+ E G +D +++ P S +G AFV + +A
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGT-IDECTVLRGPDGTS--KGCAFVKFQTHA 64
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 108 IGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCS 167
+ GL +E DLR++ G + +V +V D+ S S+GFAFV F + + AK A +
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 168 KDFKGKTIRCSMSET 182
+ G+ IR S T
Sbjct: 80 MELDGRRIRVDFSIT 94
Score = 35.0 bits (79), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 196 TEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKL 254
TE++ R+V GP D + ++ D Q+ R+RGFAFV + N D +++ AN +L
Sbjct: 28 TERDLREVFSKYGPIAD-VSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 82
Query: 255 DGNTPTVSWAEPK 267
DG V ++ K
Sbjct: 83 DGRRIRVDFSITK 95
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 282 ALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSALKAIKD 339
L V L TT + L+E+F ++G + V + +R F F+++ A +A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 340 TEKYEIDGQVLEVALA---RPQT 359
E+DG+ + V + RP T
Sbjct: 77 ANGMELDGRRIRVDFSITKRPHT 99
>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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P ++FIGGLP +++ +++L G + LVKD +G SKG+AF + V +
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 161 AIDEL 165
AI L
Sbjct: 154 AIAGL 158
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/160 (23%), Positives = 71/160 (44%), Gaps = 28/160 (17%)
Query: 101 PHGS--EVFIGGLPKDASEEDLRDLCE-----------PIGEVFEVGLVKDKDSGESKGF 147
P GS +++G +P +EE + D P V V + +DK+ F
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------F 55
Query: 148 AFVAFRSKEVAKRAIDELCSKDFKGKTIRCSMSET------NNRLFIGNVPKSWTEKEFR 201
AF+ FRS + +A+ F+G++++ ++LFIG +P + + +
Sbjct: 56 AFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 114
Query: 202 KVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
+++ GP + L+KD A ++G+AF Y + D
Sbjct: 115 ELLTSFGP-LKAFNLVKD-SATGLSKGYAFCEYVDINVTD 152
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P ++FIGGLP +++ +++L G + LVKD +G SKG+AF + V +
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 161 AIDEL 165
AI L
Sbjct: 152 AIAGL 156
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 35/154 (22%), Positives = 68/154 (44%), Gaps = 26/154 (16%)
Query: 105 EVFIGGLPKDASEEDLRDLCE-----------PIGEVFEVGLVKDKDSGESKGFAFVAFR 153
+++G +P +EE + D P V V + +DK+ FAF+ FR
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFR 59
Query: 154 SKEVAKRAIDELCSKDFKGKTIRCSMSET------NNRLFIGNVPKSWTEKEFRKVIEDV 207
S + +A+ F+G++++ ++LFIG +P + + ++++
Sbjct: 60 SVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSF 118
Query: 208 GPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
GP + L+KD A ++G+AF Y + D
Sbjct: 119 GP-LKAFNLVKD-SATGLSKGYAFCEYVDINVTD 150
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.1 bits (105), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 44/77 (57%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP++ ++++ + L IG++ LV+DK +G+S G+ FV + A +AI+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 164 ELCSKDFKGKTIRCSMS 180
L + KTI+ S +
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVT--KVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L V LP+N T + K LF G++ K+V +GF++Y++ + A KAI
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 341 EKYEIDGQVLEVALARPQT 359
++ + ++V+ ARP +
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 52/87 (59%), Gaps = 7/87 (8%)
Query: 273 SAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSS 332
S+ ++ VK L++ NLP T ++++ LF+++G+V + +++GF+H ++++
Sbjct: 2 SSGSSGMVK-LFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTA 54
Query: 333 ALKAIKDTEKYEIDGQVLEVALARPQT 359
A AI++ Y++ G + V ++ ++
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKNKS 81
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++FIG LP++A+E+++R L E G+V E ++K+ + FV K A+ AI
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 165 LCSKDFKGKTIRCSMSETNNR 185
L G I S+ ++
Sbjct: 62 LHHYKLHGVNINVEASKNKSK 82
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
+LFIGN+P+ TE+E R + E G V ++IK+ + FV + A+ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGK-VLECDIIKN---------YGFVHIEDKTAAEDAI 59
Query: 245 QKMTSANFKLDGNTPTVSWAEPKS 268
+ + ++KL G V ++ KS
Sbjct: 60 RNLH--HYKLHGVNINVEASKNKS 81
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 116 SEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDFKGKTI 175
S + LR + E G V +V + +D+ + ES+GFAFV F K A+ A+D + G+ +
Sbjct: 60 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Query: 176 RCSMSE 181
R M+
Sbjct: 120 RVQMAR 125
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 280 VKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAI 337
+ +L V NL T+ L+ +F+++G V V P + K R F F+ + ++ A A+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 338 KDTEKYEIDGQVLEVALAR 356
+ +DG+ L V +AR
Sbjct: 107 DAMDGAVLDGRELRVQMAR 125
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S ++I GL +++DL LC+P G++ + DK + + KG+ FV F S A++A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 164 EL 165
L
Sbjct: 66 AL 67
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+GGL + + ED++ E G+V + L+ DK + +GF FV F S+++ ++ + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 166 CSKDFKGKTIRC 177
+ K + C
Sbjct: 61 HFHEINNKMVEC 72
Score = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSALKAIKDT 340
++V L NTT + +K F++ G+V + K+ R FGF+ + E ++ + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 341 EKYEIDGQVLE 351
+EI+ +++E
Sbjct: 61 HFHEINNKMVE 71
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTP--PGKSGKRDFGFIHYAERSSALKAIKDT 340
L V NL T+ L+ +F+++G V V P P R F F+ + +R A A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 341 EKYEIDGQVLEVALAR 356
+ E+DG+ L V +AR
Sbjct: 76 DGAELDGRELRVQVAR 91
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 116 SEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDFKGKTI 175
S + LR + E G V +V + ++ + +GFAFV F + A+ A + + G+ +
Sbjct: 26 SPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85
Query: 176 RCSMSETNNRLFIG 189
R ++ R G
Sbjct: 86 RVQVARYGRRDLSG 99
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S++ + GLP +E+DL++ GEV V + KD +G SKGF FV F E + +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 164 E 164
+
Sbjct: 76 Q 76
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 276 AASQVKALYVKNLPENTTTKQLKELFQRHGEVTKV-VTPPGKSG-KRDFGFIHYAERSSA 333
A + L V LP TT + LKE F GEV V V K+G + FGF+ + E +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 334 LKAIKDTEKYEIDGQVLEVALARPQTNK 361
+K + ++++ IDG+ + L + ++
Sbjct: 71 VKVM--SQRHMIDGRWCDCKLPNSKQSQ 96
