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= 018159
(360 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 51/169 (30%), Positives = 91/169 (53%), Gaps = 15/169 (8%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESG--ESKGFAFVSFRSKEFAKKAI 165
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV+F +++ A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 166 DELHS-KELKGK----TIRCSLSETKN-----RLFIGNVPKNWTEDEFRKVIEDVGPGVE 215
+ LH+ K L G ++ + SE N +LFIG + K TE++ R + G +E
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ-IE 123
Query: 216 TIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTI 264
+++ P S RG +FV + A A + + M A ++P +
Sbjct: 124 ECRILRGPDGLS--RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Score = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 39/155 (25%), Positives = 74/155 (47%), Gaps = 7/155 (4%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD-PQNPSRNRGFSFVLYYNNACADYS 246
++F+G VP+ W+E + R++ E G V I +++D QNP +++G FV +Y A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 247 RQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRH 306
+ + N L G I S ++ A + + L++ I + I+ +F
Sbjct: 64 QNALHNMKV-LPGMHHPIQMKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 307 GEVTKVVMPPGKSG-KRDFGFIHYAERSSALKAVK 340
G++ + + G G R F+ + R+ A A+K
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 51/169 (30%), Positives = 91/169 (53%), Gaps = 15/169 (8%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESG--ESKGFAFVSFRSKEFAKKAI 165
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV+F +++ A +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 166 DELHS-KELKGK----TIRCSLSETKN-----RLFIGNVPKNWTEDEFRKVIEDVGPGVE 215
+ LH+ K L G ++ + SE N +LFIG + K TE++ R + G +E
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ-IE 135
Query: 216 TIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTI 264
+++ P S RG +FV + A A + + M A ++P +
Sbjct: 136 ECRILRGPDGLS--RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 182
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 39/155 (25%), Positives = 74/155 (47%), Gaps = 7/155 (4%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD-PQNPSRNRGFSFVLYYNNACADYS 246
++F+G VP+ W+E + R++ E G V I +++D QNP +++G FV +Y A +
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 247 RQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRH 306
+ + N L G I S ++ A + + L++ I + I+ +F
Sbjct: 76 QNALHNMKV-LPGMHHPIQMKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFSSF 131
Query: 307 GEVTKVVMPPGKSG-KRDFGFIHYAERSSALKAVK 340
G++ + + G G R F+ + R+ A A+K
Sbjct: 132 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
>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 = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 79/146 (54%), Gaps = 15/146 (10%)
Query: 110 FIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESG--ESKGFAFVSFRSKEFAKKAIDE 167
F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV+F +++ A +A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 168 LHS-KELKGK----TIRCSLSETKN-----RLFIGNVPKNWTEDEFRKVIEDVGPGVETI 217
LH+ K L G + + SE N +LFIG + K TE++ R G +E
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ-IEEC 125
Query: 218 ELIKDPQNPSRNRGFSFVLYYNNACA 243
+++ P S RG +FV + A A
Sbjct: 126 RILRGPDGLS--RGCAFVTFTTRAXA 149
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 39/155 (25%), Positives = 72/155 (46%), Gaps = 7/155 (4%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD-PQNPSRNRGFSFVLYYNNACADYS 246
+ F+G VP+ W+E + R++ E G V I +++D QNP +++G FV +Y A +
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 247 RQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRH 306
+ + N L G I S ++ A + + L++ I + I+ F
Sbjct: 64 QNALHNXKV-LPGXHHPIQXKPADSEKNN---AVEDRKLFIGXISKKCTENDIRVXFSSF 119
Query: 307 GEVTKVVMPPGKSG-KRDFGFIHYAERSSALKAVK 340
G++ + + G G R F+ + R+ A A+K
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIG + K +E D+R G + E R+++ + G S+G AFV+F ++ A+ AI
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKA 155
Query: 168 LHSKE 172
H +
Sbjct: 156 XHQAQ 160
>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 = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 36/132 (27%), Positives = 71/132 (53%), Gaps = 6/132 (4%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP++ ++E+ R L IG++ +L++DK +G+S G+ FV++ + A+KAI+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 167 ELHSKELKGKTIRCSLSETKN------RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ L+ KTI+ S + + L++ +PK T+ E ++ G + + L+
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 221 KDPQNPSRNRGF 232
SR GF
Sbjct: 123 DQVTGVSRGVGF 134
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 83/160 (51%), Gaps = 16/160 (10%)
Query: 185 TKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
+K L + +P+N T++EFR + +G +E+ +L++D + ++ G+ FV Y + A+
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGE-IESCKLVRD-KITGQSLGYGFVNYIDPKDAE 58
Query: 245 YSRQKMLNA--NFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKEL 302
K +N +L T +S+A P S A LYV +P + +++++L
Sbjct: 59 ----KAINTLNGLRLQTKTIKVSYARPSSASIRDA------NLYVSGLPKTMTQKELEQL 108
Query: 303 FQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVK 340
F ++G + +++++ R GFI + +R A +A+K
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 41/71 (57%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ GLPK ++++L L G + R++ D+ +G S+G F+ F + A++AI
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 167 ELHSKELKGKT 177
L+ ++ G T
Sbjct: 149 GLNGQKPSGAT 159
>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 = 66.2 bits (160), Expect = 2e-11, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 48/79 (60%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
V++G +P D +EE + DLC +G V +++M D ++G SKG+AF+ FR E + A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 169 HSKELKGKTIRCSLSETKN 187
+ +L + ++C S +
Sbjct: 66 NGYQLGSRFLKCGYSSNSD 84
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLY 237
+++G++P + TE++ + +VGP V ++++ DPQ R++G++F+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFDPQT-GRSKGYAFIEF 52
>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 = 66.2 bits (160), Expect = 2e-11, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 48/80 (60%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P V++G +P D +EE + DLC +G V +++M D ++G SKG+AF+ FR E +
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 164 AIDELHSKELKGKTIRCSLS 183
A+ L+ +L + ++C S
Sbjct: 62 AVRNLNGYQLGSRFLKCGYS 81
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLY 237
+++G++P + TE++ + +VGP V ++++ DPQ R++G++F+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFDPQT-GRSKGYAFIEF 53
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 66.2 bits (160), Expect = 3e-11, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 48/79 (60%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
V++G +P D +EE + DLC +G V +++M D ++G SKG+AF+ FR E + A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 169 HSKELKGKTIRCSLSETKN 187
+ +L + ++C S +
Sbjct: 65 NGYQLGSRFLKCGYSSNSD 83
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLY 237
+++G++P + TE++ + +VGP V ++++ DPQ R++G++F+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFDPQT-GRSKGYAFIEF 51
>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 = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 75/137 (54%), Gaps = 8/137 (5%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP++ ++++LR L IG+V +L++DK +G S G+ FV++ + + A++AI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 167 ELHSKELKGKTIRCSLSETKN------RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ L+ KTI+ S + + L+I +P+ T+ + + G + + L+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 221 KDPQNPSRNRGFSFVLY 237
Q +RG +F+ +
Sbjct: 123 D--QTTGLSRGVAFIRF 137
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 12/156 (7%)
Query: 186 KNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADY 245
+ L + +P+N T+DE R + +G VE+ +LI+D + + G+ FV Y D
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYV--TAKDA 57
Query: 246 SRQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQR 305
R +L T +S+A P S A LY+ +P + + ++++F R
Sbjct: 58 ERAINTLNGLRLQSKTIKVSYARPSSEVIKDA------NLYISGLPRTMTQKDVEDMFSR 111
Query: 306 HGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
G + ++V++ R FI + +RS A +A+
Sbjct: 112 FGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 38/63 (60%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ ++I GLP+ +++D+ D+ G + R++ D+ +G S+G AF+ F + A++AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 167 ELH 169
+
Sbjct: 149 SFN 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 75/137 (54%), Gaps = 8/137 (5%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP++ ++++LR L IG+V +L++DK +G S G+ FV++ + + A++AI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 167 ELHSKELKGKTIRCSLSETKN------RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ L+ KTI+ S + + L+I +P+ T+ + + G + + L+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 221 KDPQNPSRNRGFSFVLY 237
Q +RG +F+ +
Sbjct: 123 D--QTTGLSRGVAFIRF 137
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 73/156 (46%), Gaps = 12/156 (7%)
Query: 186 KNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADY 245
+ L + +P+N T+DE R + +G VE+ +LI+D + + G+ FV Y D
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYV--TAKDA 57
Query: 246 SRQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQR 305
R +L T +S+A P S A LY+ +P + + ++++F R
Sbjct: 58 ERAINTLNGLRLQSKTIKVSYARPSSEVIKDA------NLYISGLPRTMTQKDVEDMFSR 111
Query: 306 HGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
G + ++V++ R FI + +RS A +A+
Sbjct: 112 FGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 38/63 (60%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ ++I GLP+ +++D+ D+ G + R++ D+ +G S+G AF+ F + A++AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 167 ELH 169
+
Sbjct: 149 SFN 151
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 73/137 (53%), Gaps = 8/137 (5%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP+D ++ +L L IG + R+M+D ++G S G+AFV F S+ +++AI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 167 ELHSKELKGKTIRCSL------SETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ ++ K ++ S S L++ N+P+ T+D+ + G V+ ++
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK-NIL 122
Query: 221 KDPQNPSRNRGFSFVLY 237
+D + R RG +FV Y
Sbjct: 123 RD-KLTGRPRGVAFVRY 138
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 38/64 (59%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A++AI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 167 ELHS 170
L++
Sbjct: 150 ALNN 153
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 34/160 (21%), Positives = 76/160 (47%), Gaps = 26/160 (16%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
L + +P++ T+ E + +GP + T +++D + G+S+ + + ++ Q
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKT-----GYSYGYAFVDFTSEMDSQ 59
Query: 249 KMLNANFKLDGNTPT-----ISWADP--KSTPDHSAAASQVKALYVKNIPDNTSTEKIKE 301
+ + L+G T +S+A P +S D + LYV N+P + +++
Sbjct: 60 RAIKV---LNGITVRNKRLKVSYARPGGESIKDTN--------LYVTNLPRTITDDQLDT 108
Query: 302 LFQRHGEVT-KVVMPPGKSGK-RDFGFIHYAERSSALKAV 339
+F ++G + K ++ +G+ R F+ Y +R A +A+
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 44/161 (27%), Positives = 87/161 (54%), Gaps = 16/161 (9%)
Query: 184 ETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACA 243
++K L + +P+N T+DEF+ + +G +E+ +L++D + ++ G+ FV Y + A
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGD-IESCKLVRD-KITGQSLGYGFVNYSDPNDA 59
Query: 244 DYSRQKMLNA--NFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKE 301
D K +N KL T +S+A P S+A+ + LYV +P S +++++
Sbjct: 60 D----KAINTLNGLKLQTKTIKVSYARP------SSASIRDANLYVSGLPKTMSQKEMEQ 109
Query: 302 LFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVK 340
LF ++G + +++++ R GFI + +R A +A+K
Sbjct: 110 LFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Score = 65.1 bits (157), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 70/132 (53%), Gaps = 6/132 (4%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP++ ++++ + L IGD+ +L++DK +G+S G+ FV++ A KAI+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 167 ELHSKELKGKTIRCSLSETKN------RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ +L+ KTI+ S + + L++ +PK ++ E ++ G + + L+
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILL 124
Query: 221 KDPQNPSRNRGF 232
SR GF
Sbjct: 125 DQATGVSRGVGF 136
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 39/66 (59%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ GLPK S++++ L G + R++ D+ +G S+G F+ F + A++AI
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 167 ELHSKE 172
L+ ++
Sbjct: 151 GLNGQK 156
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVKDT 342
L V +P N + ++ K LF G++ K+V +GF++Y++ + A KA+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 343 EKYEIDGKS 351
++ K+
Sbjct: 67 NGLKLQTKT 75
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 46/72 (63%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
VF+G +P +A+EE L+D+ +G V RL+ D+E+G+ KG+ F ++ +E A A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 169 HSKELKGKTIRC 180
+ +E G+ +R
Sbjct: 71 NGREFSGRALRV 82
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
+F+GN+P TE++ + + +VGP V + L+ D + + +G+ F Y + A S
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGP-VVSFRLVYDRET-GKPKGYGFCEYQDQETA-LSAM 67
Query: 249 KMLNA 253
+ LN
Sbjct: 68 RNLNG 72
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 62.0 bits (149), Expect = 5e-10, Method: Composition-based stats.
