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= 019327
(342 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/154 (27%), Positives = 77/154 (50%), Gaps = 5/154 (3%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKD-PQNANQNRGFAFIEYYNHACAEYS 108
++F+G VPR W E D+R+ + G V I +++D QN Q++G F+ +Y A +
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 109 RQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGK 168
+ + N K + P P ++E + A + + L++ + K T++ ++ +F+ G+
Sbjct: 76 QNALHNMKVLPGMHHPI--QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 169 ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
I + I G R FV F R+ A A+K
Sbjct: 134 IEECRILRGPDGLSRG-CAFVTFTTRAMAQTAIK 166
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 63/134 (47%), Gaps = 14/134 (10%)
Query: 8 EAKGYAFVTFRTKELASQAIEELNS----------CELKGKKIKCSAAQAKHRLFIGNVP 57
++KG FVTF T++ A +A L++ ++K + + A +LFIG +
Sbjct: 57 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 116
Query: 58 RNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMSNPKF 117
+ E+D+R + G + +++ P +RG AF+ + A A+ + + M +
Sbjct: 117 KKCTENDIRVMFSSFGQ-IEECRILRGPDGL--SRGCAFVTFTTRAMAQTAIKAMHQAQT 173
Query: 118 KLDDNAP-TVSWAD 130
++P V +AD
Sbjct: 174 MEGCSSPMVVKFAD 187
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/154 (27%), Positives = 77/154 (50%), Gaps = 5/154 (3%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKD-PQNANQNRGFAFIEYYNHACAEYS 108
++F+G VPR W E D+R+ + G V I +++D QN Q++G F+ +Y A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 109 RQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGK 168
+ + N K + P P ++E + A + + L++ + K T++ ++ +F+ G+
Sbjct: 64 QNALHNMKVLPGMHHPI--QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 169 ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
I + I G R FV F R+ A A+K
Sbjct: 122 IEECRILRGPDGLSRG-CAFVTFTTRAMAQTAIK 154
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 63/134 (47%), Gaps = 14/134 (10%)
Query: 8 EAKGYAFVTFRTKELASQAIEELNS----------CELKGKKIKCSAAQAKHRLFIGNVP 57
++KG FVTF T++ A +A L++ ++K + + A +LFIG +
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 104
Query: 58 RNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMSNPKF 117
+ E+D+R + G + +++ P +RG AF+ + A A+ + + M +
Sbjct: 105 KKCTENDIRVMFSSFGQ-IEECRILRGPDGL--SRGCAFVTFTTRAMAQTAIKAMHQAQT 161
Query: 118 KLDDNAP-TVSWAD 130
++P V +AD
Sbjct: 162 MEGCSSPMVVKFAD 175
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/157 (30%), Positives = 82/157 (52%), Gaps = 10/157 (6%)
Query: 47 AKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+K L + +P+N +++ R IG + S +LV+D + Q+ G+ F+ Y + AE
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGE-IESCKLVRD-KITGQSLGYGFVNYIDPKDAE 58
Query: 107 YSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHH 166
+ ++ +L VS+A P SSA+ + LYV LPK +TQ L++LF+ +
Sbjct: 59 KAINTLNG--LRLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQY 112
Query: 167 GK-ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
G+ IT ++ G R GF+ F +R A +A+K
Sbjct: 113 GRIITSRILVDQVTGVSRG-VGFIRFDKRIEAEEAIK 148
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQ+ + LF G+I + K + YGFV++ + A KA+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 205 EKYEIDGQVLDCSLAKPQA 223
+ + + S A+P +
Sbjct: 65 NGLRLQTKTIKVSYARPSS 83
>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 = 65.5 bits (158), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 42/154 (27%), Positives = 75/154 (48%), Gaps = 5/154 (3%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKD-PQNANQNRGFAFIEYYNHACAEYS 108
+ F+G VPR W E D+R+ + G V I +++D QN Q++G F+ +Y A +
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 109 RQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGK 168
+ + N K + P P ++E + A + + L++ + K T++ ++ F+ G+
Sbjct: 64 QNALHNXKVLPGXHHPI--QXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 169 ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
I + I G R FV F R+ A A+K
Sbjct: 122 IEECRILRGPDGLSRG-CAFVTFTTRAXAQTAIK 154
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 52/109 (47%), Gaps = 13/109 (11%)
Query: 8 EAKGYAFVTFRTKELASQAIEELNSCEL----------KGKKIKCSAAQAKHRLFIGNVP 57
++KG FVTF T++ A +A L++ ++ K + + A +LFIG +
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXIS 104
Query: 58 RNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+ E+D+R + G + +++ P +RG AF+ + A A+
Sbjct: 105 KKCTENDIRVXFSSFGQ-IEECRILRGPDGL--SRGCAFVTFTTRAXAQ 150
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 46/157 (29%), Positives = 82/157 (52%), Gaps = 10/157 (6%)
Query: 47 AKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+K L + +P+N +D+ + IG + S +LV+D + Q+ G+ F+ Y + A+
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGD-IESCKLVRD-KITGQSLGYGFVNYSDPNDAD 60
Query: 107 YSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHH 166
+ ++ KL VS+A P SSA+ + LYV LPK ++Q +++LF+ +
Sbjct: 61 KAINTLNG--LKLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMSQKEMEQLFSQY 114
Query: 167 GK-ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
G+ IT ++ G R GF+ F +R A +A+K
Sbjct: 115 GRIITSRILLDQATGVSRG-VGFIRFDKRIEAEEAIK 150
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQD K LF G I + K + YGFV++++ + A KA+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 205 EKYEIDGQVLDCSLAKPQA 223
++ + + S A+P +
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
>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 = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 85/170 (50%), Gaps = 7/170 (4%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
R+++G++ GED +R+A GP + SI++ D +++GFAF+EY A+ +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVTM-KHKGFAFVEYEVPEAAQLAL 87
Query: 110 QKMSNPKF---KLDDNAPT-VSWADPR-NAESSAASQVKALYVKNLPKDITQDRLKELFA 164
++M++ + P+ + A P + + A +YV ++ +D++ D +K +F
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 147
Query: 165 HHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVL 214
GKI + + YGF+ + + S+ A+ + +++ GQ L
Sbjct: 148 AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 19/107 (17%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCS-----------------AAQAKHRLF 52
KG+AFV + E A A+E++NS L G+ IK A+A +R++
Sbjct: 70 KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY 129
Query: 53 IGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
+ +V ++ +DD++ G + S L +DP +++G+ FIEY
Sbjct: 130 VASVHQDLSDDDIKSVFEAFGK-IKSATLARDP-TTGKHKGYGFIEY 174
>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 = 60.8 bits (146), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 41/170 (24%), Positives = 85/170 (50%), Gaps = 7/170 (4%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
R+++G++ GED +R+A GP + SI++ D +++GFAF+EY A+ +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWDSVTM-KHKGFAFVEYEVPEAAQLAL 72
Query: 110 QKMSNPKF---KLDDNAPT-VSWADPR-NAESSAASQVKALYVKNLPKDITQDRLKELFA 164
++M++ + P+ + A P + + A +YV ++ +D++ D +K +F
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 165 HHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVL 214
GKI + + YGF+ + + S+ A+ + +++ GQ L
Sbjct: 133 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 182
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 19/107 (17%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKC-----------------SAAQAKHRLF 52
KG+AFV + E A A+E++NS L G+ IK A+A +R++
Sbjct: 55 KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY 114
Query: 53 IGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
+ +V ++ +DD++ G + S L +DP +++G+ FIEY
Sbjct: 115 VASVHQDLSDDDIKSVFEAFGK-IKSCTLARDP-TTGKHKGYGFIEY 159
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 58.9 bits (141), Expect = 4e-09, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 50/89 (56%)
Query: 43 SAAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
S + RLFIG +P+ +++ + + K+ GV+ + + + +NRGFAF+EY +H
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 103 ACAEYSRQKMSNPKFKLDDNAPTVSWADP 131
A +R+K+ + +L + V WA+P
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEP 91
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 77/155 (49%), Gaps = 10/155 (6%)
Query: 48 KHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEY 107
+ L + +P+N +D++R + IG V S +L++D + A + G+ F+ Y AE
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYVTAKDAER 59
Query: 108 SRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHG 167