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%)
Query: 108 IGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCS 167
+ L S + LR + E G V +V + +D+ + ES+GFAFV F K A+ A+D +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 168 KDFKGKTIRCSMS 180
G+ +R M+
Sbjct: 135 AVLDGRELRVQMA 147
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 280 VKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAI 337
+ +L V NL T+ L+ +F+++G V V P + K R F F+ + ++ A A+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 338 KDTEKYEIDGQVLEVALAR 356
+ +DG+ L V +AR
Sbjct: 130 DAMDGAVLDGRELRVQMAR 148
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 67 EGLNGQDLMGQPI 79
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 81/174 (46%), Gaps = 14/174 (8%)
Query: 175 IRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
+ S S T LFIGN+ + + E + I ++ D + D + + NR F +V +
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA--VVDVRTGT-NRKFGYVDF 61
Query: 235 YNNACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTT 294
A+ + + K+ GN + +PK AA + L KNL N T
Sbjct: 62 ---ESAEDLEKALELTGLKVFGNE--IKLEKPKGRDSKKVRAA---RTLLAKNLSFNITE 113
Query: 295 KQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQ 348
+LKE+F+ E+ ++V+ GKS + +I + + A K +++ + EIDG+
Sbjct: 114 DELKEVFEDALEI-RLVSQDGKS--KGIAYIEFKSEADAEKNLEEKQGAEIDGR 164
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEV-TKVVTPPGKSGKRDFGFIHYAERSSALKAIKD 339
K L+VK L E+TT + LKE F G V ++VT + FGF+ + A A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 340 TEKYEIDGQVLEVALARPQ 358
E EIDG + + A+P+
Sbjct: 74 MEDGEIDGNKVTLDWAKPK 92
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+ GL +D +EE L+ E +V D+++G SKGF FV F S+E AK A + +
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 166 CSKDFKGKTI 175
+ G +
Sbjct: 75 EDGEIDGNKV 84
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 180 SETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNAC 239
S+ + LF+ + + TE+ ++ + G ++ D + S ++GF FV + +
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFD----GSVRARIVTDRETGS-SKGFGFVDFNSEED 66
Query: 240 ADYSRQKMTSANFKLDGNTPTVSWAEPK 267
A +++ M ++DGN T+ WA+PK
Sbjct: 67 AKAAKEAMEDG--EIDGNKVTLDWAKPK 92
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 69 EGLNGQDLMGQPI 81
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 38/69 (55%)
Query: 110 GLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKD 169
GL +E DLR++ G + +V +V D+ S S+GFAFV F + + AK A + +
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 170 FKGKTIRCS 178
G+ IR S
Sbjct: 82 LDGRRIRVS 90
Score = 35.0 bits (79), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 196 TEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQKMTSAN-FKL 254
TE++ R+V GP D + ++ D Q+ R+RGFAFV + N D +++ AN +L
Sbjct: 28 TERDLREVFSKYGPIAD-VSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 82
Query: 255 DGNTPTVS 262
DG VS
Sbjct: 83 DGRRIRVS 90
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 282 ALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRD--FGFIHYAERSSALKAIKD 339
L V L TT + L+E+F ++G + V + +R F F+++ A +A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 340 TEKYEIDGQVLEVA 353
E+DG+ + V+
Sbjct: 77 ANGMELDGRRIRVS 90
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 67 EGLNGQDLMGQPI 79
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFR 153
++F+GGL ++E LR GEV + ++KDK + +S+GF FV F+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 17/108 (15%)
Query: 277 ASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSAL 334
A ++ L+V L +TT + L+ F ++GEV V K+ R FGF+ + + + +
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD-PNCV 71
Query: 335 KAIKDTEKYEIDGQVLEVALARPQTNKRTEGVYSCAAGVHPSGLPHAG 382
+ + + +DG+ ++ P+ G+ PSG P +G
Sbjct: 72 GTVLASRPHTLDGRNIDPKPCTPR-------------GMQPSG-PSSG 105
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKD-SGESKGFAFVAFRSKEVAKRAI 162
S++ + +P A++ ++R+L GE+ V L K +G +GF FV F +K+ AK+A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 163 DELC 166
+ LC
Sbjct: 76 NALC 79
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTP---PGKSGKRDFGFIHYAERSSALKAI 337
+ V+N+P ++++ELF GE+ V P G R FGF+ + + A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 67 EGLNGQDLMGQPI 79
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 83 EGLNGQDLMGQPI 95
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+G L K SEED+ L +P G + E +++ D G SKG AFV F S A+ AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 165 L 165
L
Sbjct: 76 L 76
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 40/71 (56%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+G L + +E LR+ + ++ D +G S+G+ FV+F S++ A+ A+D +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 166 CSKDFKGKTIR 176
+D G+ +R
Sbjct: 64 QGQDLNGRPLR 74
>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 = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ G+ ++A+EED+ D GE+ + L D+ +G KG+ V + + + A+ A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 163 DELCSKDFKGKTI 175
+ L +D G+ I
Sbjct: 82 EGLNGQDLMGQPI 94
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 101 PHGSE--VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVA 158
P GS VF+G L + + + P G + + +VKD +G+SKG+ FV+F +K A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 159 KRAIDELCSKDFKGKTIR 176
+ AI ++ + G+ IR
Sbjct: 62 ENAIQQMGGQWLGGRQIR 79
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++FI GLP ++E+L ++C+ G V ++ LV ++ +G+ KG A+V + ++ A +A+ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 165 LCSKDFKGKTIRCSMSET 182
+ K I+ ++S +
Sbjct: 78 MDGMTIKENIIKVAISNS 95
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKDTE 341
L++ LP + T ++L+E+ + HG V + ++GK + ++ Y S A +A+ +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 342 KYEIDGQVLEVALA 355
I +++VA++
Sbjct: 80 GMTIKENIIKVAIS 93
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 52/86 (60%), Gaps = 6/86 (6%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
++VK L+V+NL T + L++ F G++ +V +D+ F+H+ +R +A+KA+
Sbjct: 13 AKVKVLFVRNLATTVTEEILEKSFSEFGKLERV------KKLKDYAFVHFEDRGAAVKAM 66
Query: 338 KDTEKYEIDGQVLEVALARPQTNKRT 363
+ EI+G+ +E+ LA+P KR+
Sbjct: 67 DEMNGKEIEGEEIEIVLAKPPDKKRS 92
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 282 ALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK------RDFGFIHYAERSSALK 335
L++KNL +TT + LK +F + G + K T K K FGF+ Y + A K
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAI-KSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 336 AIKDTEKYEIDGQVLEVALARPQT 359
A+K + + +DG LEV ++ T
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERAT 89