Identities = 27/71 (38%), Positives = 48/71 (67%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++G L + +E+ LR + EP G + ++LM D E+G SKG+ F++F E AKKA+++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 169 HSKELKGKTIR 179
+ EL G+ ++
Sbjct: 89 NGFELAGRPMK 99
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 44/72 (61%), Gaps = 4/72 (5%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
RL++G++ N TED R + E G +E+I+L+ D + R++G+ F+ + ++ CA +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGR-IESIQLMMDSET-GRSKGYGFITFSDSECAKKAL 85
Query: 248 QKMLNANFKLDG 259
+++ F+L G
Sbjct: 86 EQL--NGFELAG 95
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 62.0 bits (149), Expect = 5e-10, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 49/73 (67%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S +++G L + +E+ LR + EP G + + LMKD ++G SKG+ F++F E A++A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 167 ELHSKELKGKTIR 179
+L+ EL G+ +R
Sbjct: 66 QLNGFELAGRPMR 78
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 183 SETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNAC 242
S + L++G++ N TED R + E G ++ I L+KD + R++G+ F+ + ++ C
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGK-IDNIVLMKD-SDTGRSKGYGFITFSDSEC 59
Query: 243 ADYSRQKMLNANFKLDG 259
A + +++ F+L G
Sbjct: 60 ARRALEQL--NGFELAG 74
>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 = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 72/137 (52%), Gaps = 8/137 (5%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP+D ++ +L L IG + R+ +D ++G S G+AFV F S+ +++AI
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 167 ELHSKELKGKTIRCSL------SETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
L+ ++ K ++ S S L++ N+P+ T+D+ + G V+ ++
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK-NIL 133
Query: 221 KDPQNPSRNRGFSFVLY 237
+D + R RG +FV Y
Sbjct: 134 RD-KLTGRPRGVAFVRY 149
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 38/64 (59%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A++AI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 167 ELHS 170
L++
Sbjct: 161 ALNN 164
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 33/158 (20%), Positives = 73/158 (46%), Gaps = 22/158 (13%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
L + +P++ T+ E + +GP + T + +D + G+SF + + ++ Q
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKT-----GYSFGYAFVDFTSEXDSQ 70
Query: 249 KMLNANFKLDGNTPT-----ISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELF 303
+ + L+G T +S+A P + + LYV N+P + +++ +F
Sbjct: 71 RAIKV---LNGITVRNKRLKVSYARP------GGESIKDTNLYVTNLPRTITDDQLDTIF 121
Query: 304 QRHGEVT-KVVMPPGKSGK-RDFGFIHYAERSSALKAV 339
++G + K ++ +G+ R F+ Y +R A +A+
Sbjct: 122 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 76/148 (51%), Gaps = 19/148 (12%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S V++G + + E+ +R P G + + + D + + KGFAFV + E A+ A++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 167 ELHSKELKGKTIRCS--------------LSETK---NRLFIGNVPKNWTEDEFRKVIED 209
+++S L G+ I+ L+E NR+++ +V ++ ++D+ + V E
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 210 VGPGVETIELIKDPQNPSRNRGFSFVLY 237
G +++ L +DP +++G+ F+ Y
Sbjct: 149 FGK-IKSATLARDPTT-GKHKGYGFIEY 174
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/172 (23%), Positives = 80/172 (46%), Gaps = 13/172 (7%)
Query: 187 NRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYS 246
+R+++G++ ED R+ GP +++I++ D +++GF+FV Y A +
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVT-MKHKGFAFVEYEVPEAAQLA 86
Query: 247 RQKMLNA-----NFKLDGNTPTISWADPKSTPDHSAA-ASQVKALYVKNIPDNTSTEKIK 300
++M + N K+ G I A P D A A +YV ++ + S + IK
Sbjct: 87 LEQMNSVMLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 301 ELFQRHGEVTKVVMP--PGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGK 350
+F+ G++ + P + +GFI Y + S+ AV +++ G+
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 48/78 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
VF+G L + + ED++ P G + + R++KD +G+SKG+ FVSF +K A+ AI ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 169 HSKELKGKTIRCSLSETK 186
+ L G+ IR + + K
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 47/79 (59%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
VF+G L + + ED++ P G + + R++KD +G+SKG+ FVSF +K A+ AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 168 LHSKELKGKTIRCSLSETK 186
+ + L G+ IR + + K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>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 = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 75/146 (51%), Gaps = 19/146 (13%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
V++G + + E+ +R P G + + + D + + KGFAFV + E A+ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 169 HSKELKGKTIRCS--------------LSETK---NRLFIGNVPKNWTEDEFRKVIEDVG 211
+S L G+ I+ L+E NR+++ +V ++ ++D+ + V E G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 212 PGVETIELIKDPQNPSRNRGFSFVLY 237
+++ L +DP +++G+ F+ Y
Sbjct: 136 K-IKSCTLARDPTT-GKHKGYGFIEY 159
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/171 (23%), Positives = 79/171 (46%), Gaps = 13/171 (7%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
R+++G++ ED R+ GP +++I++ D +++GF+FV Y A +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVT-MKHKGFAFVEYEVPEAAQLAL 72
Query: 248 QKMLNA-----NFKLDGNTPTISWADPKSTPDHSAA-ASQVKALYVKNIPDNTSTEKIKE 301
++M + N K+ G I A P D A A +YV ++ + S + IK
Sbjct: 73 EQMNSVMLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 129
Query: 302 LFQRHGEVTKVVMP--PGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGK 350
+F+ G++ + P + +GFI Y + S+ AV +++ G+
Sbjct: 130 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 180
>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 = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 9 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 69 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 128 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 159
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 165 KYHTVNGHNCEVRKALSK 182
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 8 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 68 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 127 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 158
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 164 KYHTVNGHNCEVRKALSK 181
>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 = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 63 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 122 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 153
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 159 KYHTVNGHNCEVRKALSK 176
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 11 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 71 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 130 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 161
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 167 KYHTVNGHNCEVRKALSK 184
>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 = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 39/137 (28%), Positives = 70/137 (51%), Gaps = 10/137 (7%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
++FIGGL D +E++LR+ G V ++++MKD +G S+GF F+SF + +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 167 ELHSKELKGKTIRCSLS------ETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
H L GK I + + ++F+G + + EF + G ++ +L+
Sbjct: 64 TQHI--LDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA-QLM 120
Query: 221 KDPQNPSRNRGFSFVLY 237
D ++ ++RGF FV Y
Sbjct: 121 LD-KDTGQSRGFGFVTY 136
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 10/74 (13%)
Query: 84 PTASVGEDEKDKHAQLLALPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKE 143
P ++ DE+DK + +F+GG+ D ++ + G + + +LM DK+
Sbjct: 75 PKRAIPRDEQDKTGK----------IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 144 SGESKGFAFVSFRS 157
+G+S+GF FV++ S
Sbjct: 125 TGQSRGFGFVTYDS 138
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 70 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 129 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 160
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 166 KYHTVNGHNCEVRKALSK 183
>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 = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
P ++FIGGL + ++E LR E G + + +M+D + S+GF FV++ + E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 163 KAIDELHSKELKGKTI------------RCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
A++ K + G+ + R T ++F+G + ++ E R E
Sbjct: 70 AAMNARPHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 211 GPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
G +E IE++ D + + RGF+FV + ++ D
Sbjct: 129 GK-IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVD 160
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK-AID 166
++F+GG+ +D E LRD E G + + +M D+ SG+ +GFAFV+F + K I
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 167 ELHSKELKGKTIRCSLSE 184
+ H+ +R +LS+
Sbjct: 166 KYHTVNGHNCEVRKALSK 183
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 48/167 (28%), Positives = 76/167 (45%), Gaps = 30/167 (17%)
Query: 174 KGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFS 233
K T RC RLF+GN+P + TE++F+++ E G E +R+RGF
Sbjct: 17 KTYTQRC-------RLFVGNLPTDITEEDFKRLFERYGEPSEVF--------INRDRGFG 61
Query: 234 FVLYYNNACADYSRQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDN 293
F+ + A+ ++ +LDG KS P A+ AL VKN+
Sbjct: 62 FIRLESRTLAEIAKA-------ELDGTI-------LKSRPLRIRFATHGAALTVKNLSPV 107
Query: 294 TSTEKIKELFQRHGEVTKVVMPPGKSGKRDF-GFIHYAERSSALKAV 339
S E +++ F + G V K V+ G+ GF+ +A + A KA+
Sbjct: 108 VSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 58/124 (46%), Gaps = 7/124 (5%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+G LP D +EED + L E G+ EV + +D +GF F+ S+ A+ A EL
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 169 HSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSR 228
LK + +R + L + N+ + + + GP VE ++ D + +
Sbjct: 79 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGP-VEKAVVVVDDRGRAT 137
Query: 229 NRGF 232
+GF
Sbjct: 138 GKGF 141
>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 = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 52/78 (66%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
G+ + + LP++ ++++LR L IG+V +L++DK +G S G+ FV++ + + A++AI
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 166 DELHSKELKGKTIRCSLS 183
+ L+ L+ KTI+ S +
Sbjct: 79 NTLNGLRLQSKTIKVSYA 96
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
L + +P+N T+DE R + +G VE+ +LI+D + + G+ FV Y D R
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYV--TAKDAERA 77
Query: 249 KMLNANFKLDGNTPTISWADP 269
+L T +S+A P
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
Score = 28.1 bits (61), Expect = 7.2, Method: Composition-based stats.