+ ++ +L VS+A P SS + LY+ LP+ +TQ ++++F+ G
Sbjct: 60 AINTLNG--LRLQSKTIKVSYARP----SSEVIKDANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 168 KITKV-VIPPAKPGQERSRYGFVHFAERSSAMKAL 201
+I V+ G R F+ F +RS A +A+
Sbjct: 114 RIINSRVLVDQTTGLSRG-VAFIRFDKRSEAEEAI 147
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQD L+ LF+ G++ + K YGFV++ A +A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 205 EKYEIDGQVLDCSLAKPQAD 224
+ + + S A+P ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 47/173 (27%), Positives = 77/173 (44%), Gaps = 27/173 (15%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIG-PGVISIELVKDPQNANQNRGFAFIEYYNHACAEYS 108
RLF+GN+P + E+D ++ + G P + I N++RGF FI + AE +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI---------NRDRGFGFIRLESRTLAEIA 74
Query: 109 RQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGK 168
+ ++ K R A+ AL VKNL ++ + L++ F+ G
Sbjct: 75 KAELDGTILK------------SRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGP 122
Query: 169 ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVLDCSLAKP 221
+ K V+ G+ + GFV FA + A KAL+ DG L + +P
Sbjct: 123 VEKAVVVVDDRGRATGK-GFVEFAAKPPARKALERCG----DGAFLLTTTPRP 170
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 77/155 (49%), Gaps = 10/155 (6%)
Query: 48 KHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEY 107
+ L + +P+N +D++R + IG V S +L++D + A + G+ F+ Y AE
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYVTAKDAER 59
Query: 108 SRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHG 167
+ ++ +L VS+A P SS + LY+ LP+ +TQ ++++F+ G
Sbjct: 60 AINTLNG--LRLQSKTIKVSYARP----SSEVIKDANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 168 KITKV-VIPPAKPGQERSRYGFVHFAERSSAMKAL 201
+I V+ G R F+ F +RS A +A+
Sbjct: 114 RIINSRVLVDQTTGLSRG-VAFIRFDKRSEAEEAI 147
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQD L+ LF+ G++ + K YGFV++ A +A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 205 EKYEIDGQVLDCSLAKPQAD 224
+ + + S A+P ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 60/106 (56%), Gaps = 9/106 (8%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
SS ++VK L+V+NL +T++ L++ F+ GK+ +V ++ Y F+HF ER
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERD 56
Query: 196 SAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSNSQKSALNPT 241
A+KA++ +++G+ ++ AKP DQK +++A P+
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKP-PDQKRKERKAQRQAASGPS 101
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 25/37 (67%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
K YAF+ F ++ A +A+EE+N +L+G+ I+ A+
Sbjct: 45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK 81
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 83/170 (48%), Gaps = 7/170 (4%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
R+++G++ GED +R+A GP + SI+ D +++GFAF+EY A+ +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDXSWDSVTX-KHKGFAFVEYEVPEAAQLAL 71
Query: 110 QKMSNPKF---KLDDNAPT-VSWADPR-NAESSAASQVKALYVKNLPKDITQDRLKELFA 164
++ ++ + P+ + A P + + A +YV ++ +D++ D +K +F
Sbjct: 72 EQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 165 HHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVL 214
GKI + + YGF+ + + S+ A+ + +++ GQ L
Sbjct: 132 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 53/107 (49%), Gaps = 19/107 (17%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCS-----------------AAQAKHRLF 52
KG+AFV + E A A+E+ NS L G+ IK A+A +R++
Sbjct: 54 KGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY 113
Query: 53 IGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
+ +V ++ +DD++ G + S L +DP +++G+ FIEY
Sbjct: 114 VASVHQDLSDDDIKSVFEAFGK-IKSCTLARDP-TTGKHKGYGFIEY 158
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 75/155 (48%), Gaps = 23/155 (14%)
Query: 48 KHRLFIGNVPRNWGEDDMRKAVTKIG-PGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+ RLF+GN+P + E++MRK K G G + I ++++GF FI AE
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------HKDKGFGFIRLETRTLAE 72
Query: 107 YSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHH 166
++ ++ DN P + A +L V+NLP+ ++ + L+E F+
Sbjct: 73 IAKVEL--------DNMPLRG----KQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVF 120
Query: 167 GKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
G++ + V+ G+ + G V F+ + +A KAL
Sbjct: 121 GQVERAVVIVDDRGRPSGK-GIVEFSGKPAARKAL 154
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 6/95 (6%)
Query: 125 TVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERS 184
T+ + R +Q L+V NLP DIT++ +++LF +GK +V I K
Sbjct: 5 TIDLKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----- 59
Query: 185 RYGFVHFAERSSAMKALKNTEKYEIDGQVLDCSLA 219
+GF+ R+ A A + + G+ L A
Sbjct: 60 -FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 93
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRLFIGNVPRNWGEDDMRKAV 69
KG+ F+ T+ LA A EL++ L+GK+++ A L + N+P+ + + +A
Sbjct: 58 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAF 117
Query: 70 TKIGPGVISIELVKD 84
+ G ++ +V D
Sbjct: 118 SVFGQVERAVVIVDD 132
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 48/194 (24%), Positives = 90/194 (46%), Gaps = 22/194 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 70
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 71 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 125
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 181
Query: 222 QADQKTSGGSNSQK 235
+ Q+ + S+SQ+
Sbjct: 182 LSKQEMASASSSQR 195
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 47 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 105
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 157
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 48/194 (24%), Positives = 90/194 (46%), Gaps = 22/194 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 69
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 70 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 180
Query: 222 QADQKTSGGSNSQK 235
+ Q+ + S+SQ+
Sbjct: 181 LSKQEMASASSSQR 194
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 104
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 156
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 48/194 (24%), Positives = 90/194 (46%), Gaps = 22/194 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 68
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 69 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 123
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 179
Query: 222 QADQKTSGGSNSQK 235
+ Q+ + S+SQ+
Sbjct: 180 LSKQEMASASSSQR 193
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 45 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 103
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 155
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 87/170 (51%), Gaps = 9/170 (5%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L++GN+ + ED +++ GP + +I+++ D N N N +AF+EY+ A + Q
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGP-IANIKIMIDKNNKNVN--YAFVEYHQSHDANIALQ 59
Query: 111 KMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHH-GKI 169
++ ++++N ++WA ++ S++ L+V +L ++ + L+ F +
Sbjct: 60 TLNGK--QIENNIVKINWA--FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 170 TKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVLDCSLA 219
+ V+ + G R YGFV F + A A+ + + +++G+ L + A
Sbjct: 116 SGHVMWDMQTGSSRG-YGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
+ LYV NL K IT+D LK+ F G I + I K + Y FV + + A AL+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 203 NTEKYEIDGQVLDCSLAKPQADQKTS 228
+I+ ++ + A Q+ Q +S
Sbjct: 60 TLNGKQIENNIVKINWA-FQSQQSSS 84
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 27/45 (60%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
M +G ++GY FV+F +++ A A++ + +L G+ ++ + A
Sbjct: 120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 46/190 (24%), Positives = 86/190 (45%), Gaps = 22/190 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 62
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 63 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 117
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 173
Query: 222 QADQKTSGGS 231
+ Q+ + S
Sbjct: 174 LSKQEMASAS 183
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 39 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 97
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 149
>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: Composition-based stats.