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+G + + ++LR L E G V E +VKD +AFV + AK AI +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 165 LCSKDFKGKTIRCSMS 180
L K+ KGK I +S
Sbjct: 63 LNGKEVKGKRINVELS 78
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 273 SAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSS 332
S+ ++ ++V N+ T+++L+ LF+R G V + +D+ F+H + +
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KDYAFVHMEKEAD 55
Query: 333 ALKAIKDTEKYEIDGQVLEVALA 355
A AI E+ G+ + V L+
Sbjct: 56 AKAAIAQLNGKEVKGKRINVELS 78
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 34/58 (58%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
++FIGGLP +++ +++L G + LVKD +G SKG+AF + V +AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 184 NRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
++LFIG +P + + ++++ GP + L+KD A ++G+AF Y + D
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKD-SATGLSKGYAFCEYVDINVTD 57
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 280 VKALYVKNLPENTTTKQLKELFQRHG--EVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
++ L V +P QL++LF+R+G E K+V R +GF+ + SSA +AI
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 338 KDTEKYEIDGQVLEVALA 355
+ I + L+VALA
Sbjct: 102 AGLNGFNILNKRLKVALA 119
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 42/75 (56%)
Query: 111 LPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDF 170
+P E LR L E G + V +V D+++ +S+G+ FV F+S A++AI L +
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109
Query: 171 KGKTIRCSMSETNNR 185
K ++ +++ + ++
Sbjct: 110 LNKRLKVALAASGHQ 124
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIG--EVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
++IG L ++EDL + +G ++ E+ +++ +G+SKGFA V S+ +K+ +D
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 164 ELCSKDFKGK 173
L ++ G+
Sbjct: 131 LLPKRELHGQ 140
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRS 154
++FIGGL + +EE LR+ E G++ + +++D S S+GF FV F S
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 181 ETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACA 240
E +LFIG + TE+ R E G D + +++DP A R+RGF FV + + A
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV-VMRDP-ASKRSRGFGFVTFSSMAEV 82
Query: 241 DYSRQKMTSANFKLDGNTPTVSWAEPK 267
D + M + +DG EPK
Sbjct: 83 DAA---MAARPHSIDGRV-----VEPK 101
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+GGL D EE +R+ GEV + L D + + +GF F+ F+ +E K+ +++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+F+GGL D EE +R+ GEV + L D + + +GF F+ F+ +E K+ ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 41/84 (48%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P G+ +FI LP++ ++DL + P G V + DK + SK F FV++ + A+
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82
Query: 161 AIDELCSKDFKGKTIRCSMSETNN 184
AI + K ++ + + N
Sbjct: 83 AIQSMNGFQIGMKRLKVQLKRSKN 106
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 56/262 (21%), Positives = 109/262 (41%), Gaps = 25/262 (9%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAF--VAFRSKEVAKRA 161
+ V + LPK ++ + + G + V D K F F + F + A A
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV----DVADSLKKNFRFARIEFARYDGALAA 97
Query: 162 IDELCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQ 221
I + + + I ++E L+ N P S+T++ R +++D+ +I L
Sbjct: 98 ITKTHKVVGQNEIIVSHLTECT--LWXTNFPPSYTQRNIRDLLQDINVVALSIRL----- 150
Query: 222 APS----RNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEPKSTPDHSAAAA 277
PS +R FA++ + A Y +K+ K++G T + P + +A
Sbjct: 151 -PSLRFNTSRRFAYIDVTSKEDARYCVEKLNG--LKIEGYTLVTKVSNPLEKSKRTDSAT 207
Query: 278 SQVKALYVKNLP-ENTTTKQLKELFQRHGEVTKVVTPPGK---SGKRDFGFIHYAERSSA 333
+ + + ++NL E L+E F+ G + K+ P G+ S F + + SA
Sbjct: 208 LEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSA 267
Query: 334 LKAIKDTEKYEIDGQVLEVALA 355
+A++ + + + V+LA
Sbjct: 268 ERALQXNRSL-LGNREISVSLA 288
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 279 QVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKA 336
++ + VKNLP++ ++ + F+ G + V S K++F F I +A AL A
Sbjct: 40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV--DVADSLKKNFRFARIEFARYDGALAA 97
Query: 337 IKDTEK 342
I T K
Sbjct: 98 ITKTHK 103
>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 = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIG-EVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V + LP+ A+E+D+R + G + EV L+++K SG+S+GFAFV F + A R ++
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+ L +SEEDL L G + E+ D + + KGFAFV F E A +A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 166 CSKDFKGKTIRC 177
+ F+G+ +
Sbjct: 71 DGQVFQGRMLHV 82
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK--RDFGFIHYAERSSALKAIKDT 340
L+V+NL ++ + L++LF +G ++++ P K + F F+ + A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA-- 68
Query: 341 EKYEIDGQVLE 351
E+DGQV +
Sbjct: 69 ---EVDGQVFQ 76
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P V+ GG+ +++ +R P G++ E+ + + KG++FV F + E A
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAH 76
Query: 161 AIDELCSKDFKGKTIRC 177
AI + +G ++C
Sbjct: 77 AIVSVNGTTIEGHVVKC 93
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKAIKDT 340
L V NL + ++ELF G + K +SG R G +H+ R+ ALKA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 96
Query: 341 EKYEIDGQVLEVALARPQTN 360
+ +DG+ +++ L Q +
Sbjct: 97 KGVPLDGRPMDIQLVASQID 116
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKAIKDT 340
L V NL + ++ELF G + K +SG R G +H+ R+ ALKA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 96
Query: 341 EKYEIDGQVLEVALARPQTN 360
+ +DG+ +++ L Q +
Sbjct: 97 KGVPLDGRPMDIQLVASQID 116
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 279 QVKALYVKNLPENTTTKQLKELFQRHGEVT--KVVTPPGKSGKRDFGFIHYAERSSALKA 336
QV LYVKNL + ++L++ F G +T KV+ G+S + FGF+ ++ A KA
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKA 71
Query: 337 IKDTEKYEIDGQVLEVALARPQTNKRT 363
+ + + + L VALA+ + +++
Sbjct: 72 VTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+++ L +E LR P G + ++ + G SKGF FV F S E A +A+ E+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 166 CSKDFKGKTIRCSMSE 181
+ K + ++++
Sbjct: 76 NGRIVATKPLYVALAQ 91
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
+YV NLP + TK ++++F ++G + + + G F F+ + + A A+ +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 343 YEIDGQVLEVALAR 356
Y+ DG L V R
Sbjct: 84 YDYDGYRLRVEFPR 97
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKG---FAFVAFRSKEVAKRA 161
+++G LP D +D+ D+ ++ G ++D D +G FAFV F A+ A
Sbjct: 24 RIYVGNLPPDIRTKDIEDV------FYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
Query: 162 IDELCSKDFKGKTIRCSMSET 182
+ D+ G +R +