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVKDT 342
L V +P N + ++++ LF GEV K++ +GF++Y A +A+
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 343 EKYEIDGKS 351
+ K+
Sbjct: 82 NGLRLQSKT 90
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 49/94 (52%)
Query: 181 SLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNN 240
S S RLFIG +PK +E + I V GV + + + +NRGF+FV Y ++
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 241 ACADYSRQKMLNANFKLDGNTPTISWADPKSTPD 274
A +R+K++ +L G+ + WA+P+ D
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD 96
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 46/106 (43%), Gaps = 21/106 (19%)
Query: 109 VFIGGLPKDASEEDLRD----LCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+FIGG+PK E++ + + E + DV DK +++GFAFV + S A A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKM--KNRGFAFVEYESHRAAAMA 68
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDV 210
R L + +L+ + +W E E V EDV
Sbjct: 69 --------------RRKLMPGRIQLWGHQIAVDWAEPEI-DVDEDV 99
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++GGL ++ ++ L P GD+ ++++ D E+ + +GFAFV F E A AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 169 HSKELKGKTIRCSLS 183
+ EL G+TIR +L+
Sbjct: 70 NESELFGRTIRVNLA 84
>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 = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 52/80 (65%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P + + + LP++ ++++LR L IG+V +L++DK +G S G+ FV++ + + A++
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 164 AIDELHSKELKGKTIRCSLS 183
AI+ L+ L+ KTI+ S +
Sbjct: 62 AINTLNGLRLQSKTIKVSYA 81
Score = 35.4 bits (80), Expect = 0.050, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 186 KNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADY 245
+ L + +P+N T+DE R + +G VE+ +LI+D + + G+ FV Y D
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYV--TAKDA 59
Query: 246 SRQKMLNANFKLDGNTPTISWADP 269
R +L T +S+A P
Sbjct: 60 ERAINTLNGLRLQSKTIKVSYARP 83
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVKDT 342
L V +P N + ++++ LF GEV K++ +GF++Y A +A+
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 343 EKYEIDGKS 351
+ K+
Sbjct: 67 NGLRLQSKT 75
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++GGL ++ ++ L P GD+ ++++ D E+ + +GFAFV F E A AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 169 HSKELKGKTIRCSLS 183
+ EL G+TIR +L+
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++GGL ++ ++ L P GD+ ++++ D E+ + +GFAFV F E A AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 169 HSKELKGKTIRCSLS 183
+ EL G+TIR +L+
Sbjct: 68 NESELFGRTIRVNLA 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 49/82 (59%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
L P+ S V++ LP + DL + G V +V +MKDK++ +SKG AF+ F K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 162 KKAIDELHSKELKGKTIRCSLS 183
+ +++K+L G+ I+ S++
Sbjct: 72 QNCTRAINNKQLFGRVIKASIA 93
Score = 31.6 bits (70), Expect = 0.63, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 279 ASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFG--FIHYAERSSAL 336
A +YV N+P + + + +F ++G+V KV + K ++ G FI + ++ SA
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 337 KAVKDTEKYEIDGK 350
+ ++ G+
Sbjct: 73 NCTRAINNKQLFGR 86
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 73/146 (50%), Gaps = 19/146 (13%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
V++G + + E+ +R P G + + D + + KGFAFV + E A+ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 169 HSKELKGKTIRCS--------------LSETK---NRLFIGNVPKNWTEDEFRKVIEDVG 211
+S L G+ I+ L+E NR+++ +V ++ ++D+ + V E G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 212 PGVETIELIKDPQNPSRNRGFSFVLY 237
+++ L +DP +++G+ F+ Y
Sbjct: 135 K-IKSCTLARDPTT-GKHKGYGFIEY 158
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 77/171 (45%), Gaps = 13/171 (7%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
R+++G++ ED R+ GP +++I+ D +++GF+FV Y A +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDXSWDSVT-XKHKGFAFVEYEVPEAAQLAL 71
Query: 248 QK-----MLNANFKLDGNTPTISWADPKSTPDHSAA-ASQVKALYVKNIPDNTSTEKIKE 301
++ + N K+ G I A P D A A +YV ++ + S + IK
Sbjct: 72 EQXNSVXLGGRNIKV-GRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 302 LFQRHGEVTKVVMP--PGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGK 350
+F+ G++ + P + +GFI Y + S+ AV +++ G+
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQ 179
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 58/121 (47%), Gaps = 6/121 (4%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S +F+G LP D +EE++R L E G EV + KD KGF F+ ++ A+ A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 167 ELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNP 226
EL + L+GK +R + L + N+P+ + + + G + ++ D P
Sbjct: 77 ELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRP 136
Query: 227 S 227
S
Sbjct: 137 S 137
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 43/161 (26%), Positives = 75/161 (46%), Gaps = 35/161 (21%)
Query: 186 KNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADY 245
++RLF+GN+P + TE+E RK+ E G E +++GF F+ A+
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF--------IHKDKGFGFIRLETRTLAEI 73
Query: 246 SRQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQR 305
++ ++ N L G + +A HSA +L V+N+P S E ++E F
Sbjct: 74 AKVEL--DNMPLRGKQLRVRFA------CHSA------SLTVRNLPQYVSNELLEEAFSV 119
Query: 306 HGEVTKVVM-------PPGKSGKRDFGFIHYAERSSALKAV 339
G+V + V+ P GK G + ++ + +A KA+
Sbjct: 120 FGQVERAVVIVDDRGRPSGK------GIVEFSGKPAARKAL 154
Score = 35.0 bits (79), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 280 SQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
+Q L+V N+P + + E++++LF+++G+ +V + K FGFI R+ A A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLAEIAK 75
Query: 340 KDTEKYEIDGKS 351
+ + + GK
Sbjct: 76 VELDNMPLRGKQ 87
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 61/253 (24%), Positives = 107/253 (42%), Gaps = 21/253 (8%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
N ++ I GLP D + +++ DL + D DK KG AFV+ + E A+ A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDL---LSDYELKYCFVDK----YKGTAFVTLLNGEQAEAA 73
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQ 224
I+ H L+ + + L T L + N+P + T+ +F +++ G +E L+ +
Sbjct: 74 INAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-E 131
Query: 225 NPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADP-KSTPDHSAAASQVK 283
+++G+ F Y A ++ +L L T + W D + TP A +
Sbjct: 132 RTGQSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQLTP----ALLHSR 185
Query: 284 ALYVKNIPD--NTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVK 340
L V +P N + L H T + G+ G+ + F + Y A +A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244
Query: 341 DTEKYEIDGKSHL 353
+ + G SHL
Sbjct: 245 QADGLSLGG-SHL 256
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
L P + + + LP +++ +L P G + L+ + +G+SKG+ F + K+ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 162 KKAIDELHSKELKGKTI 178
+A +L K L +T+
Sbjct: 151 ARAKSDLLGKPLGPRTL 167
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 61/253 (24%), Positives = 107/253 (42%), Gaps = 21/253 (8%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
N ++ I GLP D + +++ DL + D DK KG AFV+ + E A+ A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDL---LSDYELKYCFVDK----YKGTAFVTLLNGEQAEAA 73
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQ 224
I+ H L+ + + L T L + N+P + T+ +F +++ G +E L+ +
Sbjct: 74 INAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-E 131
Query: 225 NPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADP-KSTPDHSAAASQVK 283
+++G+ F Y A ++ +L L T + W D + TP A +
Sbjct: 132 RTGQSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQLTP----ALLHSR 185
Query: 284 ALYVKNIPD--NTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVK 340
L V +P N + L H T + G+ G+ + F + Y A +A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244
Query: 341 DTEKYEIDGKSHL 353
+ + G SHL
Sbjct: 245 QADGLSLGG-SHL 256
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
L P + + + LP +++ +L P G + L+ + +G+SKG+ F + K+ A
Sbjct: 91 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 162 KKAIDELHSKELKGKTI 178
+A +L K L +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 = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 61/253 (24%), Positives = 107/253 (42%), Gaps = 21/253 (8%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
N ++ I GLP D + +++ DL + D DK KG AFV+ + E A+ A
Sbjct: 19 NRRKILIRGLPGDVTNQEVHDL---LSDYELKYCFVDK----YKGTAFVTLLNGEQAEAA 71
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQ 224
I+ H L+ + + L T L + N+P + T+ +F +++ G +E L+ +
Sbjct: 72 INAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-E 129
Query: 225 NPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADP-KSTPDHSAAASQVK 283
+++G+ F Y A ++ +L L T + W D + TP A +
Sbjct: 130 RTGQSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQLTP----ALLHSR 183
Query: 284 ALYVKNIPD--NTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVK 340
L V +P N + L H T + G+ G+ + F + Y A +A +
Sbjct: 184 CLCVDRLPPGFNDVDALCRALSAVHSP-TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 242
Query: 341 DTEKYEIDGKSHL 353
+ + G SHL
Sbjct: 243 QADGLSLGG-SHL 254
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
L P + + + LP +++ +L P G + L+ + +G+SKG+ F + K+ A
Sbjct: 89 LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 148
Query: 162 KKAIDELHSKELKGKTI 178
+A +L K L +T+
Sbjct: 149 ARAKSDLLGKPLGPRTL 165
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++GGL ++ ++ L P GD+ ++++ D E+ + +GFAFV F E A AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 169 HSKELKGKTIRCSLS 183
+ EL G+TIR +L+
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 46/73 (63%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++F+GGL D +E+ L + G + EV ++KD+E+ S+GF FV+F + + AK A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 168 LHSKELKGKTIRC 180
++ K + G+ IR
Sbjct: 74 MNGKSVDGRQIRV 86
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 279 ASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRD--FGFIHYAERSSAL 336
AS L+V + +T+ + ++++F ++G++++VV+ + +R FGF+ + A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 337 KAVKDTEKYEIDGK 350
A+ +DG+
Sbjct: 69 DAMMAMNGKSVDGR 82
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++GGL ++ ++ L P GD+ ++++ D E+ + +GFAFV F E A AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 169 HSKELKGKTIRCSLS 183
+ EL G+TIR +L+
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 35/52 (67%)
Query: 114 LPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
L +D E DL++L P G + + L KDK +G+SKGFAF+SF +E A +AI
Sbjct: 23 LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSG--KRDFGFIHYAERSSALKAVKDT 342
+ V N+ ++T ++ELF+ G ++++ + K+ + F FI + R A +A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 343 EKYEID 348
+ D
Sbjct: 78 SGFGYD 83
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 47/68 (69%), Gaps = 2/68 (2%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESG--ESKGFAFVSFRSKEFAKKAI 165
++F+G +P+ SE+DLR+L E G V+E+ +++D+ +SKG FV+F +++ A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 166 DELHSKEL 173
+ LH+ ++
Sbjct: 65 NALHNMKV 72
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD-PQNPSRNRGFSFVLYYNNACA 243
++F+G VP+ W+E + R++ E G V I +++D QNP +++G FV +Y A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+GGL + + ED++ E G V + LM DK + +GF FV+F S++ +K + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 169 HSKELKGKTIRC 180
H E+ K + C
Sbjct: 61 HFHEINNKMVEC 72
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRD--FGFIHYAERSSALKAVKDT 342
++V + NT+ E +K F++ G+V ++ K+ R FGF+ + E ++ V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 343 EKYEIDGK 350
+EI+ K
Sbjct: 61 HFHEINNK 68
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 44/65 (67%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIG +P++ E+DL+ L E G ++E+ ++KD+ +G KG AF+++ +E A KA
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 168 LHSKE 172
LH ++
Sbjct: 75 LHEQK 79
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGK--SGKRDFGFIHYAERSSALKA 338
L++ IP N + +K LF+ G++ ++ + + + F+ Y ER SALKA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 31.2 bits (69), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLY 237
+LFIG +P+N E + + + E+ G + + ++KD + ++G +F+ Y
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGK-IYELTVLKD-RFTGMHKGCAFLTY 62
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+G L + +E LR+ + +M D ++G S+G+ FVSF S++ A+ A+D +
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 169 HSKELKGKTIRCSLS 183
++L G+ +R + +
Sbjct: 150 QGQDLNGRPLRINWA 164
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 80/167 (47%), Gaps = 13/167 (7%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++G L K +E+ L+ + G + +++M DK + ++ +AFV + A A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 169 HSKELKGKTIRC--------SLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELI 220
+ K+++ ++ S S+ LF+G++ N ++ R +D P + ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDF-PSYLSGHVM 120
Query: 221 KDPQNPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWA 267
D Q S +RG+ FV + + A + M + L+G I+WA
Sbjct: 121 WDMQTGS-SRGYGFVSFTSQDDAQNAMDSMQGQD--LNGRPLRINWA 164