Identities = 28/98 (28%), Positives = 54/98 (55%), Gaps = 10/98 (10%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
SS +S + L++ NLP++ T+ ++ LF +GK+ + I YGFVH +++
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53
Query: 196 SAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSNS 233
+A A++N Y++ G ++ +K ++ K S G +S
Sbjct: 54 AAEDAIRNLHHYKLHGVNINVEASKNKS--KASSGPSS 89
Score = 28.5 bits (62), Expect = 6.4, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 43 SAAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIE 98
S + +LFIGN+PR E ++R + G V+ +++K N GF IE
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGK-VLECDIIK-------NYGFVHIE 50
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 83/184 (45%), Gaps = 22/184 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 69
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 70 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 180
Query: 222 QADQ 225
+ Q
Sbjct: 181 LSKQ 184
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 104
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 156
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 45/184 (24%), Positives = 83/184 (45%), Gaps = 22/184 (11%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + ++ +R + G + +++DP N ++RGF F+ Y A E
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRDP-NTKRSRGFGFVTY---ATVEEVD 67
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQ-------VKALYVKNLPKDITQDRLKEL 162
M+ K+D +P+ A S SQ VK ++V + +D + L++
Sbjct: 68 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 122
Query: 163 FAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-IDGQVLDCSLAKP 221
F +GKI + I + ++ + FV F + S K + +KY ++G +C + K
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 178
Query: 222 QADQ 225
+ Q
Sbjct: 179 LSKQ 182
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 15/114 (13%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH----------- 49
M+ ++ ++G+ FVT+ T E A+ ++ G+ ++ A ++
Sbjct: 44 MRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTV 102
Query: 50 -RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
++F+G + + E +R + G + IE++ D + + + RGFAF+ + +H
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGK-IEVIEIMTD-RGSGKKRGFAFVTFDDH 154
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 60/120 (50%), Gaps = 8/120 (6%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ------AKHRLFIG 54
M+ +G + GYAFV F ++ + +AI+ LN ++ K++K S A+ L++
Sbjct: 36 MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVT 95
Query: 55 NVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMSN 114
N+PR +D + K G ++ +++D + RG AF+ Y A+ + ++N
Sbjct: 96 NLPRTITDDQLDTIFGKYG-SIVQKNILRDKLTG-RPRGVAFVRYNKREEAQEAISALNN 153
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 76/152 (50%), Gaps = 10/152 (6%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L + +P++ + ++ IGP + + +++D + + G+AF+++ + ++ + +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTG-YSYGYAFVDFTSEMDSQRAIK 63
Query: 111 KMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKIT 170
++ + + VS+A P ES + LYV NLP+ IT D+L +F +G I
Sbjct: 64 VLNGITVR--NKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIV 117
Query: 171 -KVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
K ++ G+ R FV + +R A +A+
Sbjct: 118 QKNILRDKLTGRPRG-VAFVRYNKREEAQEAI 148
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 42/102 (41%), Gaps = 9/102 (8%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKI-TKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
L V LP+D+T L LF G I T ++ K G Y FV F + +A+K
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG-YAFVDFTSEMDSQRAIKV 64
Query: 204 TEKYEIDGQVLDCSLAKPQADQKTSGGSNSQKSALNPTYPPH 245
+ + L S A+P GG + + + L T P
Sbjct: 65 LNGITVRNKRLKVSYARP-------GGESIKDTNLYVTNLPR 99
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ------AKHRLFIGNVPRNWGED 63
K +AF+ FR+ + +QA+ + +G+ +K H+LFIG +P +D
Sbjct: 53 KNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDD 111
Query: 64 DMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYN 101
+++ +T GP + + LVKD ++G+AF EY +
Sbjct: 112 QVKELLTSFGP-LKAFNLVKDSATG-LSKGYAFCEYVD 147
Score = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 29/131 (22%), Positives = 57/131 (43%), Gaps = 24/131 (18%)
Query: 47 AKHRLFIGNVPRNWGED---DMRKAVTKIG-----PG--VISIELVKDPQNANQNRGFAF 96
+ RL++GN+P E+ D A ++G PG V+++++ NQ++ FAF
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-------NQDKNFAF 57
Query: 97 IEYYNHACAEYSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQ 156
+E+ + + + Q M+ + + R + L++ LP +
Sbjct: 58 LEFRS---VDETTQAMAFDGIIFQGQSLKIR----RPHDYQPLPGAHKLFIGGLPNYLND 110
Query: 157 DRLKELFAHHG 167
D++KEL G
Sbjct: 111 DQVKELLTSFG 121
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+K +G +KGYAF + + QAI LN +L KK+ A
Sbjct: 129 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
>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 = 28/98 (28%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ------AKHRLFIGNVPRNWGED 63
K +AF+ FR+ + +QA+ + +G+ +K H+LFIG +P +D
Sbjct: 51 KNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDD 109
Query: 64 DMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYN 101
+++ +T GP + + LVKD ++G+AF EY +
Sbjct: 110 QVKELLTSFGP-LKAFNLVKDSATG-LSKGYAFCEYVD 145
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 29/131 (22%), Positives = 57/131 (43%), Gaps = 24/131 (18%)
Query: 47 AKHRLFIGNVPRNWGED---DMRKAVTKIG-----PG--VISIELVKDPQNANQNRGFAF 96
+ RL++GN+P E+ D A ++G PG V+++++ NQ++ FAF
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-------NQDKNFAF 55
Query: 97 IEYYNHACAEYSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQ 156
+E+ + + + Q M+ + + R + L++ LP +
Sbjct: 56 LEFRS---VDETTQAMAFDGIIFQGQSLKIR----RPHDYQPLPGAHKLFIGGLPNYLND 108
Query: 157 DRLKELFAHHG 167
D++KEL G
Sbjct: 109 DQVKELLTSFG 119
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+K +G +KGYAF + + QAI LN +L KK+ A
Sbjct: 127 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKD-PQNANQNRGFAFIEYYNHACAEYS 108
++F+G VPR W E D+R+ + G V I +++D QN Q++G F+ +Y A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 109 RQKMSNPK 116
+ + N K
Sbjct: 64 QNALHNMK 71
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 19/41 (46%), Positives = 28/41 (68%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
MK D+G +KGY F+TF E A +A+E+LN EL G+ ++
Sbjct: 38 MKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMR 78
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 138 AASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSA 197
+S LYV +L +IT+D L+ +F GKI +V+ YGF+ F++ A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 198 MKALKNTEKYEIDGQ 212
+AL+ +E+ G+
Sbjct: 61 RRALEQLNGFELAGR 75
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 49/86 (56%), Gaps = 4/86 (4%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKALKN 203
+++ L D T+D L+E F +G +T + I P RSR +GF+ F + SS + +K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKI-MKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 204 TEKYEIDGQVLDCSLAKPQADQKTSG 229
++ +DG+V+D A P+ +Q +G
Sbjct: 65 --QHILDGKVIDPKRAIPRDEQDKTG 88
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 32/154 (20%), Positives = 67/154 (43%), Gaps = 10/154 (6%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
++FIG + + ED++R+ K G V ++++KDP ++RGF F+ + + +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGT-VTDLKIMKDPATG-RSRGFGFLSFEKPSSVD--- 59
Query: 110 QKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKI 169
++ + LD A PR+ + ++V + D+ +E F+ G I
Sbjct: 60 -EVVKTQHILDGKVIDPKRAIPRDEQDKTGK----IFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 170 TKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
+ K + +GFV + + + +N
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKH 49
M KD+G+++G+ FVT+ + + + + + K +KI+ A+ +H
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPRH 167
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 76/155 (49%), Gaps = 14/155 (9%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L++G++ + E + + + GP ++SI + +D ++ G+A++ + A AE +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAERALD 75
Query: 111 KMSNPKFKLDDNAPT-VSWA--DPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHG 167
M+ F + P + W+ DP S S V +++KNL K I L + F+ G
Sbjct: 76 TMN---FDVIKGKPVRIMWSQRDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128
Query: 168 KITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
I + + G + YGFVHF + +A +A++
Sbjct: 129 NILSCKVVCDENGSKG--YGFVHFETQEAAERAIE 161
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/150 (22%), Positives = 69/150 (46%), Gaps = 15/150 (10%)
Query: 11 GYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRL--------FIGNVPRNWGE 62
GYA+V F+ A +A++ +N +KGK ++ +Q L FI N+ ++
Sbjct: 58 GYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDN 117
Query: 63 DDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMSNPKFKLDDN 122
+ + G ++S ++V D N ++G+ F+ + AE + +KM+ L+D
Sbjct: 118 KALYDTFSAFG-NILSCKVVCD---ENGSKGYGFVHFETQEAAERAIEKMNG--MLLNDR 171
Query: 123 APTVS-WADPRNAESSAASQVKALYVKNLP 151
V + + E+ ++ K Y ++P
Sbjct: 172 KVFVGRFKSRKEREAELGARAKEFYPYDVP 201
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 5 DSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
D +KGY FV F T+E A +AIE++N L +K+
Sbjct: 138 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%)
Query: 144 ALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
+LYV +L D+T+ L E F+ G I + + + Y +V+F + + A +AL
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 204 TEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
I G+ + ++ + SG N
Sbjct: 77 MNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 33/100 (33%), Positives = 59/100 (59%), Gaps = 9/100 (9%)