Sbjct: 78 VYGRDGYDYDGYRLRVEFPRS 98
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 34/65 (52%)
Query: 101 PHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR 160
P G +FI LP++ ++ DL P G V + DK + SK F FV+F + + A+
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 161 AIDEL 165
AI +
Sbjct: 98 AIKAM 102
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
L++ +LP+ T L F G V KV S + FGF+ + SA AIK
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 341 EKYEIDGQVLEVALAR 356
+++ + L+V L +
Sbjct: 103 NGFQVGTKRLKVQLKK 118
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 41/167 (24%), Positives = 75/167 (44%), Gaps = 14/167 (8%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSRQ 245
LF+GN+ + + E + I DV D + ++ +R G Y + A+ +
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKND-LAVVDVRIGMTRKFG-----YVDFESAEDLEK 63
Query: 246 KMTSANFKLDGNTPTVSWAEPKSTPDHSAAAASQVKALYVKNLPENTTTKQLKELFQRHG 305
+ K+ GN + +PK A + L KNLP T +LKE+F+
Sbjct: 64 ALELTGLKVFGNE--IKLEKPKGKDSKKERDA---RTLLAKNLPYKVTQDELKEVFEDAA 118
Query: 306 EVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQVLEV 352
E+ ++V+ GKS + +I + + A K ++ + EIDG+ + +
Sbjct: 119 EI-RLVSKDGKS--KGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 5/67 (7%)
Query: 111 LPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDF 170
LP ++++L+++ E E+ V KD G+SKG A++ F+++ A++ +E +
Sbjct: 101 LPYKVTQDELKEVFEDAAEIRLVS----KD-GKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Query: 171 KGKTIRC 177
G++I
Sbjct: 156 DGRSISL 162
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ + + LP+D ++ +L L IG + +++D +G S G+AFV F S+ ++RAI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 164 ELCSKDFKGKTIRCSMS 180
L + K ++ S +
Sbjct: 64 VLNGITVRNKRLKVSYA 80
Score = 29.6 bits (65), Expect = 3.7, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV-TKVVTPPGKSG-KRDFGFIHYAERSSALKAIKDT 340
L V LP++ T ++L LF+ G + T + K+G + F+ + + +AIK
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 341 EKYEIDGQVLEVALARP 357
+ + L+V+ ARP
Sbjct: 66 NGITVRNKRLKVSYARP 82
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKAIKDT 340
L V NL + ++ELF G + K +SG R G +H+ R+ ALKA+K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 149
Query: 341 EKYEIDGQVLEVALARPQTN 360
+ +DG+ +++ L Q +
Sbjct: 150 KGVPLDGRPMDIQLVASQID 169
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEV-GLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
S +FIG L + E+ L D G + + +++D D+G SKG+AF+ F S + + AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 163 DEL 165
+ +
Sbjct: 66 EAM 68
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 180 SETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNAC 239
S ++ +FIGN+ EK G + T ++++DP ++G+AF+ N A
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDT-GNSKGYAFI---NFAS 57
Query: 240 ADYSRQKMTSANFKLDGNTP-TVSWAEPKST 269
D S + + N + N P TVS+A K +
Sbjct: 58 FDASDAAIEAMNGQYLCNRPITVSYAFKKDS 88
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +F+ P D E +L ++ P G + EV ++ GFAFV F E A +AI+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 83
Query: 164 ELCSKDFKGKTIRCSMS 180
E+ K F + + S
Sbjct: 84 EVHGKSFANQPLEVVYS 100
Score = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
L+V+ P + +L E+F G + +V G F F+ + E SA KAI++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESAAKAIEEVHG 87
Query: 343 YEIDGQVLEVALAR 356
Q LEV ++
Sbjct: 88 KSFANQPLEVVYSK 101
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
+YV NLP + LK + G V +T G R F+HY + ++A +A+ +
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLT---WQGPRRRAFLHYPDSAAAQQAVSCLQG 78
Query: 343 YEIDGQVLEVALARPQTNK 361
+ L VALAR Q +K
Sbjct: 79 LRLGTDTLRVALARQQRDK 97
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 56/121 (46%), Gaps = 25/121 (20%)
Query: 101 PHGS-EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
P GS +FI L K + L D G + +V D++ SKG+ FV F ++E A+
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 59
Query: 160 RAIDELCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTE---------KEFRKV-IEDVGP 209
RAI+++ M + ++F+G KS E KEF V I++ GP
Sbjct: 60 RAIEKM-----------NGMLLNDRKVFVGRF-KSRKEREAELGARAKEFTNVYIKNFGP 107
Query: 210 G 210
G
Sbjct: 108 G 108
Score = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
+++KNL ++ K L + F G + ++G + +GF+H+ + +A +AI+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE---- 63
Query: 343 YEIDGQVL---EVALARPQTNKRTE 364
+++G +L +V + R ++ K E
Sbjct: 64 -KMNGMLLNDRKVFVGRFKSRKERE 87
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIG--EVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
++IG L ++EDL + +G ++ E+ +++ +G+SKGFA V S+ +K+ +D
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 164 ELCSKDFKGK 173
L ++ G+
Sbjct: 64 LLPKRELHGQ 73
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 4/79 (5%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKD 339
K L + NL + T + L+E+F++ T + P ++GK + + FI +A A +A+
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 340 TEKYEIDGQVLEVALARPQ 358
K EI+G+ + + L P+
Sbjct: 73 CNKREIEGRAIRLELQGPR 91
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGL---VKDKDSGESKGFAFVAFRSKEVAKRAI 162
+ + L A+EE L+ EVFE V +G+SKG+AF+ F S E AK A+
Sbjct: 18 LVLSNLSYSATEETLQ-------EVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 163 DELCSKDFKGKTIRCSM 179
+ ++ +G+ IR +
Sbjct: 71 NSCNKREIEGRAIRLEL 87
>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 = 0.003, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAF 152
G ++FIGGL ++E LR+ GEV E +++D + S+GF FV F
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 35.8 bits (81), Expect = 0.051, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 48/91 (52%), Gaps = 4/91 (4%)
Query: 270 PDHSAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTK--VVTPPGKSGKRDFGFIHY 327
P S +S K +++ L TT + L+E F + GEV + V+ P R FGF+ +
Sbjct: 16 PRGSHMGSSGCK-MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Query: 328 AERSSALKAIKDTEKYEIDGQVLEVALARPQ 358
+++ K + + ++E+D + ++ +A P+
Sbjct: 75 MDQAGVDKVLAQS-RHELDSKTIDPKVAFPR 104
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 179 MSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNA 238
M + ++FIG + T++ R+ G V +++DP R+RGF FV + + A
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGE-VKECLVMRDPLT-KRSRGFGFVTFMDQA 78
Query: 239 CADYSRQKMTSANFKLDGNT--PTVSW---AEPK 267
D + + + +LD T P V++ A+PK
Sbjct: 79 GVD---KVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR--AID 163
+++G + A+ E+L G V V ++ DK SG KGFA++ F KE + A+D
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 164 ELCSKDFKGKTIRCSMSETN 183
E F+G+ I+ TN