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIGGL ++ +E+ L+ + G + EV L+KD+ S +S+GFAF++F + AK A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 168 LHSKELKGKTIRC 180
++ K L GK I+
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
+LFIG + + E + V GP + + LIKD S++RGF+F+ + N A A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGP-ISEVLLIKD--RTSKSRGFAFITFENPADAKNAA 65
Query: 248 QKM 250
+ M
Sbjct: 66 KDM 68
Score = 35.0 bits (79), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVKDTE 343
L++ + T+ + +K +F +HG +++V++ ++ K R F FI + + A A KD
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 344 KYEIDGKS 351
+ GK+
Sbjct: 70 GKSLHGKA 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++G L A+ E +++L G VF V+L+ D+E+ + KGF FV + +E +AI +L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Query: 169 HSKELKGKTIRCSLSETKNRL 189
+ + G+TIR + + K L
Sbjct: 63 DNTDFMGRTIRVTEANPKKSL 83
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 282 VKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK--RDFGFIHYAERS 333
++ +YV N+ + ++E++KELF + G+V V + + K + FGF+ E S
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES 54
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 99 LLALPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSK 158
L PP+ ++F+G L K SE+D+R L E G++ E +++ + G SKG AFV + S
Sbjct: 8 CLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSH 66
Query: 159 EFAKKAIDELHSKE 172
A+ AI+ LH +
Sbjct: 67 AEAQAAINALHGSQ 80
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNA 241
+LF+G + K +ED+ R++ E G +E +++ P S +G +FV Y ++A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFG-NIEECTILRGPDGNS--KGCAFVKYSSHA 67
>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 = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 48/84 (57%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P G+ +FI LP++ ++DL + P G+V ++ DK++ SK F FVS+ + A+
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82
Query: 164 AIDELHSKELKGKTIRCSLSETKN 187
AI ++ ++ K ++ L +KN
Sbjct: 83 AIQSMNGFQIGMKRLKVQLKRSKN 106
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 73/148 (49%), Gaps = 4/148 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++G L D +E L + P G + +R+ +D + S G+A+V+F+ A++A+D
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 167 ELHSKELKGKTIRCSLSETKNRL---FIGNV-PKNWTEDEFRKVIEDVGPGVETIELIKD 222
++ +KGK +R S+ L +GN+ KN + K + D I K
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 135
Query: 223 PQNPSRNRGFSFVLYYNNACADYSRQKM 250
+ + ++G+ FV + A+ + +KM
Sbjct: 136 VCDENGSKGYGFVHFETQEAAERAIEKM 163
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/152 (22%), Positives = 72/152 (47%), Gaps = 10/152 (6%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
L++G++ + TE + GP + +I + +D R+ G+++V + A A+ +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAERALD 75
Query: 249 KMLNANFKLDGNTPT-ISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHG 307
M NF + P I W S D S S V +++KN+ + + + + F G
Sbjct: 76 TM---NFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128
Query: 308 EVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
+ + ++G + +GF+H+ + +A +A+
Sbjct: 129 NILSCKVVCDENGSKGYGFVHFETQEAAERAI 160
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 44/65 (67%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++F+G +P+ E+DL+ L E G ++E+ ++KD+ +G KG AF+++ +++ A KA
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 168 LHSKE 172
LH ++
Sbjct: 77 LHEQK 81
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKV-VMPPGKSG-KRDFGFIHYAERSSALKA 338
L+V IP + +K LF+ G + ++ V+ +G + F+ Y R SALKA
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 73/148 (49%), Gaps = 4/148 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++G L D +E L + P G + +R+ +D + S G+A+V+F+ A++A+D
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 167 ELHSKELKGKTIRCSLSETKNRLF---IGNV-PKNWTEDEFRKVIEDVGPGVETIELIKD 222
++ +KGK +R S+ L +GN+ KN + K + D I K
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 130
Query: 223 PQNPSRNRGFSFVLYYNNACADYSRQKM 250
+ + ++G+ FV + A+ + +KM
Sbjct: 131 VCDENGSKGYGFVHFETQEAAERAIEKM 158
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/152 (22%), Positives = 72/152 (47%), Gaps = 10/152 (6%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
L++G++ + TE + GP + +I + +D R+ G+++V + A A+ +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAERALD 70
Query: 249 KMLNANFKLDGNTPT-ISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHG 307
M NF + P I W S D S S V +++KN+ + + + + F G
Sbjct: 71 TM---NFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 308 EVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
+ + ++G + +GF+H+ + +A +A+
Sbjct: 124 NILSCKVVCDENGSKGYGFVHFETQEAAERAI 155
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 49/77 (63%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ + + LP++ ++++ + L IGD+ +L++DK +G+S G+ FV++ A KAI+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 167 ELHSKELKGKTIRCSLS 183
L+ +L+ KTI+ S +
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 8/90 (8%)
Query: 184 ETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACA 243
++K L + +P+N T+DEF+ + +G +E+ +L++D + ++ G+ FV Y + A
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIG-DIESCKLVRD-KITGQSLGYGFVNYSDPNDA 59
Query: 244 DYSRQKMLNA--NFKLDGNTPTISWADPKS 271
D K +N KL T +S+A P S
Sbjct: 60 D----KAINTLNGLKLQTKTIKVSYARPSS 85
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 46/86 (53%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ V++GGL + SE L +L G V + KD+ +G+ +G+ FV F S+E A AI
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 167 ELHSKELKGKTIRCSLSETKNRLFIG 192
+ +L GK IR + + N+ G
Sbjct: 76 IMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 280 SQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGK-SGK-RDFGFIHYAERSSALK 337
+Q +YV + + S + ELF + G V MP + +G+ + +GF+ + A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 338 AVKDTEKYEIDGK 350
A+K + ++ GK
Sbjct: 73 AIKIMDMIKLYGK 85
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 50/92 (54%)
Query: 95 KHAQLLALPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVS 154
+H A P + + GL +E DLR++ G + +V ++ D++S S+GFAFV
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 155 FRSKEFAKKAIDELHSKELKGKTIRCSLSETK 186
F + + AK+A + + EL G+ IR S TK
Sbjct: 95 FENVDDAKEAKERANGMELDGRRIRVDFSITK 126
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 199 TEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNAN-FKL 257
TE + R+V GP + + ++ D Q+ R+RGF+FV + N D +++ AN +L
Sbjct: 59 TERDLREVFSKYGP-IADVSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 113
Query: 258 DGNTPTISWADPK 270
DG + ++ K
Sbjct: 114 DGRRIRVDFSITK 126
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 45/76 (59%)
Query: 111 IGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS 170
+ GL +E DLR++ G + +V ++ D++S S+GFAFV F + + AK+A + +
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 171 KELKGKTIRCSLSETK 186
EL G+ IR S TK
Sbjct: 77 MELDGRRIRVDFSITK 92
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 199 TEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNAN-FKL 257
TE + R+V GP + + ++ D Q+ R+RGF+FV + N D +++ AN +L
Sbjct: 25 TERDLREVFSKYGP-IADVSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 79
Query: 258 DGNTPTISWADPK 270
DG + ++ K
Sbjct: 80 DGRRIRVDFSITK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 44/74 (59%)
Query: 113 GLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKE 172
GL +E DLR++ G + +V ++ D++S S+GFAFV F + + AK+A + + E
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 173 LKGKTIRCSLSETK 186
L G+ IR S TK
Sbjct: 82 LDGRRIRVDFSITK 95
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 199 TEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNAN-FKL 257
TE + R+V GP + + ++ D Q+ R+RGF+FV + N D +++ AN +L
Sbjct: 28 TERDLREVFSKYGP-IADVSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 82
Query: 258 DGNTPTISWADPK 270
DG + ++ K
Sbjct: 83 DGRRIRVDFSITK 95
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+++F+GG+P + E +LR+ + G V EV ++ D E +GF F++F ++ +A++
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 167 ELHSKELKGKTIRCSLSETKN 187
+H ++ GK + +E ++
Sbjct: 71 -MHFHDIMGKKVEVKRAEPRD 90
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 7/87 (8%)
Query: 187 NRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYS 246
N++F+G +P N E E R+ + G E + +I D + R RGF F+ + + D
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVV-MIYDAEK-QRPRGFGFITFEDEQSVD-- 66
Query: 247 RQKMLNANFK-LDGNTPTISWADPKST 272
+ +N +F + G + A+P+ +
Sbjct: 67 --QAVNMHFHDIMGKKVEVKRAEPRDS 91
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVM--PPGKSGKRDFGFIHYAERSSALKAVKDT 342
++V IP N +++E F++ G VT+VVM K R FGFI + + S +AV +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 343 EKYEIDGK 350
++I GK
Sbjct: 72 HFHDIMGK 79
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+FIGGL D +++DL+D G+V + L D +G S+GF FV F+ E K +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 169 HSKELKGKTI 178
K L GK I
Sbjct: 62 EHK-LNGKVI 70
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S++ + GLP +E+DL++ G+V V++ KD ++G SKGF FV F E K +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 167 ELHSKELKGKTIRCSLSETK 186
+ H + G+ C L +K
Sbjct: 76 QRHM--IDGRWCDCKLPNSK 93
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 278 AASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKV-VMPPGKSG-KRDFGFIHYAERSSA 335
A + L V +P T+ + +KE F GEV V V K+G + FGF+ + E +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 336 LKAVKDTEKYEIDGK 350
+K + ++++ IDG+
Sbjct: 71 VKVM--SQRHMIDGR 83
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIG LP++A+E+++R L E G V E ++K+ + FV K A+ AI
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 168 LHSKELKGKTIRCSLSETKNR 188
LH +L G I S+ K++
Sbjct: 62 LHHYKLHGVNINVEASKNKSK 82
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 46/74 (62%), Gaps = 6/74 (8%)
Query: 276 SAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSA 335
S+ +S + L++ N+P + ++I+ LF+++G+V + + +++GF+H ++++A
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAA 55
Query: 336 LKAVKDTEKYEIDG 349
A+++ Y++ G
Sbjct: 56 EDAIRNLHHYKLHG 69
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD 222
+LFIGN+P+ TE E R + E G +E ++IK+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLEC-DIIKN 43
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 6/77 (7%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S +F+G LP D +EE++R L E G EV + KD KGF F+ ++ A+ A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 167 ELHSKELKGKTIRCSLS 183
EL + L+GK +R +
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 186 KNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADY 245
++RLF+GN+P + TE+E RK+ E G E +++GF F+ A+
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF--------IHKDKGFGFIRLETRTLAEI 66
Query: 246 SRQKMLNANFKLDGNTPTISWA 267
++ ++ N L G + +A
Sbjct: 67 AKVEL--DNMPLRGKQLRVRFA 86
Score = 35.0 bits (79), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 280 SQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
+Q L+V N+P + + E++++LF+++G+ +V + K FGFI R+ A A
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLAEIAK 68
Query: 340 KDTEKYEIDGK 350
+ + + GK
Sbjct: 69 VELDNMPLRGK 79
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 2/70 (2%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIG--DVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
++IG L ++EDL + +G D+ E++ +++ +G+SKGFA V S+ +KK +D
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 167 ELHSKELKGK 176
L +EL G+
Sbjct: 64 LLPKRELHGQ 73
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 2/85 (2%)
Query: 104 PNGSE--VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
P GS VF+G L + + + P G + + R++KD +G+SKG+ FVSF +K A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 162 KKAIDELHSKELKGKTIRCSLSETK 186
+ AI ++ + L G+ IR + + K
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++F+G L K ++ED+R + EP G + E +++ + G SKG AFV F++ A+ AI+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 168 LHS 170
LHS
Sbjct: 73 LHS 75
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNA 241
+LF+G + K T+++ RK+ E G ++ +++ P S +G +FV + +A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGT-IDECTVLRGPDGTS--KGCAFVKFQTHA 64
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 2/70 (2%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIG--DVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
++IG L ++EDL + +G D+ E++ +++ +G+SKGFA V S+ +KK +D
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 167 ELHSKELKGK 176
L +EL G+
Sbjct: 131 LLPKRELHGQ 140
>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 = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 42/71 (59%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+G L + +E LR+ + +M D ++G S+G+ FVSF S++ A+ A+D +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 169 HSKELKGKTIR 179
++L G+ +R
Sbjct: 64 QGQDLNGRPLR 74
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ GL +D +EE L+ E R++ D+E+G SKGF FV F S+E AK A + +
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 169 HSKELKGKTIRCSLSETK 186
E+ G + ++ K
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 283 KALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSG-KRDFGFIHYAERSSALKAVKD 341
K L+VK + ++T+ E +KE F G V ++ ++G + FGF+ + A A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 342 TEKYEIDG 349