Query: 133 NAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFA 192
+ + ++VK L+V+NL +T++ L++ F+ GK+ +V ++ Y FVHF
Sbjct: 6 SGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFE 57
Query: 193 ERSSAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
+R +A+KA+ EI+G+ ++ LAKP D+K SG S+
Sbjct: 58 DRGAAVKAMDEMNGKEIEGEEIEIVLAKP-PDKKRSGPSS 96
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 76/155 (49%), Gaps = 14/155 (9%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L++G++ + E + + + GP ++SI + +D ++ G+A++ + A AE +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRD-MITRRSLGYAYVNFQQPADAERALD 70
Query: 111 KMSNPKFKLDDNAPT-VSWA--DPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHG 167
M+ F + P + W+ DP S S V +++KNL K I L + F+ G
Sbjct: 71 TMN---FDVIKGKPVRIMWSQRDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 168 KITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
I + + G + YGFVHF + +A +A++
Sbjct: 124 NILSCKVVCDENGSKG--YGFVHFETQEAAERAIE 156
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 54/111 (48%), Gaps = 12/111 (10%)
Query: 11 GYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRL--------FIGNVPRNWGE 62
GYA+V F+ A +A++ +N +KGK ++ +Q L FI N+ ++
Sbjct: 53 GYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDN 112
Query: 63 DDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMS 113
+ + G ++S ++V D N ++G+ F+ + AE + +KM+
Sbjct: 113 KALYDTFSAFG-NILSCKVVCDE---NGSKGYGFVHFETQEAAERAIEKMN 159
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 5 DSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
D +KGY FV F T+E A +AIE++N L +K+
Sbjct: 133 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%)
Query: 144 ALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
+LYV +L D+T+ L E F+ G I + + + Y +V+F + + A +AL
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 204 TEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
I G+ + ++ + SG N
Sbjct: 72 MNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 33/105 (31%), Positives = 55/105 (52%), Gaps = 17/105 (16%)
Query: 133 NAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQ-ERSR----YG 187
+ + S VK LYV+NL +++ +++ F + KPG ER + Y
Sbjct: 6 SGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNN-----------IKPGAVERVKKIRDYA 54
Query: 188 FVHFAERSSAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
FVHF+ R A++A+K +DG ++ +LAKP D+ +SG S+
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP-VDKDSSGPSS 98
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V NL ++ ++ELFA G + K + + G+ VHF R+ A+KA+K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQY 149
Query: 205 EKYEIDGQVLDCSLAKPQAD 224
+ +DG+ +D L Q D
Sbjct: 150 KGVPLDGRPMDIQLVASQID 169
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V NL ++ ++ELFA G + K + + G+ VHF R+ A+KA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD-VHFERRADALKAMKQY 96
Query: 205 EKYEIDGQVLDCSLAKPQAD 224
+ +DG+ +D L Q D
Sbjct: 97 KGVPLDGRPMDIQLVASQID 116
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V NL ++ ++ELFA G + K + + G+ VHF R+ A+KA+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD-VHFERRADALKAMKQY 96
Query: 205 EKYEIDGQVLDCSLAKPQAD 224
+ +DG+ +D L Q D
Sbjct: 97 KGVPLDGRPMDIQLVASQID 116
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 72/168 (42%), Gaps = 21/168 (12%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKI----GPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
LF+GN+ N +++ ++ + V+ + + R F ++++ AE
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRI-------GMTRKFGYVDF---ESAE 59
Query: 107 YSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHH 166
+ + K+ N + P+ +S + L KNLP +TQD LKE+F
Sbjct: 60 DLEKALELTGLKVFGNE--IKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDA 117
Query: 167 GKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVL 214
+I V +K G+ + ++ F + A K + + EIDG+ +
Sbjct: 118 AEIRLV----SKDGKSKG-IAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 7 GEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
G++KG A++ F+T+ A + EE E+ G+ I
Sbjct: 127 GKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 41/81 (50%)
Query: 139 ASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAM 198
A +YV NLP +T + L +F+ +GK+ KV I K ++ F+ F ++ SA
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 199 KALKNTEKYEIDGQVLDCSLA 219
+ ++ G+V+ S+A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93
Score = 35.8 bits (81), Expect = 0.032, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
MK KD+ ++KG AF+ F K+ A +N+ +L G+ IK S A
Sbjct: 49 MKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 138 AASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSA 197
A + L V LP T+ LKE F+ G++ V + +GFV F E +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 198 MKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSNS 233
+K + ++++ IDG+ DC L P + Q G +S
Sbjct: 71 VKVM--SQRHMIDGRWCDCKL--PNSKQSQDSGPSS 102
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKALKN 203
+++ L +++T+D + E+F+ +GKI + +P + S+ Y +V F A KALK+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 204 TEKYEIDGQVLDCS 217
+ +IDGQ + +
Sbjct: 67 MDGGQIDGQEITAT 80
Score = 31.2 bits (69), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 25/39 (64%)
Query: 9 AKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQA 47
+KGYA+V F + A +A++ ++ ++ G++I +A A
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 27/41 (65%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
M ++G +KGY F+TF E A +A+E+LN EL G+ +K
Sbjct: 59 MMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 133 NAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFA 192
N + +A ++ LYV +L +IT+D L+ +F G+I + + YGF+ F+
Sbjct: 18 NLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 193 ERSSAMKALKNTEKYEIDGQ 212
+ A KAL+ +E+ G+
Sbjct: 77 DSECAKKALEQLNGFELAGR 96
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 77/173 (44%), Gaps = 13/173 (7%)
Query: 40 IKCSAAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
++ S + LFIGN+ N +++ A++++ +L NR F ++++
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISEL---FAKNDLAVVDVRTGTNRKFGYVDF 61
Query: 100 YNHACAEYSRQKMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRL 159
AE + + K+ N + P+ +S + L KNL +IT+D L
Sbjct: 62 ---ESAEDLEKALELTGLKVFGNE--IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDEL 116
Query: 160 KELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQ 212
KE+F +I V ++ G+ + ++ F + A K L+ + EIDG+
Sbjct: 117 KEVFEDALEIRLV----SQDGKSKG-IAYIEFKSEADAEKNLEEKQGAEIDGR 164
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%)
Query: 142 VKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
++ L V +P + + +L++LF +G I V I + ++ YGFV F SSA +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 202 KNTEKYEIDGQVLDCSLA 219
+ I + L +LA
Sbjct: 102 AGLNGFNILNKRLKVALA 119
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHR 50
+++ +++GY FV F++ A QAI LN + K++K + A + H+
Sbjct: 78 RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 141 QVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
+ K L + NL T++ L+E+F K T + +P + G+ + Y F+ FA A +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGKSKG-YAFIEFASFEDAKEA 69
Query: 201 LKNTEKYEIDGQVLDCSLAKPQAD 224
L + K EI+G+ + L P+
Sbjct: 70 LNSCNKREIEGRAIRLELQGPRGS 93
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 7 GEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
G++KGYAF+ F + E A +A+ N E++G+ I+
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR 84
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 75/152 (49%), Gaps = 10/152 (6%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L + +P++ + ++ IGP + + + +D + + G+AF+++ + ++ + +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKTG-YSFGYAFVDFTSEXDSQRAIK 74
Query: 111 KMSNPKFKLDDNAPTVSWADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKIT 170
++ + + VS+A P ES + LYV NLP+ IT D+L +F +G I
Sbjct: 75 VLNGITVR--NKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIV 128
Query: 171 -KVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
K ++ G+ R FV + +R A +A+
Sbjct: 129 QKNILRDKLTGRPRG-VAFVRYNKREEAQEAI 159
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/116 (25%), Positives = 43/116 (37%), Gaps = 14/116 (12%)
Query: 130 DPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFV 189
DPR + ++ L V LP+D T L LF G I I Y FV
Sbjct: 9 DPRASNTN-------LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFV 61
Query: 190 HFAERSSAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSNSQKSALNPTYPPH 245
F + +A+K + + L S A+P GG + + + L T P
Sbjct: 62 DFTSEXDSQRAIKVLNGITVRNKRLKVSYARP-------GGESIKDTNLYVTNLPR 110
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSC 33
++ K +G +G AFV + +E A +AI LN+
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNV 165
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/93 (25%), Positives = 44/93 (47%)
Query: 139 ASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAM 198
AS L+V L D + L+++F+ +G+I++VV+ + Q +GFV F A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 199 KALKNTEKYEIDGQVLDCSLAKPQADQKTSGGS 231
A+ +DG+ + A +D ++ S
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+K +++ ++G+ FVTF + A A+ +N + G++I+ A
Sbjct: 45 VKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 40/79 (50%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQD K LF G I + K + YGFV++++ + A KA+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 205 EKYEIDGQVLDCSLAKPQA 223
++ + + S A+P +
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 18/85 (21%), Positives = 47/85 (55%)
Query: 142 VKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
+++++V N+P + T+++LK++F+ G + + + + YGF + ++ +A+ A+
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 202 KNTEKYEIDGQVLDCSLAKPQADQK 226