Sbjct: 69 E---SLFRGRQIKVIPKRTN 85
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAF--RSKEVAKRAID 163
V++G + ++ +DL G + + ++ DK SG KG+A++ F R+ A A+D
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 164 ELCSKDFKGKTIRCSMSETN 183
E F+G+TI+ TN
Sbjct: 99 ETV---FRGRTIKVLPKRTN 115
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKR--AID 163
+++G + A+ E+L G V V ++ DK SG KGFA++ F KE + A+D
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 164 ELCSKDFKGKTIRCSMSETN 183
E F+G+ I+ TN
Sbjct: 68 E---SLFRGRQIKVIPKRTN 84
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +F+ P D E +L ++ P G + EV ++ GFAFV F E A +AI+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 56
Query: 164 ELCSKDFKGKTIRCSMS 180
E+ K F + + S
Sbjct: 57 EVHGKSFANQPLEVVYS 73
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
L+V+ P + +L E+F G + +V G F F+ + E SA KAI++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESAAKAIEEVHG 60
Query: 343 YEIDGQVLEVALAR 356
Q LEV ++
Sbjct: 61 KSFANQPLEVVYSK 74
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFE--------VGLVKDKDSGESKGFAFVAFRSKEV 157
+F+ GL ++ + E + D + IG + + L D+++G+ KG A V+F
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 158 AKRAIDELCSKDFKGKTIRCSMS 180
AK AID K+F G I+ S +
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A+ AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 164 EL 165
L
Sbjct: 74 AL 75
Score = 35.0 bits (79), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVT-KVVTPPGKSGK-RDFGFIHYAERSSALKAIKDT 340
LYV NLP T QL +F ++G + K + +G+ R F+ Y +R A +AI
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 341 EKYEIDG--QVLEVALA 355
+G Q L V LA
Sbjct: 76 NNVIPEGGSQPLSVRLA 92
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFE--------VGLVKDKDSGESKGFAFVAFRSKEV 157
+F+ GL ++ + E + D + IG + + L D+++G+ KG A V+F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 158 AKRAIDELCSKDFKGKTIRCSMS 180
AK AID K+F G I+ S +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSK----EVAKR 160
++FIGGL ++E LR+ GEV E +++D + S+GF FV F + +V +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 161 AIDELCSKDFKGK 173
+ EL SK K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTK--VVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
+++ L TT + L+E F + GEV + V+ P R FGF+ + +++ K + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 341 EKYEIDGQVLEVALA 355
++E+D + ++ +A
Sbjct: 63 -RHELDSKTIDPKVA 76
Score = 29.3 bits (64), Expect = 4.9, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 185 RLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACADYSR 244
++FIG + T++ R+ G V +++DP R+RGF FV + + A D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGE-VKECLVMRDPLT-KRSRGFGFVTFMDQAGVD--- 56
Query: 245 QKMTSANFKLDGNT--PTVSW 263
+ + + +LD T P V++
Sbjct: 57 KVLAQSRHELDSKTIDPKVAF 77
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
K L+V N+P L+++F + G++ V + G + FGF+ + + A +A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 341 EKYEIDGQVLEV--ALARPQTN 360
++G+ +EV A AR TN
Sbjct: 76 HGTVVEGRKIEVNNATARVMTN 97
Score = 37.0 bits (84), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 182 TNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLYYNNACAD 241
T RL + N+P + + + R++ G +D +E+I + + ++GF FV + N+A AD
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILD-VEIIFNERG---SKGFGFVTFENSADAD 69
Query: 242 YSRQKM 247
+R+K+
Sbjct: 70 RAREKL 75
Score = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 108 IGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCS 167
+ +P + DLR + G++ +V ++ ++ SKGF FV F + A RA ++L
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 77
Query: 168 KDFKGKTIRCSMSETNN 184
+G+ I E NN
Sbjct: 78 TVVEGRKI-----EVNN 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEV--TKVVTPPGKSGKRDFGFIHYAERSSALKAIK 338
LYV LP+ + K++++LF ++G + ++++ R GFI + +R A +AIK
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ +++ GLPK S++++ L G + ++ D+ +G S+G F+ F + A+ AI
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 164 EL 165
L
Sbjct: 62 GL 63
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+ ++I LP E++L ++ +P G+V +++D SG S+G F S E + I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 164 ELCSKDFKGKTIR 176
F GK I+
Sbjct: 85 H-----FNGKFIK 92
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 186 LFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFA 230
L+I N+P S E+E +++ G + T +++D SR GFA
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVIST-RILRDSSGTSRGVGFA 71
>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 = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKR--DFGFIHYAERSSALKAIKDT 340
LYV NL TT +Q+ ELF + G++ K++ K K F F+ Y R+ A A++
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 341 EKYEIDGQVL 350
+D +++
Sbjct: 102 NGTRLDDRII 111
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 47/90 (52%), Gaps = 8/90 (8%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
S V +++KNL ++ K L + F G + ++G + +GF+H+ + +A +AI
Sbjct: 9 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 68
Query: 338 KDTEKYEIDGQVL---EVALARPQTNKRTE 364
+ +++G +L +V + R ++ K E
Sbjct: 69 E-----KMNGMLLNDRKVFVGRFKSRKERE 93
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+FI L K + L D G + +V D++ SKG+ FV F ++E A+RAI+++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFE--------VGLVKDKDSGESKGFAFVAFRSK 155
S +++ GL + +DL D + G V + + DK++G+ KG A V++
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 156 EVAKRAIDELCSKDFKGKTIRCSMS 180
AK A++ KDF+G ++ S++
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G VFI L D+ EE L ++ + G++ V +V D+ SKG AF F ++E A++ +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.4 bits (85), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
VF+GG+ E ++R G V EV ++ D+ +G SKG+ FV+F + ++ ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 166 CSKDFKGKTIRC 177
+F GK ++
Sbjct: 72 I--NFHGKKLKL 81
>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 = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
VF+GG+ E ++R G V EV ++ D+ +G SKG+ FV+F + ++ ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 166 CSKDFKGKTIRC 177
+F GK ++
Sbjct: 71 I--NFHGKKLKL 80
>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 = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKR-DFGFIHYAERSSALKAIKDTE 341
LYV NL TT +Q+ ELF + G++ K++ K F F+ Y R+ A A++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 342 KYEIDGQVL 350
+D +++
Sbjct: 81 GTRLDDRII 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 = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
VF+GG+ E ++R G V EV ++ D+ +G SKG+ FV+F + ++ ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 166 CSKDFKGKTIR 176