E EIDG
Sbjct: 74 MEDGEIDG 81
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 183 SETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNAC 242
S+ LF+ + ++ TE+ ++ + G ++ D + S ++GF FV + +
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFD----GSVRARIVTDRETGS-SKGFGFVDFNSEED 66
Query: 243 ADYSRQKMLNANFKLDGNTPTISWADPK 270
A +++ M + ++DGN T+ WA PK
Sbjct: 67 AKAAKEAMEDG--EIDGNKVTLDWAKPK 92
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 42/75 (56%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S ++I GL +++DL LC+P G + + + DK + + KG+ FV F S A+KA+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 167 ELHSKELKGKTIRCS 181
L + ++ + + S
Sbjct: 66 ALKASGVQAQMAKQS 80
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 278 AASQVKALYVKNIPDNTSTEKIKELFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSA 335
+S LY++ + T+ + + +L Q +G++ TK ++ + + +GF+ + S+A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 336 LKAV 339
KAV
Sbjct: 61 QKAV 64
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 45/81 (55%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P G +FI LP++ ++ DL P G+V ++ DK++ SK F FVSF + + A+
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 164 AIDELHSKELKGKTIRCSLSE 184
AI ++ ++ K ++ L +
Sbjct: 98 AIKAMNGFQVGTKRLKVQLKK 118
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 47/79 (59%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+ + + + LP+D ++ +L L IG + R+M+D ++G S G+AFV F S+ +++A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 165 IDELHSKELKGKTIRCSLS 183
I L+ ++ K ++ S +
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 42/69 (60%)
Query: 113 GLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKE 172
GL +E DLR++ G + +V ++ D++S S+GFAFV F + + AK+A + + E
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 173 LKGKTIRCS 181
L G+ IR S
Sbjct: 82 LDGRRIRVS 90
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 199 TEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNAN-FKL 257
TE + R+V GP + + ++ D Q+ R+RGF+FV + N D +++ AN +L
Sbjct: 28 TERDLREVFSKYGP-IADVSIVYDQQS-RRSRGFAFVYFEN---VDDAKEAKERANGMEL 82
Query: 258 DGNTPTIS 265
DG +S
Sbjct: 83 DGRRIRVS 90
>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 = 9e-06, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 38/58 (65%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+++F+GGLP ++ LR E GD+ E ++ D+++G+S+G+ FV+ + A++A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTK-VVMPPGKSGK-RDFGFIHYAERSSALKAVKDT 342
++V +P +T+ +++ F+ G++ + VV+ ++GK R +GF+ A+R++A +A KD
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 343 EKYEIDGK 350
IDG+
Sbjct: 80 NPI-IDGR 86
>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 = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 49/83 (59%), Gaps = 2/83 (2%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIG-DVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID- 166
V + LP+ A+E+D+R + G EVRLM++K SG+S+GFAFV F + A + ++
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Query: 167 ELHSKELKGKTIRCSLSETKNRL 189
HS + G+ + S+ K ++
Sbjct: 64 NQHSLNILGQKVSMHYSDPKPKI 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 114 LPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKEL 173
+P E LR L E G + V+++ D+E+ +S+G+ FV F+S A++AI L+ +
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109
Query: 174 KGKTIRCSLSETKNR 188
K ++ +L+ + ++
Sbjct: 110 LNKRLKVALAASGHQ 124
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 282 VKALYVKNIPDNTSTEKIKELFQRHG--EVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
++ L V IP ++++LF+R+G E K+V R +GF+ + SSA +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 340 KDTEKYEIDGK 350
+ I K
Sbjct: 102 AGLNGFNILNK 112
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 54/121 (44%), Gaps = 6/121 (4%)
Query: 58 GASEKDQSAEANRNDDDTPHVEEEEKPTASVGEDEKDKHAQLLALPPNGSEVFIGGLPKD 117
G + QS + R D P E P+ V +P + ++FIGGLP
Sbjct: 72 GIIFQGQSLKIRRPHDYQPLPGMSENPSVYV------PGVVSTVVPDSAHKLFIGGLPNY 125
Query: 118 ASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKT 177
+++ +++L G + L+KD +G SKG+AF + +AI L+ +L K
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 178 I 178
+
Sbjct: 186 L 186
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 34/172 (19%), Positives = 70/172 (40%), Gaps = 44/172 (25%)
Query: 109 VFIGGLPKDASEEDLRDLCE-----------PIGDVFEVRLMKDKESGESKGFAFVSFRS 157
+++G +P +EE + D P V V++ +DK FAF+ FRS
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 158 KEFAKKAID----ELHSKELKGK---------------------TIRCSLSETKNRLFIG 192
+ +A+ + LK + + + ++ ++LFIG
Sbjct: 61 VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 193 NVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
+P +D+ ++++ GP ++ L+KD ++G++F Y + D
Sbjct: 121 GLPNYLNDDQVKELLTSFGP-LKAFNLVKDSAT-GLSKGYAFCEYVDINVTD 170
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FI GLP ++E+L ++C+ G V ++RL+ ++ +G+ KG A+V + ++ A +A+ +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 168 LHSKELKGKTIRCSLSET 185
+ +K I+ ++S +
Sbjct: 78 MDGMTIKENIIKVAISNS 95
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVKDTE 343
L++ +P + + E+++E+ + HG V + + ++GK + ++ Y S A +AV +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 344 KYEI 347
I
Sbjct: 80 GMTI 83
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 110 FIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELH 169
F+GGL D S++DL+D G+V + + D +G S+GF F+ F+ +K +D+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 170 SKELKGKTI 178
+ L G+ I
Sbjct: 75 HR-LDGRVI 82
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 184 ETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACA 243
E + F+G + + ++ + + G V+ IK N R+RGF F+L+ + A
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCT--IKXDPNTGRSRGFGFILFKDAA-- 64
Query: 244 DYSRQKMLNAN-FKLDG 259
S +K+L+ +LDG
Sbjct: 65 --SVEKVLDQKEHRLDG 79
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P ++FIGGLP +++ +++L G + L+KD +G SKG+AF + +
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 164 AIDELHSKELKGKTI 178
AI L+ +L K +
Sbjct: 154 AIAGLNGMQLGDKKL 168
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/160 (22%), Positives = 71/160 (44%), Gaps = 28/160 (17%)
Query: 104 PNGS--EVFIGGLPKDASEEDLRDLCE-----------PIGDVFEVRLMKDKESGESKGF 150
P GS +++G +P +EE + D P V V++ +DK F
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------F 55
Query: 151 AFVSFRSKEFAKKAIDELHSKELKGKTIRCSLSE------TKNRLFIGNVPKNWTEDEFR 204
AF+ FRS + +A+ +G++++ ++LFIG +P +D+ +
Sbjct: 56 AFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVK 114
Query: 205 KVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
+++ GP ++ L+KD ++G++F Y + D
Sbjct: 115 ELLTSFGP-LKAFNLVKDSAT-GLSKGYAFCEYVDINVTD 152
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P ++FIGGLP +++ +++L G + L+KD +G SKG+AF + +
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 164 AIDELHSKELKGKTI 178
AI L+ +L K +
Sbjct: 152 AIAGLNGMQLGDKKL 166
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 68/153 (44%), Gaps = 26/153 (16%)
Query: 109 VFIGGLPKDASEEDLRDLCE-----------PIGDVFEVRLMKDKESGESKGFAFVSFRS 157
+++G +P +EE + D P V V++ +DK FAF+ FRS
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 158 KEFAKKAIDELHSKELKGKTIRCSLSE------TKNRLFIGNVPKNWTEDEFRKVIEDVG 211
+ +A+ +G++++ ++LFIG +P +D+ ++++ G
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 212 PGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
P ++ L+KD ++G++F Y + D
Sbjct: 120 P-LKAFNLVKDSAT-GLSKGYAFCEYVDINVTD 150
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKE-SGESKGFAFVSFRSKEFAKKAI 165
S++ + +P A++ ++R+L G++ VRL K +G +GF FV F +K+ AKKA
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 166 DEL-HSKELKGKTI 178
+ L HS L G+ +
Sbjct: 76 NALCHSTHLYGRRL 89
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMP---PGKSGKRDFGFIHYAERSSALKA 338
+ V+NIP + +I+ELF GE+ V +P G R FGF+ + + A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 111 IGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS 170
+ L S + LR + E G V +V + +D+ + ES+GFAFV F K A+ A+D +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 171 KELKGKTIRCSLS 183
L G+ +R ++
Sbjct: 135 AVLDGRELRVQMA 147
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++F+G L K SEED+ L +P G + E +++ + G SKG AFV F S A+ AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 168 LHSKE 172
LH +
Sbjct: 76 LHGSQ 80
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
N ++F+G + + ++LR L E G V E ++KD +AFV + AK A
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAA 59
Query: 165 IDELHSKELKGKTIRCSLS 183
I +L+ KE+KGK I LS
Sbjct: 60 IAQLNGKEVKGKRINVELS 78
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 276 SAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSA 335
S ++ ++V N+ ++++++ LF+R G V + + +D+ F+H + + A
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KDYAFVHMEKEADA 56
Query: 336 LKAVKDTEKYEIDGK 350
A+ E+ GK
Sbjct: 57 KAAIAQLNGKEVKGK 71
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+G ++FIGGL ++E LR+ G+V E +M+D + S+GF FV+F + K
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 165 IDELHSKELKGKTI 178
+ + EL KTI
Sbjct: 84 LAQ-SRHELDSKTI 96
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 10/88 (11%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
++FIG + T++ R+ G E + +++DP R+RGF FV + + A D
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECL-VMRDPLT-KRSRGFGFVTFMDQAGVD--- 81
Query: 248 QKMLNANFKLDGNT--PTISW---ADPK 270
+ + + +LD T P +++ A PK
Sbjct: 82 KVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 38/66 (57%)
Query: 119 SEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTI 178
S + LR + E G V +V + +D+ + ES+GFAFV F K A+ A+D + L G+ +
Sbjct: 60 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Query: 179 RCSLSE 184
R ++
Sbjct: 120 RVQMAR 125
>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 = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 44/73 (60%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
G +F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 166 DELHSKELKGKTI 178
+ L+ ++L G+ I
Sbjct: 82 EGLNGQDLMGQPI 94
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRS 157
+FIGGL + +EE LR+ E G + + +M+D S S+GF FV+F S
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 187 NRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
+LFIG + TE+ R E G + + +++DP + R+RGF FV + + A D
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCV-VMRDPAS-KRSRGFGFVTFSSMAEVD 83
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++ L +E LR P G + ++M E G SKGF FV F S E A KA+ E+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 169 HSKELKGKTIRCSLSETK 186
+ + + K + +L++ K
Sbjct: 76 NGRIVATKPLYVALAQRK 93
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 281 QVKALYVKNIPDNTSTEKIKELFQRHGEVT--KVVMPPGKSGKRDFGFIHYAERSSALKA 338
QV LYVKN+ D E++++ F G +T KV+M G+S + FGF+ ++ A KA
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKA 71
Query: 339 VKDTEKYEIDGKSHLHFPVFV 359
V E++G+ P++V
Sbjct: 72 VT-----EMNGRIVATKPLYV 87
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +F+ P D E +L ++ P G + EV+++ GFAFV F E A KAI+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 83
Query: 167 ELHSKELKGKTIRCSLS 183
E+H K + + S
Sbjct: 84 EVHGKSFANQPLEVVYS 100
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 11/76 (14%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEK 344
L+V+ P + ++ E+F G + +V + G F F+ + E SA KA++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESAAKAIE---- 83
Query: 345 YEIDGKSHLHFPVFVL 360
E+ GKS + P+ V+
Sbjct: 84 -EVHGKSFANQPLEVV 98
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 HSKELKGKTI 178
+ ++L G+ I
Sbjct: 70 NGQDLMGQPI 79
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +F+ P D E +L ++ P G + EV+++ GFAFV F E A KAI+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 56
Query: 167 ELHSKELKGKTIRCSLS 183
E+H K + + S
Sbjct: 57 EVHGKSFANQPLEVVYS 73
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEK 344
L+V+ P + ++ E+F G + +V + G F F+ + E SA KA++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESAAKAIE---- 56
Query: 345 YEIDGKSHLHFPV 357
E+ GKS + P+
Sbjct: 57 -EVHGKSFANQPL 68
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEV-RLMKDKESGESKGFAFVSFRSKEFAKKAI 165
S +FIG L + E+ L D G + + ++M+D ++G SKG+AF++F S + + AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 166 DELHSKELKGKTIRCSLSETKN 187
+ ++ + L + I S + K+
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKD 87
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIGGL ++E LR+ G+V E +M+D + S+GF FV+F + K + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 168 LHSKELKGKTI 178
EL KTI
Sbjct: 62 -SRHELDSKTI 71
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
++FIG + T++ R+ G E + +++DP R+RGF FV + + A D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECL-VMRDPLT-KRSRGFGFVTFMDQAGVD--- 56
Query: 248 QKMLNANFKLDGNTPTISWADPK 270
+ + + +LD T DPK
Sbjct: 57 KVLAQSRHELDSKT-----IDPK 74
>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 = 1e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 HSKELKGKTI 178
+ ++L G+ I
Sbjct: 70 NGQDLMGQPI 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 = 1e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFR 156