+N E G+ L A + +++
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKE 92
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
+F+GN+P E+ ++ +++GP V+S LV D + + +G+ F EY + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGP-VVSFRLVYD-RETGKPKGYGFCEYQDQETALSAMR 68
Query: 111 KMSNPKF 117
++ +F
Sbjct: 69 NLNGREF 75
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 3/80 (3%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
K L+VK L +D T++ LKE F G + ++ + G + +GFV F A A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKG-FGFVDFNSEEDAKAAKE 72
Query: 203 NTEKYEIDGQVLDCSLAKPQ 222
E EIDG + AKP+
Sbjct: 73 AMEDGEIDGNKVTLDWAKPK 92
Score = 32.3 bits (72), Expect = 0.35, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+++G +KG+ FV F ++E A A E + E+ G K+ A+ K
Sbjct: 48 RETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 18/88 (20%), Positives = 46/88 (52%), Gaps = 7/88 (7%)
Query: 45 AQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHAC 104
+Q LF+ + + E+ ++++ G + +V D + + ++GF F+++ +
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFD----GSVRARIVTDRETGS-SKGFGFVDFNSEED 66
Query: 105 AEYSRQKMSNPKFKLDDNAPTVSWADPR 132
A+ +++ M + + +D N T+ WA P+
Sbjct: 67 AKAAKEAMEDGE--IDGNKVTLDWAKPK 92
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGK-ITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
LYV LPK ++Q +++LF+ +G+ IT ++ G R GF+ F +R A +A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRG-VGFIRFDKRIEAEEAIK 61
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/118 (23%), Positives = 52/118 (44%), Gaps = 29/118 (24%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCS-------------------------- 43
K +AF+ FR+ + +QA+ + +G+ +K
Sbjct: 51 KNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTV 109
Query: 44 AAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYN 101
+ H+LFIG +P +D +++ +T GP + + LVKD ++G+AF EY +
Sbjct: 110 VPDSAHKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATG-LSKGYAFCEYVD 165
Score = 31.2 bits (69), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+K +G +KGYAF + + QAI LN +L KK+ A
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+++TQD L+ LF+ G++ + K YGFV++ A +A+
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 205 EKYEIDGQVLDCSLAKP 221
+ + + S A+P
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 138 AASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAK--PGQERSR-YGFVHFAER 194
+S L++KNL T++ LK +F+ G I I K G S +GFV + +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 195 SSAMKALKNTEKYEIDGQVLDCSLAK 220
A KALK + + +DG L+ +++
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISE 86
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 36/77 (46%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP++ TQD L+ LF+ G++ + K YGFV++ A +A+
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 205 EKYEIDGQVLDCSLAKP 221
+ + + S A+P
Sbjct: 82 NGLRLQSKTIKVSYARP 98
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITK-VVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
++V LP T L++ F G I + VVI + G+ R YGFV A+R++A +A K+
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG-YGFVTMADRAAAERACKD 78
Query: 204 TEKYEIDGQVLDCSLA 219
IDG+ + +LA
Sbjct: 79 PNPI-IDGRKANVNLA 93
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 144 ALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
LYV NL T++++ ELF+ G I K+++ K + + FV + R+ A A++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 204 TEKYEIDGQVL 214
+D +++
Sbjct: 101 INGTRLDDRII 111
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGP-GVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
L++GN+ E+ + + +K G I + L K + A GF F+EYY+ A AE +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC---GFCFVEYYSRADAENAM 98
Query: 110 QKMSNPKFKLDDNAPTVSW 128
+ ++ +LDD W
Sbjct: 99 RYINGT--RLDDRIIRTDW 115
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 9/79 (11%)
Query: 141 QVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHF---AERSS 196
Q + L++ L + T++ L+ + GK+T V+ P +RSR +GFV F AE +
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM-RDPASKRSRGFGFVTFSSMAEVDA 84
Query: 197 AMKALKNTEKYEIDGQVLD 215
AM A + IDG+V++
Sbjct: 85 AMAA----RPHSIDGRVVE 99
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
++V +P + + L+E F G +T+VV+ Q +GF+ F + S +A+ N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 205 EKYEIDGQVLDCSLAKPQADQKTSGGSN 232
++I G+ ++ A+P+ D K+SG S+
Sbjct: 72 HFHDIMGKKVEVKRAEPR-DSKSSGPSS 98
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 49 HRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYS 108
+++F+G +P N GE ++R+ K G V + ++ D + + RGF FI + + E S
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGV-VTEVVMIYDAEK-QRPRGFGFITFED----EQS 64
Query: 109 RQKMSNPKF-KLDDNAPTVSWADPRNAESSAAS 140
+ N F + V A+PR+++SS S
Sbjct: 65 VDQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPS 97
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
SS +S + LY+ NL +T D L++LF +P A +S Y FV + +++
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQN 55
Query: 196 SAMKALKN-TEKYEIDGQVLDC 216
A++A++ + K E+ G++++
Sbjct: 56 WAIRAIETLSGKVELHGKIMEV 77
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 30/120 (25%), Positives = 53/120 (44%), Gaps = 9/120 (7%)
Query: 106 EYSRQKMSNPKFKLDDNAPTVSWADPRNAESSAAS--QVKALYVKNLPKDITQDRLKELF 163
EY + K LD+ +P + + A + ++ + VKNLPK Q+++ + F
Sbjct: 3 EYGHHARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYF 62
Query: 164 AHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYE-----IDGQVLDCSL 218
H G I V + A ++ R+ + FA A+ A+ T K I + +C+L
Sbjct: 63 KHCGPIIHVDV--ADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTL 120
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 75/158 (47%), Gaps = 11/158 (6%)
Query: 51 LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQ 110
L+ N P ++ + ++R + I +SI L N +R FA+I+ + A Y +
Sbjct: 120 LWXTNFPPSYTQRNIRDLLQDINVVALSIRL--PSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 111 KMSNPKFKLDDNAPTVSWADPRNAESSAAS-QVKALYVKNLPKDIT-QDRLKELFAHHGK 168
K++ K + VS ++ + +A+ + + + ++NL ++ ++ L+E F G
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGS 237
Query: 169 ITKVVIPPAKPGQERSRY----GFVHFAERSSAMKALK 202
I K+ IP GQ+ + F F + SA +AL+
Sbjct: 238 IEKINIP---AGQKEHSFNNCCAFXVFENKDSAERALQ 272
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKALKN 203
+++ L TQ+ L+E F G++ + ++ P +RSR +GFV F +++ K L
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 204 TEKYEIDGQVLDCSLAKPQADQ 225
+ ++E+D + +D +A P+ Q
Sbjct: 87 S-RHELDSKTIDPKVAFPRRAQ 107
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 7/93 (7%)
Query: 140 SQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMK 199
+Q L+V NLP DIT++ +++LF +GK +V I K +GF+ R+ A
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEI 66
Query: 200 ALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
A + + G+ L A A TSG S+
Sbjct: 67 AKVELDNMPLRGKQLRVRFACHSASL-TSGPSS 98
Score = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 10/68 (14%)
Query: 48 KHRLFIGNVPRNWGEDDMRKAVTKIG-PGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+ RLF+GN+P + E++MRK K G G + I ++++GF FI AE
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------HKDKGFGFIRLETRTLAE 65
Query: 107 YSRQKMSN 114
++ ++ N
Sbjct: 66 IAKVELDN 73
Score = 28.5 bits (62), Expect = 5.0, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
KG+ F+ T+ LA A EL++ L+GK+++ A
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 86
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 49 HRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYN 101
H+LFIG +P +D +++ +T GP + + LVKD ++G+AF EY +
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATG-LSKGYAFCEYVD 52
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
+K +G +KGYAF + + QAI LN +L KK+
Sbjct: 34 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 73
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LFIG + R E ++ K GP + + L+KD +++RGFAFI + N A A+ +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGP-ISEVLLIKD--RTSKSRGFAFITFENPADAKNAA 65
Query: 110 QKMS 113
+ M+
Sbjct: 66 KDMN 69
Score = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
+ +++G+AF+TF A A +++N L GK IK A+
Sbjct: 44 TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 141 QVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
QV LYVKNL I +RL++ F+ G IT + G +GFV F+ A KA
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSSPEEATKA 71
Query: 201 LKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
+ + + L +LA+ + +++ SG S+
Sbjct: 72 VTEMNGRIVATKPLYVALAQ-RKEERQSGPSS 102
Score = 31.6 bits (70), Expect = 0.63, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 5 DSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+ G +KG+ FV F + E A++A+ E+N + K + + AQ K
Sbjct: 50 EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 1/93 (1%)
Query: 128 WADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYG 187
W DP N ++ K L+V + D T+ +L+ F +G I ++ + +K + Y
Sbjct: 89 W-DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 188 FVHFAERSSAMKALKNTEKYEIDGQVLDCSLAK 220
F+ + A K+ + +IDG+ + + +
Sbjct: 148 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 3/76 (3%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKALKN 203
+++ L TQ+ L+E F G++ + ++ P +RSR +GFV F +++ K L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 204 TEKYEIDGQVLDCSLA 219
+ ++E+D + +D +A
Sbjct: 62 S-RHELDSKTIDPKVA 76
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V NL ++ ++ELFA G + K + + G+ VHF ++ A+KA+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD-VHFERKADALKAMKQY 89
Query: 205 EKYEIDGQVLDCSLA 219
+DG+ ++ L
Sbjct: 90 NGVPLDGRPMNIQLV 104
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKC 42
+G +KGYAF+ FR E ++ A+ LN +L + +KC
Sbjct: 40 TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 76