+F GK ++
Sbjct: 70 -QINFHGKKLK 79
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 3/68 (4%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDT 340
+ L KNL N T +LKE+F+ E+ ++V+ GKS + +I + + A K +++
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEI-RLVSQDGKS--KGIAYIEFKSEADAEKNLEEK 73
Query: 341 EKYEIDGQ 348
+ EIDG+
Sbjct: 74 QGAEIDGR 81
Score = 28.5 bits (62), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 111 LPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDF 170
L + +E++L+++ E + E+ LV G+SKG A++ F+S+ A++ ++E +
Sbjct: 24 LSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEKQGAEI 78
Query: 171 KGKTI 175
G+++
Sbjct: 79 DGRSV 83
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 278 SQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAI 337
SQ K L+V N+P L+++F + G++ V + G + FGF+ + + A +A
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAR 86
Query: 338 KDTEKYEIDGQVLEV 352
+ ++G+ +EV
Sbjct: 87 EKLHGTVVEGRKIEV 101
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 171 KGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFA 230
+G + RL + N+P + + + R++ G +D +E+I + + ++GF
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD-VEIIFNERG---SKGFG 72
Query: 231 FVLYYNNACADYSRQKM 247
FV + N+A AD +R+K+
Sbjct: 73 FVTFENSADADRAREKL 89
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 108 IGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCS 167
+ +P + DLR + G++ +V ++ ++ SKGF FV F + A RA ++L
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 91
Query: 168 KDFKGKTIRCSMSETNN 184
+G+ I E NN
Sbjct: 92 TVVEGRKI-----EVNN 103
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
G +F+ + ++A E+++++ GE+ + L D+ +G SKG+A V + + + A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 163 DELCSKDFKGKTIR 176
+ L + G+TI+
Sbjct: 86 EALNGAEIMGQTIQ 99
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.034, Method: Composition-based stats.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 13/93 (13%)
Query: 98 ALPPHGSE----VFIGGLP-KDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAF 152
L P GS +FIG LP K+ S+EDL + P G + ++ + F F+ F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQF 64
Query: 153 RSKEVAKRAIDELCSKDFKGKTIRCSMSETNNR 185
+ + + AI+ + GK + +S +N R
Sbjct: 65 DNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 36.2 bits (82), Expect = 0.042, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 10/88 (11%)
Query: 99 LPPHGSEVFIGGLP-KDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEV 157
+PP S +FIG LP K+ S+EDL + P G + ++ + F F+ F + +
Sbjct: 7 IPPK-SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQS 57
Query: 158 AKRAIDELCSKDFKGKTIRCSMSETNNR 185
+ AI+ + GK + +S +N R
Sbjct: 58 VRDAIECESQEMNFGKKLILEVSSSNAR 85
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 36.2 bits (82), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 275 AAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKV-VTPPGKSGK-RDFGFIHYAERSS 332
A K L+V + +TT +L+ F+ +G + ++ + +SGK R + FI Y
Sbjct: 97 AQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERD 156
Query: 333 ALKAIKDTEKYEIDGQVLEVALARPQTNK 361
A K + +IDG+ + V + R +T K
Sbjct: 157 MHSAYKHADGKKIDGRRVLVDVERGRTVK 185
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+ + D +E LR E G + + +V K SG+ +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 166 CSKDFKGKTI 175
K G+ +
Sbjct: 165 DGKKIDGRRV 174
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 35.8 bits (81), Expect = 0.056, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
VF+G L EE L +L G + +V + KD++ G+ K F FV F+ E AI L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 166 CSKDFKGKTIRCS 178
G+ I S
Sbjct: 78 NGIRLYGRPINVS 90
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAI 337
+ ++V NL + L ELF + G +TKV + GK + FGF+ + S AI
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI 74
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.8 bits (81), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 11/80 (13%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S VF+G D +E++LR+ G+V +V + K + FAFV F ++A+
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQ---- 56
Query: 164 ELCSKDF--KGKTIRCSMSE 181
LC +D KG ++ S +E
Sbjct: 57 SLCGEDLIIKGISVHISNAE 76
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 35.8 bits (81), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 12/87 (13%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
GS+VF+G +D + E+L+ GEV +V + K + FAFV F +VA+
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQ--- 62
Query: 163 DELCSKDF--KGKTIRCSMSE-TNNRL 186
LC +D KG ++ S +E +N+L
Sbjct: 63 -SLCGEDLIIKGISVHISNAEPKHNKL 88
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.4 bits (80), Expect = 0.062, Method: Composition-based stats.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 13/93 (13%)
Query: 98 ALPPHGSE----VFIGGLP-KDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAF 152
L P GS +FIG LP K+ S+EDL + P G + ++ + F F+ F
Sbjct: 13 GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQF 64
Query: 153 RSKEVAKRAIDELCSKDFKGKTIRCSMSETNNR 185
+ + + AI+ + GK + +S +N R
Sbjct: 65 DNPQSVRDAIECESQEMNFGKKLILEVSSSNAR 97
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKAIKDT 340
L V NL + ++ELF G + K +SG R G +H+ ++ ALKA+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAMKQY 89
Query: 341 EKYEIDGQVLEVALA 355
+DG+ + + L
Sbjct: 90 NGVPLDGRPMNIQLV 104
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 275 AAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKV-VTPPGKSGK-RDFGFIHYAERSS 332
A K L+V + +TT +L+ F+ +G + ++ + +SGK R + FI Y
Sbjct: 97 AQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERD 156
Query: 333 ALKAIKDTEKYEIDGQVLEVALARPQTNK 361
A K + +IDG+ + V + R +T K
Sbjct: 157 MHSAYKHADGKKIDGRRVLVDVERGRTVK 185
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
+F+ + D +E LR E G + + +V K SG+ +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 166 CSKDFKGKTI 175
K G+ +
Sbjct: 165 DGKKIDGRRV 174
>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 = 35.0 bits (79), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 30/115 (26%), Positives = 55/115 (47%), Gaps = 10/115 (8%)
Query: 66 GSHINTEDAVEDEDKRTASISEDEKEKHDQLLALPPHGSE---VFIGGLPKDASEEDLRD 122
GS NT +A+ S E D+L P E +F+ + ++A E+++++
Sbjct: 39 GSDSNTREAIH-------SYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQE 91
Query: 123 LCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDELCSKDFKGKTIRC 177
GE+ + L D+ +G SKG+A V + + + A A + L + G+TI+
Sbjct: 92 KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 104 SEVFIGGLP-KDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