++F+GGL ++E LR G+V + +MKDK + +S+GF FV F+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Score = 31.2 bits (69), Expect = 0.84, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 279 ASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK--RDFGFIHYAERSSAL 336
A ++ L+V + +T+ E ++ F ++GEV V+ K+ R FGF+ + + + +
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD-PNCV 71
Query: 337 KAVKDTEKYEIDGKS 351
V + + +DG++
Sbjct: 72 GTVLASRPHTLDGRN 86
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 169 HSKELKGKTI 178
+ ++L G+ I
Sbjct: 72 NGQDLMGQPI 81
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 169 HSKELKGKTI 178
+ ++L G+ I
Sbjct: 70 NGQDLMGQPI 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P V+ GG+ +++ +R P G + E+R+ + KG++FV F + E A
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAH 76
Query: 164 AIDELHSKELKGKTIRC 180
AI ++ ++G ++C
Sbjct: 77 AIVSVNGTTIEGHVVKC 93
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID-E 167
+F+GGL D EE +R+ G+V + L D ++ + +GF F++F+ +E KK ++ +
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 168 LHSKELKGKTIRCSLS 183
H+ L I+ ++S
Sbjct: 64 YHNVGLSKCEIKVAMS 79
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 282 VKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPP-GKSGK-RDFGFIHYAE 331
VK ++V + +T EKI+E F GEV + +P K+ K R F FI + E
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE 52
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 45/74 (60%), Gaps = 6/74 (8%)
Query: 276 SAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSA 335
S+ ++VK L+V+N+ + + E +++ F + G++ +V +D+ FIH+ ER A
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV------KKLKDYAFIHFDERDGA 58
Query: 336 LKAVKDTEKYEIDG 349
+KA+++ +++G
Sbjct: 59 VKAMEEMNGKDLEG 72
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ L +EE L G + V+ +KD +AF+ F ++ A KA++E+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 169 HSKELKGKTI 178
+ K+L+G+ I
Sbjct: 66 NGKDLEGENI 75
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 39/71 (54%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
++FIGGLP +++ +++L G + L+KD +G SKG+AF + +AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 168 LHSKELKGKTI 178
L+ +L K +
Sbjct: 63 LNGMQLGDKKL 73
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 187 NRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
++LFIG +P +D+ ++++ GP ++ L+KD ++G++F Y + D
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSAT-GLSKGYAFCEYVDINVTD 57
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
+ PN VF+GG+ E ++R G V EV+++ D+ +G SKG+ FVSF +
Sbjct: 7 IMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63
Query: 162 KKAIDE---LHSKELK-GKTIR 179
+K ++ H K+LK G IR
Sbjct: 64 QKIVESQINFHGKKLKLGPAIR 85
>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 = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 43/70 (61%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ G+ ++A+EED+ D G++ + L D+ +G KG+ V + + + A+ A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 169 HSKELKGKTI 178
+ ++L G+ I
Sbjct: 86 NGQDLMGQPI 95
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ L +SEEDL L G + E+ D + + KGFAFV+F E A KA E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 169 HSKELKGKTIRCSLSETK 186
+ +G+ + S K
Sbjct: 71 DGQVFQGRMLHVLPSTIK 88
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK--RDFGFIHYAERSSALKAVKDT 342
L+V+N+ +S E +++LF +G ++++ P K + F F+ + A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA-- 68
Query: 343 EKYEIDGK 350
E+DG+
Sbjct: 69 ---EVDGQ 73
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+F+GGL D EE +R+ G+V + L D ++ + +GF F++F+ +E KK ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGK--SGKRDFGFIHYAERSSALKAV 339
++V + +T EKI+E F GEV + +P + +R F FI + E K +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFE--------VRLMKDKESGESKGFAFVSFRSKEF 160
+F+ GL ++ + E + D + IG + + L D+E+G+ KG A VSF
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 161 AKKAIDELHSKELKGKTIRCSLS 183
AK AID KE G I+ S +
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFE--------VRLMKDKESGESKGFAFVSFRSKEF 160
+F+ GL ++ + E + D + IG + + L D+E+G+ KG A VSF
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 161 AKKAIDELHSKELKGKTIRCSLS 183
AK AID KE G I+ S +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFA 92
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 46/216 (21%), Positives = 94/216 (43%), Gaps = 14/216 (6%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAF--VSFRSKEFAKKA 164
+ V + LPK ++ + + G + V D K F F + F + A A
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV----DVADSLKKNFRFARIEFARYDGALAA 97
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQ 224
I + H + + I L+E L+ N P ++T+ R +++D+ +I L
Sbjct: 98 ITKTHKVVGQNEIIVSHLTECT--LWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF 155
Query: 225 NPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADPKSTPDHSAAAS-QVK 283
N SR F+++ + A Y +K+ K++G T ++P + +A+ + +
Sbjct: 156 NTSRR--FAYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR 211
Query: 284 ALYVKNIPDNTSTEK-IKELFQRHGEVTKVVMPPGK 318
+ ++N+ E ++E F+ G + K+ +P G+
Sbjct: 212 EIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ 247
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 76/177 (42%), Gaps = 20/177 (11%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
++ P ++ ++RDL + I V + S+ FA++ SKE A+ +++L
Sbjct: 120 LWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 169 HSKELKGKTIRCSLS---ETKNR----------LFIGNVPKNWT-EDEFRKVIEDVGPGV 214
+ +++G T+ +S E R + I N+ E+ R+ E G +
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFG-SI 238
Query: 215 ETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTP-TISWADPK 270
E I + + S N +F ++ N A ++ L N L GN ++S AD K
Sbjct: 239 EKINIPAGQKEHSFNNCCAFXVFENKDSA----ERALQXNRSLLGNREISVSLADKK 291
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE- 167
VF+GG+ E ++R G V EV+++ D+ +G SKG+ FVSF + +K ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 168 --LHSKELK-GKTIR 179
H K+LK G IR
Sbjct: 72 INFHGKKLKLGPAIR 86
>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 = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE- 167
VF+GG+ E ++R G V EV+++ D+ +G SKG+ FVSF + +K ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 168 --LHSKELK-GKTIR 179
H K+LK G IR
Sbjct: 71 INFHGKKLKLGPAIR 85
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
VF+G L EE L +L G + +V + KD+E G+ K F FV F+ E AI L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 169 HSKELKGKTIRCS 181
+ L G+ I S
Sbjct: 78 NGIRLYGRPINVS 90
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 283 KALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGK-RDFGFIHYAERSSALKAVKD 341
+ ++V N+ E + ELF + G +TKV + + GK + FGF+ + S A+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 342 TEKYEIDGK 350
+ G+
Sbjct: 77 LNGIRLYGR 85
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 4/74 (5%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+ + L A+EE L+++ E + + ++G+SKG+AF+ F S E AK+A++
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 169 HSKELKGKTIRCSL 182
+ +E++G+ IR L
Sbjct: 74 NKREIEGRAIRLEL 87
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 40/69 (57%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ GLPK S++++ L G + R++ D+ +G S+G F+ F + A++AI
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 167 ELHSKELKG 175
L+ ++ G
Sbjct: 62 GLNGQKPLG 70
Score = 34.7 bits (78), Expect = 0.076, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEV--TKVVMPPGKSGKRDFGFIHYAERSSALKAVK 340
LYV +P S +++++LF ++G + +++++ R GFI + +R A +A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 47/88 (53%), Gaps = 6/88 (6%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
G VFI L D+ EE L ++ + GD+ VR++ ++ SKG AF F ++E A+K +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 166 ------DELHSKELKGKTIRCSLSETKN 187
E +L G+ ++ L+ T++
Sbjct: 75 AAASLEAEGGGLKLDGRQLKVDLAVTRD 102
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 284 ALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKR--DFGFIHYAERSSALKAVK 340
LYV N+ T+ E+I ELF + G++ K++M K K F F+ Y R+ A A++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Score = 34.7 bits (78), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
L +++G L +EE + +L GD+ ++ + DK + GF FV + S+ A
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94
Query: 162 KKAIDELHSKELKGKTIR 179
+ A+ ++ L + IR
Sbjct: 95 ENAMRYINGTRLDDRIIR 112
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 44/74 (59%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
G +F+ + ++A E+++++ G++ + L D+ +G SKG+A V + + + A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 166 DELHSKELKGKTIR 179
+ L+ E+ G+TI+
Sbjct: 86 EALNGAEIMGQTIQ 99
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ ++I LP E++L ++ +P G V R+++D SG S+G F S E + I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 167 ELHSKELK 174
+ K +K
Sbjct: 85 HFNGKFIK 92
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 280 SQVKALYVKNIPDNTSTEKIKELFQ--RHGEVTKVVMPPGKSGKRDFGFIHYAERSSALK 337
S VK LYV+N+ +TS E I++ F + G V +V RD+ F+H++ R A++
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVE 66
Query: 338 AVKDTEKYEIDG 349
A+K +DG
Sbjct: 67 AMKALNGKVLDG 78
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFE--------VRLMKDKESGESKGFAFVSFRSK 158
S +++ GL + +DL D + G V + + DKE+G+ KG A VS+
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 159 EFAKKAIDELHSKELKGKTIRCSLSETK 186
AK A++ K+ +G ++ SL+ K
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 44/74 (59%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
G +F+ + ++A E+++++ G++ + L D+ +G SKG+A V + + + A A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 166 DELHSKELKGKTIR 179
+ L+ E+ G+TI+
Sbjct: 132 EALNGAEIMGQTIQ 145
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 45/174 (25%), Positives = 78/174 (44%), Gaps = 13/174 (7%)
Query: 178 IRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLY 237
+ S S T LFIGN+ N + E + I ++ +L NR F +V +
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISEL---FAKNDLAVVDVRTGTNRKFGYVDF 61
Query: 238 YNNACADYSRQKMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTE 297
+ D + L K+ GN I PK A+ + L KN+ N + +
Sbjct: 62 --ESAEDLEKALELTG-LKVFGNE--IKLEKPKGRDSKKVRAA--RTLLAKNLSFNITED 114
Query: 298 KIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGKS 351
++KE+F+ E+ ++V GKS + +I + + A K +++ + EIDG+S
Sbjct: 115 ELKEVFEDALEI-RLVSQDGKS--KGIAYIEFKSEADAEKNLEEKQGAEIDGRS 165
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 51/97 (52%), Gaps = 16/97 (16%)
Query: 82 EKPTASVGEDEKDKHAQLLALPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKD 141
EKP G D K A L N L + +E++L+++ E D E+RL+
Sbjct: 86 EKPK---GRDSKKVRAARTLLAKN--------LSFNITEDELKEVFE---DALEIRLVS- 130
Query: 142 KESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTI 178
+ G+SKG A++ F+S+ A+K ++E E+ G+++
Sbjct: 131 -QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 43/174 (24%), Positives = 83/174 (47%), Gaps = 27/174 (15%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMK--DKESGESKGFAFVSFRSKEFAKKAID 166
+FIG L + S +L+ I ++F + D +G ++ F +V F S E +KA+
Sbjct: 16 LFIGNLNPNKSVAELK---VAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL- 71
Query: 167 ELHSKELKGKTIRCSLSETKNR----------LFIGNVPKNWTEDEFRKVIEDVGPGVET 216
EL ++ G I+ L + K R L N+ N TEDE ++V ED
Sbjct: 72 ELTGLKVFGNEIK--LEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFED------A 123
Query: 217 IELIKDPQNPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADPK 270
+E I+ +++G +++ + + A A+ + ++ A ++DG + ++ + K
Sbjct: 124 LE-IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA--EIDGRSVSLYYTGEK 174
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++G + A+ E+L G V V ++ DK SG KGFA++ F KE + ++ L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 169 HSKELKGKTIR 179
+G+ I+
Sbjct: 68 DESLFRGRQIK 78
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
+ + +++G + A+ E+L G V V ++ DK SG KGFA++ F KE
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 162 KKAIDELHSKELKGKTIR 179
+ ++ L +G+ I+
Sbjct: 61 RTSL-ALDESLFRGRQIK 77
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 38/64 (59%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ +++ LP+ +++ L + G + + +++DK +G +G AFV + +E A++AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 167 ELHS 170
L++
Sbjct: 74 ALNN 77
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGE-VTKVVMPPGKSGK-RDFGFIHYAERSSALKAV 339
LYV N+P + +++ +F ++G V K ++ +G+ R F+ Y +R A +A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 34/75 (45%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDE 167
EV L + E L+D+C G+V EV ++ + + G A V F S AK+ +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 168 LHSKELKGKTIRCSL 182
LH + G I L
Sbjct: 68 LHLTSVMGNIIHAQL 82
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 42/163 (25%), Positives = 71/163 (43%), Gaps = 13/163 (7%)
Query: 189 LFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQ 248
LF+GN+ N + E + I DV +L R F +V + + D +
Sbjct: 10 LFVGNLNFNKSAPELKTGISDV---FAKNDLAVVDVRIGMTRKFGYVDF--ESAEDLEKA 64
Query: 249 KMLNANFKLDGNTPTISWADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGE 308
L K+ GN I PK S + L KN+P + +++KE+F+ E
Sbjct: 65 LELTG-LKVFGNE--IKLEKPKGK--DSKKERDARTLLAKNLPYKVTQDELKEVFEDAAE 119
Query: 309 VTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGKS 351
+ ++V GKS + +I + + A K ++ + EIDG+S