Score = 34.7 bits (78), Expect = 0.079, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKAL 201
+ +Y+ ++P D T++++ +L ++ G + + + P RS+ Y F+ F + S+ A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMM-FDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 202 KNTEKYEIDGQVLDC 216
+N Y++ + L C
Sbjct: 62 RNLNGYQLGSRFLKC 76
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 39/83 (46%)
Query: 130 DPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFV 189
DP N ++ K L+V + D T+ +L+ F +G I ++ + +K + Y F+
Sbjct: 90 DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 190 HFAERSSAMKALKNTEKYEIDGQ 212
+ A K+ + +IDG+
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGR 172
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 1/93 (1%)
Query: 139 ASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAM 198
A ++ L+V L TQ+ L+ F+ +G++ VI K + +GFV F + +
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72
Query: 199 KALKNTEKYEIDGQVLDCSLAKPQADQKTSGGS 231
L + + +DG+ +D P+ Q + S
Sbjct: 73 TVLA-SRPHTLDGRNIDPKPCTPRGMQPSGPSS 104
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHAC 104
+LF+G + + ++ +R ++ G V+ ++KD + NQ+RGF F+++ + C
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGE-VVDCVIMKD-KTTNQSRGFGFVKFKDPNC 70
>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 = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKC 42
+G +KGYAF+ FR E ++ A+ LN +L + +KC
Sbjct: 41 TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 77
Score = 34.3 bits (77), Expect = 0.095, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKAL 201
+ +Y+ ++P D T++++ +L ++ G + + + P RS+ Y F+ F + S+ A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMM-FDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 202 KNTEKYEIDGQVLDC 216
+N Y++ + L C
Sbjct: 63 RNLNGYQLGSRFLKC 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 5 DSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
D +KGY FV F T+E A +AIE++N L +K+
Sbjct: 46 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 81
Score = 35.0 bits (79), Expect = 0.065, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 129 ADPRNAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGF 188
ADP S S V +++KNL K I L + F+ G I + + G + YGF
Sbjct: 2 ADP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGF 55
Query: 189 VHFAERSSAMKALK 202
VHF + +A +A++
Sbjct: 56 VHFETQEAAERAIE 69
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.6 bits (83), Expect = 0.023, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+Y + +T +++ F+ G+I ++ + P K Y FV F+ SA A+ +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVSV 81
Query: 205 EKYEIDGQVLDCSLAKPQADQKTSGGSN 232
I+G V+ C K D TSG S+
Sbjct: 82 NGTTIEGHVVKCYWGKESPDM-TSGPSS 108
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKC 42
KGY+FV F T E A+ AI +N ++G +KC
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 36.2 bits (82), Expect = 0.024, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 142 VKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
++ +YV NL T +++KELF+ GK+ V + + ++ +GFV E S + +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAI 59
Query: 202 KNTEKYEIDGQVLDCSLAKPQ 222
+ + G+ + + A P+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPK 80
>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 = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+G++KGY FV+F K A AI+++ L G++I+ + A K
Sbjct: 44 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 36.2 bits (82), Expect = 0.028, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 146 YVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKALKNT 204
+V L D ++ LK+ F G++ I P RSR +GF+ F + +S K L
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIK-XDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 205 EKYEIDGQVLD 215
E + +DG+V+D
Sbjct: 74 E-HRLDGRVID 83
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
+ F+G + + + D++ TK G V+ + DP N ++RGF FI + + A E
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGE-VVDCTIKXDP-NTGRSRGFGFILFKDAASVE 67
>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 = 36.2 bits (82), Expect = 0.028, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKC 42
+G +KGYAF+ FR E ++ A+ LN +L + +KC
Sbjct: 42 TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 78
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKAL 201
+ +Y+ ++P D T++++ +L ++ G + + + P RS+ Y F+ F + S+ A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMM-FDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 202 KNTEKYEIDGQVLDC 216
+N Y++ + L C
Sbjct: 64 RNLNGYQLGSRFLKC 78
>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 = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 7/71 (9%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+++KNL K I L + F+ G I + + G + YGFVHF + +A +A++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIE-- 63
Query: 205 EKYEIDGQVLD 215
+++G +L+
Sbjct: 64 ---KMNGMLLN 71
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 5 DSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
D +KGY FV F T+E A +AIE++N L +K+
Sbjct: 40 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 141 QVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
++ + VKNLPK Q+++ + F H G I V + A ++ R+ + FA A+ A
Sbjct: 3 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV--ADSLKKNFRFARIEFARYDGALAA 60
Query: 201 LKNTEKYE-----IDGQVLDCSL 218
+ T K I + +C+L
Sbjct: 61 ITKTHKVVGQNEIIVSHLTECTL 83
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 36 KGKKIKCSAAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFA 95
+G + RL + N+P + + D+R+ + G ++ +E++ N ++GF
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIF---NERGSKGFG 72
Query: 96 FIEYYNHACAEYSRQKM 112
F+ + N A A+ +R+K+
Sbjct: 73 FVTFENSADADRAREKL 89
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 140 SQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMK 199
SQ K L+V N+P L+++F GKI V I + G + +GFV F + A +
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADR 84
Query: 200 ALKNTEKYEIDGQVLDCSLA 219
A + ++G+ ++ + A
Sbjct: 85 AREKLHGTVVEGRKIEVNNA 104
Score = 32.0 bits (71), Expect = 0.47, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 9 AKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+KG+ FVTF A +A E+L+ ++G+KI+ + A A+
Sbjct: 68 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
LYV NLP+ IT D+L +F +G I + I K FV + +R A +A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.040, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHFAERSSAMKAL 201
+ V+N+P Q ++ELF+ G++ V +P G R +GFV F + A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>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 = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+G++KGY FV+F K A AI+++ L G++I+ + A K
Sbjct: 53 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKV-VIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
++V +L +IT + +K FA G+I+ V+ G+ + YGFV F + A A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQ 76
Query: 204 TEKYEIDGQVLDCSLA--KPQADQKT 227
+ G+ + + A KP A + T
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKST 102
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
RL + N+P + + D+R+ + G ++ +E++ N ++GF F+ + N A A+ +R
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIF---NERGSKGFGFVTFENSADADRAR 72
Query: 110 QKM 112
+K+
Sbjct: 73 EKL 75
Score = 32.0 bits (71), Expect = 0.49, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 9 AKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+KG+ FVTF A +A E+L+ ++G+KI+ + A A+
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 93
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALK 202
K L+V N+P L+++F GKI V I + G + +GFV F + A +A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 73
Query: 203 NTEKYEIDGQVLDCSLA 219
++G+ ++ + A
Sbjct: 74 KLHGTVVEGRKIEVNNA 90
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.068, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+YV NLP DI ++++F +G I + + + G + FV F + A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP---FAFVEFEDPRDAEDAVYGR 81
Query: 205 EKYEIDGQVLDCSLAKPQADQKTSGGSNS 233
+ Y+ DG L P++ + T G +S
Sbjct: 82 DGYDYDGYRLRVEF--PRSGRGTGSGPSS 108
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
L++ +P+++ + LK LF GKI ++ + + F+ + ER SA+KA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 34.3 bits (77), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
+LFIG +PRN E D++ + G + + ++KD + ++G AF+ Y
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGK-IYELTVLKD-RFTGMHKGCAFLTY 62
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.7 bits (78), Expect = 0.075, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
M+ D+G +KGYAF+ F + + + AIE +N L + I S A K
Sbjct: 39 MRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK 86
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%)
Query: 137 SAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSS 196
S +Q +YV L + +++ L ELF G + +P + + YGFV F
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 197 AMKALKNTEKYEIDGQ 212
A A+K + ++ G+
Sbjct: 70 ADYAIKIMDMIKLYGK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 34.7 bits (78), Expect = 0.086, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
+G+AFV F E A+ AI+ +N EL G+ I+ + A+
Sbjct: 47 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 34.7 bits (78), Expect = 0.086, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
+G+AFV F E A+ AI+ +N EL G+ I+ + A+
Sbjct: 49 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
S + L KNL +IT+D LKE+F +I V ++ G+ + ++ F +
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKG-IAYIEFKSEA 64
Query: 196 SAMKALKNTEKYEIDGQ 212
A K L+ + EIDG+
Sbjct: 65 DAEKNLEEKQGAEIDGR 81
Score = 28.1 bits (61), Expect = 7.7, Method: Composition-based stats.