S +FIG LP K+ S+EDL + P G + ++ + F F+ F + + + AI
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 54
Query: 163 DELCSKDFKGKTIRCSMSETNNR 185
+ + GK + +S +N R
Sbjct: 55 ECESQEMNFGKKLILEVSSSNAR 77
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 35.0 bits (79), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V+I G P DA+ +D+++ E G+V + + + KG FV F S E AK+ ++
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 168
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
PP + +IG +P A+E DL L + G + D KG F+ + + E A
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQ------NFGFILDFKHYPEKGCCFIKYDTHEQAA 77
Query: 160 RAIDELCSKDFKGKTIR 176
I L + F+G+ +R
Sbjct: 78 VCIVALANFPFQGRNLR 94
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 283 LYVKNLPENTTTKQ-LKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTE 341
+++ NL K ++ +F ++G++ G S + F F+ Y +A A+ +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIV------GCSVHKGFAFVQYVNERNARAAVAGED 71
Query: 342 KYEIDGQVLEVAL-ARPQTNK 361
I GQVL++ L A P+ N+
Sbjct: 72 GRMIAGQVLDINLAAEPKVNR 92
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 10/91 (10%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
+++ +G + + ++LR E G V E +VKD +AFV E A AI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 164 ELCSKDFKGKTIRCSMSETNNRLFIGNVPKS 194
L + +F+GK + +S +RL + P S
Sbjct: 63 GLDNTEFQGKRMHVQLS--TSRLRTASGPSS 91
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEK 342
L+V N+ T ++L+ F+ +G V + +D+ F+H A++AI+ +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIV------KDYAFVHMERAEDAVEAIRGLDN 66
Query: 343 YEIDGQVLEVALA 355
E G+ + V L+
Sbjct: 67 TEFQGKRMHVQLS 79
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
++F+ LP D + + L+D G V + ++G+SKG V F S EVA+RA
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACRM 67
Query: 165 LCSKDFKGKTI 175
+ G+ I
Sbjct: 68 MNGMKLSGREI 78
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 33.9 bits (76), Expect = 0.23, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
S +F+ LP D + + L+D G V + ++G+SKG V F S EVA+RA
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR 63
Query: 164 ELCSKDFKGKTI 175
+ G+ I
Sbjct: 64 MMNGMKLSGREI 75
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V+I G P DA+ +D+++ E G+V + + + KG FV F S E AK+ ++
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 70
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V+I G P DA+ +D+++ E G+V + + KG FV F S E AK+ ++
Sbjct: 114 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 170
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V+I G P DA+ +D+++ E G+V + + KG FV F S E AK+ ++
Sbjct: 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 169
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 29/63 (46%)
Query: 90 KEKHDQLLALPPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAF 149
+E D L VF L DL D +G+V +V ++ D++S SKG A+
Sbjct: 12 REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71
Query: 150 VAF 152
V F
Sbjct: 72 VEF 74
>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 = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKAIKDT 340
L V NL + ++ELF G + K +SG R G +H+ ++ ALKA K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAXKQY 90
Query: 341 EKYEIDGQVLEVALA 355
+DG+ + L
Sbjct: 91 NGVPLDGRPXNIQLV 105
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 100 PPHGSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAK 159
PP+ ++G LP + + D+ + + + + V LV+DKD+ + KGF +V F + K
Sbjct: 14 PPY--TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70
Query: 160 RAI 162
A+
Sbjct: 71 EAL 73
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.3 bits (72), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIG--EVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAID 163
V++G +++ L + IG +V E+ +++ +G+SKG+A V S+ + ++
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 164 ELCSKDFKGKTI 175
L K G+ +
Sbjct: 118 LLPGKVLNGEKV 129
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 31/75 (41%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDE 164
EV L + E L+D+C GEV EV ++ + + G A V F S AK +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 165 LCSKDFKGKTIRCSM 179
L G I +
Sbjct: 68 LHLTSVMGNIIHAQL 82
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 17/112 (15%)
Query: 105 EVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKD-------KDSGESKGFAFVAFRSKEV 157
+VF+GGLP D E+++ G LV D K KG+AF+ F+ +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQEESS 64
Query: 158 AKRAIDELCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGP 209
+ ID +D GK C S T + P + ++ +F + D GP
Sbjct: 65 VQALIDACLEED--GKLYLCVSSPTIKDKPVQIRPWNLSDSDF---VMDSGP 111
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 29/52 (55%)
Query: 297 LKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQ 348
+ ++F + G++T P + + F+ YA + A+ A+K+ + Y++D Q
Sbjct: 24 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 29/52 (55%)
Query: 297 LKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSALKAIKDTEKYEIDGQ 348
+ ++F + G++T P + + F+ YA + A+ A+K+ + Y++D Q
Sbjct: 38 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 274 AAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSSA 333
++ +S + LY+ NL T L++LF K+ K + F+ Y +++ A
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDR----KLPLAGQVLLKSGYAFVDYPDQNWA 57
Query: 334 LKAIKD-TEKYEIDGQVLEV 352
++AI+ + K E+ G+++EV
Sbjct: 58 IRAIETLSGKVELHGKIMEV 77
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPG 315
+ KNLP T +++E F R G + +V+ P G
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG 45
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 70/169 (41%), Gaps = 20/169 (11%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAF--VAFRSKEVAKRA 161
+ V + LPK ++ + + G + V D K F F + F + A A
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV----DVADSLKKNFRFARIEFARYDGALAA 60
Query: 162 IDELCSKDFKGKTIRCSMSETNNRLFIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQ 221
I + + + I ++E L++ N P S+T++ R +++D+ +I L
Sbjct: 61 ITKTHKVVGQNEIIVSHLTECT--LWMTNFPPSYTQRNIRDLLQDINVVALSIRL----- 113
Query: 222 APS----RNRGFAFVLYYNNACADYSRQKMTSANFKLDGNTPTVSWAEP 266
PS +R FA++ + A Y +K+ K++G T + P
Sbjct: 114 -PSLRFNTSRRFAYIDVTSKEDARYCVEKLNG--LKIEGYTLVTKVSNP 159
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 279 QVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGF--IHYAERSSALKA 336
++ + VKNLP++ ++ + F+ G + V S K++F F I +A AL A
Sbjct: 3 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV--DVADSLKKNFRFARIEFARYDGALAA 60
Query: 337 IKDTEK 342
I T K