Sbjct: 120 I-RLVSKDGKS--KGIAYIEFKTEADAEKTFEEKQGTEIDGRS 159
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 5/65 (7%)
Query: 114 LPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKEL 173
LP ++++L+++ E D E+RL+ + G+SKG A++ F+++ A+K +E E+
Sbjct: 101 LPYKVTQDELKEVFE---DAAEIRLVS--KDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Query: 174 KGKTI 178
G++I
Sbjct: 156 DGRSI 160
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGF--IHYAERSSALKAVKDT 342
L V N+ S I+ELF G + K + +SG R G +H+ R+ ALKA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 96
Query: 343 EKYEIDGK 350
+ +DG+
Sbjct: 97 KGVPLDGR 104
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGF--IHYAERSSALKAVKDT 342
L V N+ S I+ELF G + K + +SG R G +H+ R+ ALKA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 96
Query: 343 EKYEIDGK 350
+ +DG+
Sbjct: 97 KGVPLDGR 104
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMP--PGKSGKRDFGFIHYAERSSALKAVKDT 342
L V N+ TS + ++ +F+++G V V +P P R F F+ + +R A A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 343 EKYEIDGK 350
+ E+DG+
Sbjct: 76 DGAELDGR 83
Score = 35.0 bits (79), Expect = 0.066, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 38/82 (46%)
Query: 111 IGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS 170
+ L S + LR + E G V +V + ++ + +GFAFV F + A+ A +
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 171 KELKGKTIRCSLSETKNRLFIG 192
EL G+ +R ++ R G
Sbjct: 78 AELDGRELRVQVARYGRRDLSG 99
>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 = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIG--DVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+ V++G +++ L + IG DV E++ +++ +G+SKG+A V S+ K
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 165 IDELHSKELKGKTI 178
++ L K L G+ +
Sbjct: 116 LELLPGKVLNGEKV 129
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSF--RSKEFAKKAID 166
V++G + ++ +DL G + + ++ DK SG KG+A++ F R+ A A+D
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 167 ELHSKELKGKTIR 179
E +G+TI+
Sbjct: 99 E---TVFRGRTIK 108
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 42/65 (64%), Gaps = 5/65 (7%)
Query: 114 LPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKEL 173
L + +E++L+++ E D E+RL+ + G+SKG A++ F+S+ A+K ++E E+
Sbjct: 24 LSFNITEDELKEVFE---DALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 78
Query: 174 KGKTI 178
G+++
Sbjct: 79 DGRSV 83
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 273 PDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAER 332
P S + L KN+ N + +++KE+F+ E+ ++V GKS + +I +
Sbjct: 7 PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-RLVSQDGKS--KGIAYIEFKSE 63
Query: 333 SSALKAVKDTEKYEIDGKS 351
+ A K +++ + EIDG+S
Sbjct: 64 ADAEKNLEEKQGAEIDGRS 82
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGF--IHYAERSSALKAVKDT 342
L V N+ S I+ELF G + K + +SG R G +H+ R+ ALKA+K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVHFERRADALKAMKQY 149
Query: 343 EKYEIDGK 350
+ +DG+
Sbjct: 150 KGVPLDGR 157
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 111 IGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS 170
+ +P + DLR + G + +V ++ ++ SKGF FV+F + A +A ++LH
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 77
Query: 171 KELKGKTI 178
++G+ I
Sbjct: 78 TVVEGRKI 85
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 4/66 (6%)
Query: 185 TKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACAD 244
T RL + N+P + + + R++ G + +E+I + + ++GF FV + N+A AD
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIFNERG---SKGFGFVTFENSADAD 69
Query: 245 YSRQKM 250
+R+K+
Sbjct: 70 RAREKL 75
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 283 KALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDT 342
K L+V NIP ++++F + G++ V + + G + FGF+ + + A +A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 343 EKYEIDGK 350
++G+
Sbjct: 76 HGTVVEGR 83
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 36/60 (60%), Gaps = 6/60 (10%)
Query: 280 SQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
++VK L+V+N+ + E +++ F G++ +V +D+ F+H+ +R +A+KA+
Sbjct: 13 AKVKVLFVRNLATTVTEEILEKSFSEFGKLERV------KKLKDYAFVHFEDRGAAVKAM 66
>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 = 0.025, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 111 IGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS 170
+ +P + DLR + G + +V ++ ++ SKGF FV+F + A +A ++LH
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 91
Query: 171 KELKGKTI 178
++G+ I
Sbjct: 92 TVVEGRKI 99
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 269 PKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIH 328
P+ + ++ SQ K L+V NIP ++++F + G++ V + + G + FGF+
Sbjct: 16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 75
Query: 329 YAERSSALKAVKDTEKYEIDGK 350
+ + A +A + ++G+
Sbjct: 76 FENSADADRAREKLHGTVVEGR 97
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 188 RLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSR 247
RL + N+P + + + R++ G + +E+I N ++GF FV + N+A AD +R
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIF---NERGSKGFGFVTFENSADADRAR 86
Query: 248 QKM 250
+K+
Sbjct: 87 EKL 89
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 278 AASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPP--GKSG---KRDFGFIHYAER 332
+S L++KN+ +T+ E +K +F + G + + K+G FGF+ Y +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 333 SSALKAVKDTEKYEIDG 349
A KA+K + + +DG
Sbjct: 61 EQAQKALKQLQGHTVDG 77
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGE---SKGFAFVSFRSKEFAKK 163
S +FI L +EE L+ + +G + + K K S GF FV ++ E A+K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 164 AIDELHSKELKGKTIRCSLSE 184
A+ +L + G + +SE
Sbjct: 66 ALKQLQGHTVDGHKLEVRISE 86
>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 = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKR-DFGFIHYAERSSALKAVKDTE 343
LYV N+ T+ E+I ELF + G++ K++M K F F+ Y R+ A A++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 344 KYEIDGK 350
+D +
Sbjct: 81 GTRLDDR 87
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++G L +EE + +L GD+ ++ + DK + GF FV + S+ A+ A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAMRYI 79
Query: 169 HSKELKGKTIR 179
+ L + IR
Sbjct: 80 NGTRLDDRIIR 90
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
VF L DL D +G V +VR++ D+ S SKG A+V F + AI L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-L 86
Query: 169 HSKELKGKTIRCSLSET-KNRL 189
+ L G I S+ KNRL
Sbjct: 87 TGQRLLGVPIIVQASQAEKNRL 108
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 266 WADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGK-SGK-RD 323
W DP + P+ A K L+V + +T+ K++ F+ +G + ++ M K SGK R
Sbjct: 89 W-DPHNDPN--AQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 324 FGFIHYAERSSALKAVKDTEKYEIDGKSHL 353
+ FI Y A K + +IDG+ L
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 34/70 (48%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ + D +E LR E G + + ++ K SG+ +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 169 HSKELKGKTI 178
K++ G+ +
Sbjct: 165 DGKKIDGRRV 174
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 35.4 bits (80), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
++F+ LP D + + L+D G V + E+G+SKG V F S E A++A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR 66
Query: 167 ELHSKELKGKTI 178
++ +L G+ I
Sbjct: 67 MMNGMKLSGREI 78
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S +F+ LP D + + L+D G V + E+G+SKG V F S E A++A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR 63
Query: 167 ELHSKELKGKTI 178
++ +L G+ I
Sbjct: 64 MMNGMKLSGREI 75
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
V+I G P DA+ +D+++ E G V +++ + KG FV F S E AKK ++
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 70
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 35.4 bits (80), Expect = 0.053, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 12/89 (13%)
Query: 102 LPPNGSEVFIGGLP-KDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEF 160
+PP S +FIG LP K+ S+EDL + P G + ++ + F F+ F + +
Sbjct: 7 IPPK-SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQS 57
Query: 161 AKKAIDELHSKELK-GKTIRCSLSETKNR 188
+ AI E S+E+ GK + +S + R
Sbjct: 58 VRDAI-ECESQEMNFGKKLILEVSSSNAR 85
>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 = 35.4 bits (80), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
V+I G P DA+ +D+++ E G V +++ + KG FV F S E AKK ++
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 168
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 266 WADPKSTPDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGK-SGK-RD 323
W DP + P +A K L+V + +T+ K++ F+ +G + ++ M K SGK R
Sbjct: 89 W-DPHNDP--NAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 324 FGFIHYAERSSALKAVKDTEKYEIDGKSHL 353
+ FI Y A K + +IDG+ L
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 34/70 (48%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+F+ + D +E LR E G + + ++ K SG+ +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 169 HSKELKGKTI 178
K++ G+ +
Sbjct: 165 DGKKIDGRRV 174
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.0 bits (79), Expect = 0.059, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 107 SEVFIGGLP-KDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
S +FIG LP K+ S+EDL + P G + ++ + F F+ F + + + AI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
Query: 166 DELHSKELK-GKTIRCSLSETKNR 188
E S+E+ GK + +S + R
Sbjct: 75 -ECESQEMNFGKKLILEVSSSNAR 97
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.0 bits (79), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S VF+G D +E++LR+ GDV +V + K + FAFV+F + A+
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60
Query: 167 ELHSKELKGKTIRCSLSETKN 187
E +KG ++ S +E K+
Sbjct: 61 E--DLIIKGISVHISNAEPKH 79
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 183 SETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNAC 242
S + +F+G + TEDE R+ G + D P R F+FV + ++
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGD-------VMDVFIPKPFRAFAFVTFADDQI 54
Query: 243 ADYSRQKMLNANFKLDGNTPTISWADPK 270
A Q + + + G + IS A+PK
Sbjct: 55 A----QSLCGEDLIIKGISVHISNAEPK 78
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.0 bits (79), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGF--IHYAERSSALKAVKDT 342
L V N+ S I+ELF G + K + +SG R G +H+ ++ ALKA+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAMKQY 89
Query: 343 EKYEIDGK 350
+DG+
Sbjct: 90 NGVPLDGR 97
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 35.0 bits (79), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 37/165 (22%), Positives = 70/165 (42%), Gaps = 12/165 (7%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAF--VSFRSKEFAKKA 164
+ V + LPK ++ + + G + V D K F F + F + A A
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHV----DVADSLKKNFRFARIEFARYDGALAA 60
Query: 165 IDELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQ 224
I + H + + I L+E L++ N P ++T+ R +++D+ +I L
Sbjct: 61 ITKTHKVVGQNEIIVSHLTECT--LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF 118
Query: 225 NPSRNRGFSFVLYYNNACADYSRQKMLNANFKLDGNTPTISWADP 269
N SR F+++ + A Y +K+ K++G T ++P
Sbjct: 119 NTSRR--FAYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNP 159
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEK 344
+YV N+P + T+ I+++F ++G + + + + G F F+ + + A AV +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 345 YEIDG-KSHLHFP 356
Y+ DG + + FP
Sbjct: 84 YDYDGYRLRVEFP 96
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 105 NGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
N +++G LP D +D+ D+ G + ++ L K++ G FAFV F A+ A
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDA 77
Query: 165 I 165
+
Sbjct: 78 V 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 35.0 bits (79), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+++ +G + + ++LR E G V E ++KD +AFV E A +AI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 167 ELHSKELKGKTIRCSLSETKNRLFIG 192
L + E +GK + LS ++ R G
Sbjct: 63 GLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEK 344
L+V NI + ++++ F+ +G V + + +D+ F+H A++A++ +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIV------KDYAFVHMERAEDAVEAIRGLDN 66
Query: 345 YEIDGK 350
E GK
Sbjct: 67 TEFQGK 72
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 187 NRLFIGNVPKNWTEDEFRKVIEDVGPGVETIELIKD 222
+L +GN+ T E R E+ GP +E +++KD
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIEC-DIVKD 45
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 34.7 bits (78), Expect = 0.076, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 107 SEVFIGGLP-KDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
S +FIG LP K+ S+EDL + P G + ++ + F F+ F + + + AI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
Query: 166 DELHSKELK-GKTIRCSLSETKNR 188
E S+E+ GK + +S + R
Sbjct: 75 -EXESQEMNFGKKLILEVSSSNAR 97
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 133 VFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHS----KELKGKTIRCSLSET 185
V +RL+KDK++ +++GFAFV S A + + L S ++ GKTI +++
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 107 SEVFIGGLP-KDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
S +FIG LP K+ S+EDL + P G + ++ + F F+ F + + + AI
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 54
Query: 166 DELHSKELK-GKTIRCSLSETKNR 188
E S+E+ GK + +S + R
Sbjct: 55 -ECESQEMNFGKKLILEVSSSNAR 77