Identities = 10/34 (29%), Positives = 22/34 (64%)
Query: 7 GEAKGYAFVTFRTKELASQAIEELNSCELKGKKI 40
G++KG A++ F+++ A + +EE E+ G+ +
Sbjct: 50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+G+AFV F E A+ AI+ +N EL G+ I+ + A
Sbjct: 44 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 9/94 (9%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAK----PGQERSRYGFVHFAERSSAM 198
K LY+KNL +T+ L LFA + + PP + G+ R + F+ F + A
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFA---RFQEKKGPPIQFRMMTGRMRGQ-AFITFPNKEIAW 81
Query: 199 KALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
+AL Y++ G++L K Q++SG S+
Sbjct: 82 QALHLVNGYKLYGKILVIEFGK-NKKQRSSGPSS 114
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+G +G AF+TF KE+A QA+ +N +L GK + + K
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 8 EAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
E++G+AFV F K A A++ ++ L G++++ A+
Sbjct: 87 ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
M+ +G + GYAFV F ++ + +AI+ LN ++ K++K S A+
Sbjct: 36 MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 30/77 (38%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V LP+D+T L LF G I I Y FV F + +A+K
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 205 EKYEIDGQVLDCSLAKP 221
+ + L S A+P
Sbjct: 66 NGITVRNKRLKVSYARP 82
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
+ ++V NL + ++ L ELF G +TKV I + G+ +S +GFV F S A+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS-FGFVCFKHPESVSYAI 74
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
+G+AFV F E A+ AI+ +N EL G+ I+ + A+
Sbjct: 54 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L+V+ P D+ + L E+F G + +V I + + FV F E SA KA++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85
Query: 205 EKYEIDGQVLDCSLAK 220
Q L+ +K
Sbjct: 86 HGKSFANQPLEVVYSK 101
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 7/94 (7%)
Query: 138 AASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSA 197
+S ++V D+T+D L+E F+ +G + V IP KP + + FV FA+ A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP--KPFRA---FAFVTFADDQIA 55
Query: 198 MKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGS 231
E I G + S A+P+ + + S
Sbjct: 56 QSLCG--EDLIIKGISVHISNAEPKHNSNSGPSS 87
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
LYV NL T++++ ELF+ G I K+++ K + + FV + R+ A A++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADAENAMRYI 79
Query: 205 EKYEIDGQVL 214
+D +++
Sbjct: 80 NGTRLDDRII 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L+V+NL +++ L++LF+ +G ++++ P ++ + FV F A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA-- 68
Query: 205 EKYEIDGQVL 214
E+DGQV
Sbjct: 69 ---EVDGQVF 75
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAA 45
+G+AFV F E A+ AI+ +N EL G+ I+ + A
Sbjct: 105 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 38/83 (45%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L++ +LP++ L ++F G + + K +GFV + SA A+++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 205 EKYEIDGQVLDCSLAKPQADQKT 227
++I + L L + + D K+
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKS 110
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
+G++KGY FV+F K A AI + L G++I+ + A K
Sbjct: 53 TGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKV-VIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
++V +L +IT + +K FA GKI+ V+ G+ + YGFV F + A A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKG-YGFVSFYNKLDAENAIVH 76
Query: 204 TEKYEIDGQVLDCSLA 219
+ G+ + + A
Sbjct: 77 MGGQWLGGRQIRTNWA 92
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 49 HR-LFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
HR LF+G + + EDD+R+ G + +++ P ++G AF++Y +HA A+
Sbjct: 15 HRKLFVGMLNKQQSEDDVRRLFEAFG-NIEECTILRGPD--GNSKGCAFVKYSSHAEAQ 70
>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 = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
L V NLP +TQ + +EL G + + + ++ + YGF + ++ SA +A
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
Score = 27.7 bits (60), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 3 GKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCS 43
G+D G+ KG+A + + T E+A +A ++ + L G ++ S
Sbjct: 218 GQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 257
>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 = 32.7 bits (73), Expect = 0.28, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCS-AAQAKH 49
+G ++GY FV+F +++ A A++ + +L G+ ++ + AA+ +H
Sbjct: 39 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLEH 83
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
L V NLP +TQ + +EL G + + + ++ + YGF + ++ SA +A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 3 GKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCS 43
G+D G+ KG+A + + T E+A +A ++ + L G ++ S
Sbjct: 220 GQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 259
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
L V NLP +TQ + +EL G + + + ++ + YGF + ++ SA +A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 3 GKDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCS 43
G+D G+ KG+A + + T E+A +A ++ + L G ++ S
Sbjct: 220 GQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 259
>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 = 32.7 bits (73), Expect = 0.31, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L V NL ++ ++ELFA G + K + + G+ VHF ++ A+KA K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD-VHFERKADALKAXKQY 90
Query: 205 EKYEIDGQVLDCSL 218
+DG+ + L
Sbjct: 91 NGVPLDGRPXNIQL 104
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 32/76 (42%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L++ +LP++ T L F G + + K +GFV F SA A+K
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 205 EKYEIDGQVLDCSLAK 220
+++ + L L K
Sbjct: 103 NGFQVGTKRLKVQLKK 118
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 8 EAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQ 46
E++G+AFV F K A A++ ++ L G++++ A+
Sbjct: 110 ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 144 ALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKN 203
L V L T+ L+E+F+ +G I V I + + + FV+F A +A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 204 TEKYEIDGQVL--DCSLAK 220
E+DG+ + D S+ K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
S ++G+AFV F + A +A E N EL G++I+ + K
Sbjct: 84 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 62 EDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQK 111
E D+R+ +K GP + + +V D Q + ++RGFAF+ + N A+ ++++
Sbjct: 60 ERDLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFENVDDAKEAKER 107
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQA 47
+ S ++G+AFV F + A +A E N EL G++I+ S +
Sbjct: 51 QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
Score = 31.2 bits (69), Expect = 0.95, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 62 EDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQK 111
E D+R+ +K GP + + +V D Q + ++RGFAF+ + N A+ ++++
Sbjct: 29 ERDLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFENVDDAKEAKER 76
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 155 TQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQVL 214
T+ L+E+F+ +G I V I + + + FV+F A +A + E+DG+ +
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 215 DCS 217
S
Sbjct: 88 RVS 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 32.0 bits (71), Expect = 0.48, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L+V+ P D+ + L E+F G + +V I + + FV F E SA KA++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 58
Query: 205 EKYEIDGQVLDCSLAK 220
Q L+ +K
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 32.0 bits (71), Expect = 0.49, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 133 NAESSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFA 192
+ S + LYV L IT+ L+ F G+I + + +R + F+ FA
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITV------VQRQQCAFIQFA 56
Query: 193 ERSSA-MKALKNTEKYEIDGQVLD 215
R +A + A K+ K ++G+ L+
Sbjct: 57 TRQAAEVAAEKSFNKLIVNGRRLN 80
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 31.6 bits (70), Expect = 0.64, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 5/81 (6%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+YV NLP+D LK G +P Q R F+H+ + ++A +A+
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGS-----VPLRLTWQGPRRRAFLHYPDSAAAQQAVSCL 76
Query: 205 EKYEIDGQVLDCSLAKPQADQ 225
+ + L +LA+ Q D+
Sbjct: 77 QGLRLGTDTLRVALARQQRDK 97
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 31.6 bits (70), Expect = 0.72, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 62 EDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQK 111
E D+R+ +K GP + + +V D Q + ++RGFAF+ + N A+ ++++
Sbjct: 29 ERDLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFENVDDAKEAKER 76
Score = 31.2 bits (69), Expect = 0.88, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
+ S ++G+AFV F + A +A E N EL G++I+
Sbjct: 51 QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 155 TQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQ 212
T+ L+E+F+ +G I V I + + + FV+F A +A + E+DG+
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKA 200
L+V +P+ + + LK LF G+I ++ + + F+ + R SA+KA
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 50 RLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSR 109
+LF+G +PR E D++ + G + + ++KD + ++G AF+ Y CA S
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGR-IYELTVLKD-RLTGLHKGCAFLTY----CARDSA 70
Query: 110 QK 111
K
Sbjct: 71 LK 72
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 31.6 bits (70), Expect = 0.73, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 62 EDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQK 111
E D+R+ +K GP + + +V D Q + ++RGFAF+ + N A+ ++++
Sbjct: 26 ERDLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFENVDDAKEAKER 73
Score = 31.2 bits (69), Expect = 0.89, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
+ S ++G+AFV F + A +A E N EL G++I+
Sbjct: 48 QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 155 TQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEIDGQ 212
T+ L+E+F+ +G I V I + + + FV+F A +A + E+DG+
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 82
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 31.6 bits (70), Expect = 0.74, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIK 41
+ +G +KGYA V + T + A A E LN E+ G+ I+
Sbjct: 62 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 99
>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 = 31.2 bits (69), Expect = 0.77, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 43 SAAQAKHRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNH 102
S + KH+LFI +P + ++++ + + K V + LV + A + +G A++EY N
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEE-ICKAHGTVKDLRLVTN--RAGKPKGLAYVEYENE 68
Query: 103 ACAEYSRQKMSNPKFK 118
+ A + KM K
Sbjct: 69 SQASQAVMKMDGMTIK 84
Score = 27.7 bits (60), Expect = 9.7, Method: Composition-based stats.
Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 137 SAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSS 196
S + + L++ LP T++ L+E+ HG + + + + G+ + +V + S
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG-LAYVEYENESQ 70
Query: 197 AMKALKNTEKYEIDGQVLDCSLA 219
A +A+ + I ++ +++
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAIS 93
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+YV NL + + L+ F ++G + V + PG + FV F + A A++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG-----FAFVEFEDPRDAADAVR-- 128
Query: 205 EKYEIDGQVL 214
E+DG+ L
Sbjct: 129 ---ELDGRTL 135
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.2 bits (69), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 32/76 (42%)
Query: 138 AASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSA 197
+S LY++ L T L +L +GKI K + YGFV F S+A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 198 MKALKNTEKYEIDGQV 213
KA+ + + Q+
Sbjct: 61 QKAVTALKASGVQAQM 76
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 21/26 (80%)
Query: 2 KGKDSGEAKGYAFVTFRTKELASQAI 27
K K +G++KG+AF++F +E A++AI
Sbjct: 49 KDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 13 AFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRL 51
AFVT+ E A QA+ ELN +++ ++K + A+ + L
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML 114
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 13 AFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRLFIG 54
AFVT+ E A QA+ ELN +++ ++K + A+ + L G
Sbjct: 52 AFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
S ++ ++V N+ T L+ LF G++ + + Y FVH + +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54
Query: 196 SAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
A A+ E+ G+ ++ L+ QK SG S+
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELS--TKGQKKSGPSS 89
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 10 KGYAFVTFRTKELASQAIEELNSCELKGKKI 40
K YAFV + A AI +LN E+KGK+I
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRI 73
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 144 ALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKAL 201
++V NL + +LKE+F+ G + + I K G+ R G V F + A++A+
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG-IGTVTFEQSIEAVQAI 73
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 150 LPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNTEKYEI 209
L + Q L+E FA HGK+ V + P Q ++ V A+ A+ + +Y+I
Sbjct: 21 LSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKA---VVQMENLQDAIGAVNSLHRYKI 77
Query: 210 DGQVLDCSLA 219
+ + SLA
Sbjct: 78 GSKKILVSLA 87
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 56 VPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
+P+ EDD+R + G + L+++ +++ Q+RGFAF+E+
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRN-KSSGQSRGFAFVEF 51
Score = 28.5 bits (62), Expect = 5.3, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 1 MKGKDSGEAKGYAFVTFRTKELASQAIE-ELNSCELKGKKIKCSAAQAKHRL 51
M+ K SG+++G+AFV F + A++ +E +S + G+K+ + K ++
Sbjct: 35 MRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKI 86
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
+YV NL + + L+ F ++G + V + PG + FV F + A A++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG-----FAFVEFEDPRDAADAVR-- 128
Query: 205 EKYEIDGQVL 214
++DG+ L
Sbjct: 129 ---DLDGRTL 135
>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 = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 6 SGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCS 43
+G +KGYA V + T + A A E LN E+ G+ I+
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVI 174
+ LY++NLP IT + + ++F +G I ++ +
Sbjct: 19 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKVVI 174
+ LY++NLP IT + + ++F +G I ++ +
Sbjct: 13 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 44
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 4 KDSGEAKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAK 48
K++G+ KG A V++ A A+E + + +G K+K S A+ K
Sbjct: 59 KETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>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 = 2.8, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 143 KALYVKNLPKDITQDRLKELFAHHGKITKV 172
+ LY++NLP IT + + ++F +G I ++
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQI 38
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 75 GVISIELVKDPQNANQNRGFAFIEYYNHACAEYSRQKMS--NPKFKLDDNAPTVSWA 129
V +I L+KD Q QNRGFAF++ + A Q + +P K+D V +A
Sbjct: 37 AVNNIRLIKDKQT-QQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.3 bits (64), Expect = 3.6, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 7/97 (7%)
Query: 136 SSAASQVKALYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERS 195
SS +S ++V+NLP D T LK+ F G + I + G+ + G V F
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKG-CGVVKFESPE 59
Query: 196 SAMKALKNTEKYEIDGQVLDCSLAKPQADQKTSGGSN 232
A +A + ++ G+ +D + D+ SG S+
Sbjct: 60 VAERACRMMNGMKLSGREIDVRI-----DRNASGPSS 91
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 52 FIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEY 99
F+GN+P + E+ +++ G + ++ L ++P N + +GF + E+
Sbjct: 19 FLGNLPYDVTEESIKEFFR--GLNISAVRLPREPSNPERLKGFGYAEF 64
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 146 YVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSR-YGFVHF 191
++ NLP D+T++ +KE F I+ V +P ER + +G+ F
Sbjct: 19 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEF 64
>pdb|1US1|A Chain A, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1US1|B Chain B, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1PU4|A Chain A, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|1PU4|B Chain B, Crystal Structure Of Human Vascular Adhesion Protein-1
pdb|2Y73|A Chain A, The Native Structures Of Soluble Human Primary Amine
Oxidase Aoc3
pdb|2Y73|B Chain B, The Native Structures Of Soluble Human Primary Amine
Oxidase Aoc3
pdb|2Y74|A Chain A, The Crystal Structure Of Human Soluble Primary Amine
Oxidase Aoc3 In The Off-Copper Conformation
pdb|2Y74|B Chain B, The Crystal Structure Of Human Soluble Primary Amine
Oxidase Aoc3 In The Off-Copper Conformation
Length = 763
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 85 PQNANQNRGFAFIEYYNHACAEYSRQKMSNPKFKLDD-NAPTVSWADPRNAESSAASQVK 143
PQN++ RGF++ Y + S+ F +D APTV ++D N E+ A +
Sbjct: 616 PQNSSMARGFSWERYQLAVTQRKEEEPSSSSVFNQNDPWAPTVDFSDFINNETIAGKDLV 675
Query: 144 A 144
A
Sbjct: 676 A 676
>pdb|3ALA|A Chain A, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|B Chain B, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|C Chain C, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|D Chain D, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|E Chain E, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|F Chain F, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
pdb|3ALA|G Chain G, Crystal Structure Of Vascular Adhesion Protein-1 In Space
Group C2
Length = 748
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 85 PQNANQNRGFAFIEYYNHACAEYSRQKMSNPKFKLDD-NAPTVSWADPRNAESSAASQVK 143
PQN++ RGF++ Y + S+ F +D APTV ++D N E+ A +
Sbjct: 601 PQNSSMARGFSWERYQLAVTQRKEEEPSSSSVFNQNDPWAPTVDFSDFINNETIAGKDLV 660
Query: 144 A 144
A
Sbjct: 661 A 661
>pdb|2C10|A Chain A, The Structure Of A Truncated, Soluble Version Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C10|B Chain B, The Structure Of A Truncated, Soluble Version Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C10|C Chain C, The Structure Of A Truncated, Soluble Version Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C10|D Chain D, The Structure Of A Truncated, Soluble Version Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C11|A Chain A, Crystal Structure Of The 2-Hydrazinopyridine Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C11|B Chain B, Crystal Structure Of The 2-Hydrazinopyridine Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C11|C Chain C, Crystal Structure Of The 2-Hydrazinopyridine Of
Semicarbazide-Sensitive Amine Oxidase
pdb|2C11|D Chain D, Crystal Structure Of The 2-Hydrazinopyridine Of
Semicarbazide-Sensitive Amine Oxidase
Length = 735
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 85 PQNANQNRGFAFIEYYNHACAEYSRQKMSNPKFKLDD-NAPTVSWADPRNAESSAASQVK 143
PQN++ RGF++ Y + S+ F +D APTV ++D N E+ A +
Sbjct: 588 PQNSSMARGFSWERYQLAVTQRKEEEPSSSSVFNQNDPWAPTVDFSDFINNETIAGKDLV 647
Query: 144 A 144
A
Sbjct: 648 A 648
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 9 AKGYAFVTFRTKELASQAIEELNSCELKGKKIKCSAAQAKHRLFIG 54
K YAFV E A +AI L++ E +GK++ + ++ R G
Sbjct: 43 VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
L+V N+ T L+ F +G + + I Y FVH A++A++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 205 EKYEIDGQVLDCSLAKPQADQKTSGGSNS 233
+ E G+ + L+ + +T+ G +S
Sbjct: 65 DNTEFQGKRMHVQLSTSRL--RTASGPSS 91
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.1 bits (61), Expect = 7.6, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 145 LYVKNLPKDITQDRLKELFAHHGKITKVVIPPAKPGQERSRYGFVHFAERSSAMKALKNT 204
++V L + T + +K F GK+ ++ K +GFV F E ++ +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 205 EKYEIDGQVLDCSLA 219
+EI+ ++++C A
Sbjct: 61 HFHEINNKMVECKKA 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 11/58 (18%), Positives = 30/58 (51%)
Query: 49 HRLFIGNVPRNWGEDDMRKAVTKIGPGVISIELVKDPQNANQNRGFAFIEYYNHACAE 106
++F+G +P + ED++ + + GP V+ + ++ +G+AF+ + + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 9.8, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 6/93 (6%)
Query: 141 QVKALYVKNLPKDITQDRLKELFAHHG--KITKVVIPPAKPGQERSRYGFVHFAERSSAM 198
Q + LYV NL +D+T+ + +LF+ G K K++ Y FV F E A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT----SNDPYCFVEFYEHRDAA 69
Query: 199 KALKNTEKYEIDGQVLDCSLAKPQADQKTSGGS 231
AL +I G+ + + A + QK+ S
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
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
0.314 0.131 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,383,202
Number of Sequences: 62578
Number of extensions: 337961
Number of successful extensions: 1027
Number of sequences better than 100.0: 152
Number of HSP's better than 100.0 without gapping: 116
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 741
Number of HSP's gapped (non-prelim): 304
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)