Sbjct: 61 ITKTHK 66
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 104 SEVFIGGLPKDASEEDLRDLCEPIGEVFEVGL-VKDKDSGESKGFAFVAFRSKEVAKRAI 162
++V IG L ++ +++ + ++ G++ + + V+ SKG+A+V F + + A++A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 163 DELCSKDFKGKTIRCS 178
+ G+ I +
Sbjct: 65 KHMDGGQIDGQEITAT 80
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSG---KRDFGFIHYAERSSALKAIKD 339
+++ L N T + E+F +G++ + P + + + ++ + A KA+K
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 340 TEKYEIDGQ 348
+ +IDGQ
Sbjct: 67 MDGGQIDGQ 75
>pdb|2DKJ|A Chain A, Crystal Structure Of T.Th.Hb8 Serine
Hydroxymethyltransferase
pdb|2DKJ|B Chain B, Crystal Structure Of T.Th.Hb8 Serine
Hydroxymethyltransferase
Length = 407
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 156 EVAKRAIDELCSKDFKGKTIRCSMSETNNRLFIGNV-PKSWTEKEFRKVIEDVGPGVDTI 214
E AKR +EL + + R T+N LF+ ++ PK T KE + ++ VG V+
Sbjct: 288 ENAKRLAEELARRGY-----RIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKN 342
Query: 215 ELIKDPQAPSRNRGF 229
+ DP+ P G
Sbjct: 343 AIPFDPKPPRVTSGI 357
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 187 FIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
F+GN+P TE+ ++ G + + L ++P P R +GF + +
Sbjct: 19 FLGNLPYDVTEESIKEFFR--GLNISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 187 FIGNVPKSWTEKEFRKVIEDVGPGVDTIELIKDPQAPSRNRGFAFVLY 234
F+GN+P TE+ ++ G + + L ++P P R +GF + +
Sbjct: 23 FLGNLPYDVTEESIKEFFR--GLNISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 273 SAAAASQVKALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGKRDFGFIHYAERSS 332
S+ + LYV L + T L+ F + GE+ + ++ FI +A R +
Sbjct: 5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITV----VQRQQCAFIQFATRQA 60
Query: 333 A-LKAIKDTEKYEIDGQVLEVALAR 356
A + A K K ++G+ L V R
Sbjct: 61 AEVAAEKSFNKLIVNGRRLNVKWGR 85
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.0 bits (66), Expect = 3.0, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 8/88 (9%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGK----SGK-RDFGFIHYAERSSALK 335
K LY+KNL T + L LF R E PP + +G+ R FI + + A +
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKG---PPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 336 AIKDTEKYEIDGQVLEVALARPQTNKRT 363
A+ Y++ G++L + + + + +
Sbjct: 83 ALHLVNGYKLYGKILVIEFGKNKKQRSS 110
>pdb|2VMN|A Chain A, Crystal Structure Of N341absshmt Internal Aldimine
pdb|2VMO|A Chain A, Crystal Structure Of N341absshmt Gly External Aldimine
pdb|2VMP|A Chain A, Crystal Structure Of N341absshmt L-Ser External Aldimine
pdb|2VMQ|A Chain A, Structure Of N341absshmt Crystallized In The Presence Of
L- Allo-Thr
Length = 405
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 155 KEVAKRAID--ELCSKDFKGKTIRCSMSETNNRLFIGNV-PKSWTEKEFRKVIEDVGPGV 211
K AKR +D + + + + T+N L + ++ P+ T K KV+++VG V
Sbjct: 279 KAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITV 338
Query: 212 DTIELIKDPQAPSRNRGF 229
+ + DP++P G
Sbjct: 339 NKATIPYDPESPFVTSGI 356
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 103 GSEVFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAI 162
GS VF+ L + L+++ G V +++DKD G+S+G V F A +AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI 73
Query: 163 DELCSKDFKGKTIRCSMSE 181
+ + + M E
Sbjct: 74 SMFNGQLLFDRPMHVKMDE 92
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 283 LYVKNLPENTTTKQLKELFQRHGEVTKVVTPPGKSGK-RDFGFIHYAERSSALKAIKDTE 341
++V NL K+LKE+F G V + K GK R G + + + A++AI
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS--- 74
Query: 342 KYEIDGQVL 350
+GQ+L
Sbjct: 75 --MFNGQLL 81
>pdb|2VMV|A Chain A, Crystal Structure Of F351gbsshmt Internal Aldimine
pdb|2VMX|A Chain A, Crystal Structure Of F351gbsshmt In Complex With
L-Allo-Thr
pdb|2VMY|A Chain A, Crystal Structure Of F351gbsshmt In Complex With Gly And
Fthf
pdb|2VMY|B Chain B, Crystal Structure Of F351gbsshmt In Complex With Gly And
Fthf
pdb|2VMW|A Chain A, Crystal Structure Of F351gbsshmt In Complex With L-Ser
pdb|2VMZ|A Chain A, Crystal Structure Of F351gbsshmt In Complex With Gly
Length = 405
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 155 KEVAKRAID--ELCSKDFKGKTIRCSMSETNNRLFIGNV-PKSWTEKEFRKVIEDVGPGV 211
K AKR +D + + + + T+N L + ++ P+ T K KV+++VG V
Sbjct: 279 KAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITV 338
Query: 212 DTIELIKDPQAPSRNRGF 229
+ + DP++P G
Sbjct: 339 NKNTIPYDPESPGVTSGI 356
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 28.9 bits (63), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 106 VFIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSKEVAKRAIDEL 165
V + GLP S +DL+D G+V + KD G V + KE + A+ +L
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKL 70
Query: 166 CSKDFK 171
F+
Sbjct: 71 DDTKFR 76
>pdb|3D37|A Chain A, The Crystal Structure Of The Tail Protein From Neisseria
Meningitidis Mc58
pdb|3D37|B Chain B, The Crystal Structure Of The Tail Protein From Neisseria
Meningitidis Mc58
Length = 381
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 16/98 (16%)
Query: 89 EKEKHDQLLALPPHGSEVFIGGLPKDASEEDLR-DLCEPI--GEVFEVGLVKDKDSGESK 145
E+ D +P + IG L +A+ DL + CE + G++ G++ + G+SK
Sbjct: 23 ERYDIDSDFLIPADSFDFVIGRLGPEAAIPDLSGESCEVVIDGQIVMTGIIGSQRHGKSK 82
Query: 146 GFAFVAFRSKEVAKRAIDELCSKDFKGKTIRCSMSETN 183
G S+E++ L +D G + CS + N
Sbjct: 83 G-------SRELS------LSGRDLAGFLVDCSAPQLN 107
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.9 bits (63), Expect = 6.9, Method: Composition-based stats.
Identities = 8/30 (26%), Positives = 21/30 (70%)
Query: 281 KALYVKNLPENTTTKQLKELFQRHGEVTKV 310
+ LY++NLP T +++ ++F ++G + ++
Sbjct: 13 RILYIRNLPYKITAEEMYDIFGKYGPIRQI 42
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 97 LALPPHGSEV-FIGGLPKDASEEDLRDLCEPIGEVFEVGLVKDKDSGESKGFAFVAFRSK 155
+ LPP + + +I LP + E++ D+ G + ++ + ++ E++G A+V +
Sbjct: 1 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDI 57
Query: 156 EVAKRAIDEL 165
AK A+D L
Sbjct: 58 FDAKNAVDHL 67
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
0.312 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,830,253
Number of Sequences: 62578
Number of extensions: 535114
Number of successful extensions: 1506
Number of sequences better than 100.0: 200
Number of HSP's better than 100.0 without gapping: 150
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 1071
Number of HSP's gapped (non-prelim): 406
length of query: 479
length of database: 14,973,337
effective HSP length: 103
effective length of query: 376
effective length of database: 8,527,803
effective search space: 3206453928
effective search space used: 3206453928
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)