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGF--IHYAERSSALKAVKDT 342
L V N+ S I+ELF G + K + +SG R G +H+ ++ ALKA K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAXKQY 90
Query: 343 EKYEIDGK 350
+DG+
Sbjct: 91 NGVPLDGR 98
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
V+I G P DA+ +D+++ E G V ++ + KG FV F S E AKK ++
Sbjct: 114 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 170
>pdb|1X4O|A Chain A, Solution Structure Of Surp Domain In Splicing Factor 4
Length = 78
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 196 KNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFVLYYNNACADYSRQKM 250
KN E + + I D GP VETI L QN N+ FSF+ N+ Y RQK+
Sbjct: 18 KNLAE-KLARFIADGGPEVETIAL----QNNRENQAFSFLYDPNSQGYRYYRQKL 67
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
V+I G P DA+ +D+++ E G V ++ + KG FV F S E AKK ++
Sbjct: 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 169
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 190 FIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFV 235
F+GN+P + TE+ ++ G + + L ++P NP R +GF +
Sbjct: 23 FLGNLPYDVTEESIKEFFR--GLNISAVRLPREPSNPERLKGFGYA 66
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGES-KGFAFVSF 155
F+G LP D +EE +++ + ++ VRL ++ + E KGF + F
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 68
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 123 LRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIRCSL 182
L L G V + D+ +G++KGF FV S AKK I H K L
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL--------- 79
Query: 183 SETKNRLFI 191
+ K+RLF+
Sbjct: 80 -DLKHRLFL 87
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 120 EEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIR 179
++ L L G V + D+ +G++KGF FV S AKK I H K L
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL------ 79
Query: 180 CSLSETKNRLFI 191
+ K+RLF+
Sbjct: 80 ----DLKHRLFL 87
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 190 FIGNVPKNWTEDEFRKVIEDVGPGVETIELIKDPQNPSRNRGFSFV 235
F+GN+P + TE+ ++ G + + L ++P NP R +GF +
Sbjct: 19 FLGNLPYDVTEESIKEFFR--GLNISAVRLPREPSNPERLKGFGYA 62
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGES-KGFAFVSF 155
F+G LP D +EE +++ + ++ VRL ++ + E KGF + F
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 34/67 (50%)
Query: 273 PDHSAAASQVKALYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAER 332
D S S V +++KN+ + + + + F G + + ++G + +GF+H+ +
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQ 61
Query: 333 SSALKAV 339
+A +A+
Sbjct: 62 EAAERAI 68
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 136 VRLMKDKESGESKGFAFVSFRSKEFAK--KAIDELH-SKELKGKTIRCSLSETKNR 188
VR++KDK++ ++GFAF+ + E A+ + + LH + GKTI ++ R
Sbjct: 55 VRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAKGSKR 110
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 72/169 (42%), Gaps = 16/169 (9%)
Query: 55 SKAGASEKDQSAEANRNDDDTPHVEEEEKPTASVGEDEKDKHAQL-------------LA 101
S AGAS + S+ A N +D P + + +V + EK + QL L
Sbjct: 6 SDAGASNEYDSSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLV 65
Query: 102 LPPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFA 161
+P G + LP S+ +C P+ + E +LM K+ G S S SKE
Sbjct: 66 MPTGGGKSLCYQLPALCSDGFTLVIC-PLISLMEDQLMVLKQLGISATMLNAS-SSKEHV 123
Query: 162 KKAIDELHSKELKGKTIRCSLSET-KNRLFIGNVPKNWTEDEFRKVIED 209
K E+ +K + K I + + K+++F+ + K + F ++ D
Sbjct: 124 KWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVD 172
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 32.7 bits (73), Expect = 0.31, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 103 PPNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAK 162
PP + +IG +P A+E DL L + G + + + + KG F+ + + E A
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAA 77
Query: 163 KAIDELHSKELKGKTIR 179
I L + +G+ +R
Sbjct: 78 VCIVALANFPFQGRNLR 94
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 110 FIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELH 169
++G LP + + D+ + + + + VRL++DK++ + KGF +V F + K+A+
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYD 76
Query: 170 SKELKGKTIRCSLSETKNR 188
L +++R ++E + +
Sbjct: 77 GALLGDRSLRVDIAEGRKQ 95
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P ++V++G LP+DA DL+ +G V +RL + AF+ + A++
Sbjct: 17 PLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQG----PRRRAFLHYPDSAAAQQ 71
Query: 164 AIDELHSKELKGKTIRCSLSETK 186
A+ L L T+R +L+ +
Sbjct: 72 AVSCLQGLRLGTDTLRVALARQQ 94
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P +V++G L + ++ +L G + V + ++ GFAFV F A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAAD 125
Query: 164 AIDELHSKELKGKTIRCSLSETKNR 188
A+ EL + L G +R LS + R
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEKR 150
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 31/60 (51%)
Query: 299 IKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEKYEIDGKSHLHFPVF 358
I ++F + G++T P + + F+ YA + A+ AVK+ + Y++D + +F
Sbjct: 38 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPG 317
+ KN+P T +I+E F R G + +V++P G
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG 45
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.6 bits (70), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 299 IKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAVKDTEKYEID 348
I ++F + G++T P + + F+ YA + A+ AVK+ + Y++D
Sbjct: 24 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSK---EFAKKAI 165
V + GLP S +DL+D GDV + KD G V + K E+A + +
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKL 70
Query: 166 DELHSKELKGKT 177
D+ + +G+T
Sbjct: 71 DDTKFRSHEGET 82
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
GS+VF+G +D + E+L+ G+V +V + K + FAFV+F + A+
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSLC 65
Query: 166 DELHSKELKGKTIRCSLSETK-NRL 189
E +KG ++ S +E K N+L
Sbjct: 66 GE--DLIIKGISVHISNAEPKHNKL 88
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGE-SKGFAFVSFRSKEFAKKAI 165
++V IG L ++ +++ + ++ G + + + ++ SKG+A+V F + + A+KA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 166 DELHSKELKGKTIRCS 181
+ ++ G+ I +
Sbjct: 65 KHMDGGQIDGQEITAT 80
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 31.2 bits (69), Expect = 1.00, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 39/75 (52%)
Query: 109 VFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDEL 168
+++ P ++ ++RDL + I V + S+ FA++ SKE A+ +++L
Sbjct: 6 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 65
Query: 169 HSKELKGKTIRCSLS 183
+ +++G T+ +S
Sbjct: 66 NGLKIEGYTLVTKVS 80
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 104 PNGSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKK 163
P +V++G L + ++ +L G + V + ++ GFAFV F A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAAD 125
Query: 164 AIDELHSKELKGKTIRCSLSETKNR 188
A+ +L + L G +R LS + R
Sbjct: 126 AVRDLDGRTLCGCRVRVELSNGEKR 150
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 47/107 (43%), Gaps = 7/107 (6%)
Query: 108 EVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMK--DKESGESKGFAFVSFRSKEFAKKAI 165
+VF+GGLP D E+++ G + K K KG+AF+ F+ + + I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 166 DELHSKELKGKTIRCSLSETKNRLFIGNVPKNWTEDEFRKVIEDVGP 212
D ++ GK C S T + P N ++ +F + D GP
Sbjct: 70 DACLEED--GKLYLCVSSPTIKDKPVQIRPWNLSDSDF---VMDSGP 111
>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 = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 10/55 (18%), Positives = 30/55 (54%)
Query: 285 LYVKNIPDNTSTEKIKELFQRHGEVTKVVMPPGKSGKRDFGFIHYAERSSALKAV 339
+++KN+ + + + + F G + + ++G + +GF+H+ + +A +A+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 120 EEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIR 179
EE ++ E G+V E+ + D G +V FR +E A+KA+ +L+++ G+ I
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 180 CSLS 183
LS
Sbjct: 100 AELS 103
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
S + + LP+D++ C+ + D+ + +K +K AFV+ + E A+ AI
Sbjct: 6 SGILVKNLPQDSN-------CQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 167 ELHSKELKGKTIRCSLSETKNRLFIG 192
H +GK + L T L G
Sbjct: 59 MFHQYSFRGKDLIVQLQPTDALLCSG 84
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 100 LALPPNGSEV-FIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSK 158
+ LPP + + +I LP + E++ D+ G + ++R+ + E++G A+V +
Sbjct: 1 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDI 57
Query: 159 EFAKKAIDEL 168
AK A+D L
Sbjct: 58 FDAKNAVDHL 67
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAID 166
+ V + GLP S +DL+D GDV + +D G V F KE A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 69
Query: 167 ELHSKELK 174
+L + + +
Sbjct: 70 KLDNTKFR 77
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 109 VFIGGLPKDASEEDLRDLC----EPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKA 164
+++ L +E DL L E G + R+M +G +G AF++F +KE A +A
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQA 83
Query: 165 IDELHSKELKGKTIRCSLSETKNR 188
+ ++ +L GK + + K +
Sbjct: 84 LHLVNGYKLYGKILVIEFGKNKKQ 107
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKE---FAKK 163
+ V + GLP S +DL+D GDV + +D G V F KE +A +
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 68
Query: 164 AIDELHSKELKGKT 177
+D + +G+T
Sbjct: 69 KLDNTKFRSHEGET 82
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 107 SEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKE---FAKK 163
+ V + GLP S +DL+D GDV + +D G V F KE +A +
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 68
Query: 164 AIDELHSKELKGKT 177
+D + +G+T
Sbjct: 69 KLDNTKFRSHEGET 82
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 106 GSEVFIGGLPKDASEEDLRDLCEPIGDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAI 165
GS VF+ L + L+++ G V +++DK+ G+S+G V+F A +AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI 73
Query: 166 DELHSKELKGKTIRCSLSE 184
+ + L + + + E
Sbjct: 74 SMFNGQLLFDRPMHVKMDE 92
>pdb|3J20|Q Chain Q, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 158
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 213 GVETIELIKDPQNPSRNRGFSFVL 236
G+ +++L KDP NP+RN + +L
Sbjct: 59 GIPSVKLFKDPDNPNRNLTITRIL 82
>pdb|1OXY|A Chain A, Crystallographic Analysis Of Oxygenated And Deoxygenated
States Of Arthropod Hemocyanin Shows Unusual Differences
Length = 628
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 61/132 (46%), Gaps = 17/132 (12%)
Query: 123 LRDLCEPIGDVFEVRLMKDKES-GESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIRCS 181
LRDL GD+ +++ +E +S +V S++ + K +DELH ++ G + S
Sbjct: 258 LRDL----GDIEISEMVRMRERILDSIHLGYVI--SEDGSHKTLDELHGTDILGALVESS 311
Query: 182 LSETKNRLFIGNVPKNWTEDEFRKVIEDVG-----PGV--ETIELIKDPQNPSRNRGFSF 234
E+ N + GN+ NW ++ + G PGV +T ++DP + +R
Sbjct: 312 Y-ESVNHEYYGNL-HNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDN 369
Query: 235 VLY-YNNACADY 245
+ + Y N Y
Sbjct: 370 IFHEYKNTLKPY 381
>pdb|1LLA|A Chain A, Crystal Structure Of Deoxygenated Limulus Polyphemus
Subunit Ii Hemocyanin At 2.18 Angstroms Resolution:
Clues For A Mechanism For Allosteric Regulation
pdb|1NOL|A Chain A, Oxygenated Hemocyanin (Subunit Type Ii)
Length = 628
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 61/132 (46%), Gaps = 17/132 (12%)
Query: 123 LRDLCEPIGDVFEVRLMKDKES-GESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIRCS 181
LRDL GD+ +++ +E +S +V S++ + K +DELH ++ G + S
Sbjct: 258 LRDL----GDIEISEMVRMRERILDSIHLGYVI--SEDGSHKTLDELHGTDILGALVESS 311
Query: 182 LSETKNRLFIGNVPKNWTEDEFRKVIEDVG-----PGV--ETIELIKDPQNPSRNRGFSF 234
E+ N + GN+ NW ++ + G PGV +T ++DP + +R
Sbjct: 312 Y-ESVNHEYYGNL-HNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDN 369
Query: 235 VLY-YNNACADY 245
+ + Y N Y
Sbjct: 370 IFHEYKNTLKPY 381
>pdb|1LL1|A Chain A, Hydroxo Bridge Met Form Hemocyanin From Limulus
Length = 628
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 61/132 (46%), Gaps = 17/132 (12%)
Query: 123 LRDLCEPIGDVFEVRLMKDKES-GESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIRCS 181
LRDL GD+ +++ +E +S +V S++ + K +DELH ++ G + S
Sbjct: 258 LRDL----GDIEISEMVRMRERILDSIHLGYVI--SEDGSHKTLDELHGTDILGALVESS 311
Query: 182 LSETKNRLFIGNVPKNWTEDEFRKVIEDVG-----PGV--ETIELIKDPQNPSRNRGFSF 234
E+ N + GN+ NW ++ + G PGV +T ++DP + +R
Sbjct: 312 Y-ESVNHEYYGNL-HNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIFYNWHRFIDN 369
Query: 235 VLY-YNNACADY 245
+ + Y N Y
Sbjct: 370 IFHEYKNTLKPY 381
>pdb|1AC6|A Chain A, Crystal Structure Of A Variable Domain Mutant Of A T-Cell
Receptor Alpha Chain
pdb|1AC6|B Chain B, Crystal Structure Of A Variable Domain Mutant Of A T-Cell
Receptor Alpha Chain
Length = 110
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 131 GDVFEVRLMKDKESGESKGFAFVSFRSKEFAKKAIDELHSKELKGKTIRCSLSETKNRLF 190
G F R +DKE G S+GF + +KE + + +E C+LS N+L
Sbjct: 42 GPQFLFRASRDKEKGSSRGFE--ATYNKEATSFHLQKASVQESDSAVYYCALSGGNNKLT 99
Query: 191 IG 192
G
Sbjct: 100 FG 101
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
0.311 0.130 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,161,828
Number of Sequences: 62578
Number of extensions: 429919
Number of successful extensions: 1716
Number of sequences better than 100.0: 204
Number of HSP's better than 100.0 without gapping: 155
Number of HSP's successfully gapped in prelim test: 49
Number of HSP's that attempted gapping in prelim test: 1322
Number of HSP's gapped (non-prelim): 379
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
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: 52 (24.6 bits)