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= 011693
(479 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 65.1 bits (157), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 46/166 (27%), Positives = 83/166 (50%), Gaps = 13/166 (7%)
Query: 180 AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAE 239
+K L + +P+N E+ + + +G + +LV+D K + + G+ F+ Y + K AE
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGE-IESCKLVRD-KITGQSLGYGFVNYIDPKDAE 58
Query: 240 YSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHH 299
+ + +L T VS+A P SS + + +YV LP+ +TQ +L++LF +
Sbjct: 59 KAINTLNG--LRLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMTQKELEQLFSQY 112
Query: 300 GRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQ 345
GRI + + +GF+ F +R A +A+K L+GQ
Sbjct: 113 GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG-----LNGQ 153
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 70/137 (51%), Gaps = 8/137 (5%)
Query: 109 IPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEF 168
+P + ++ + R SIGE+ ++++ K + ++ G+ FV + + + A KAI+ LN
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 169 KGKKIRCST---SQAKYR---LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSS 222
+ K I+ S S A R L++ +P+ ++L+++ S+ G +T LV + S
Sbjct: 70 QTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS 129
Query: 223 NNRGFAFIEYHNHKCAE 239
RG FI + AE
Sbjct: 130 --RGVGFIRFDKRIEAE 144
Score = 36.6 bits (83), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V LP+N+TQ++ + LF G I + K + GFV++ + A KA+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 338 EKYELDGQALECSLAKPQA 356
L + ++ S A+P +
Sbjct: 65 NGLRLQTKTIKVSYARPSS 83
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 30/63 (47%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+ G+P ++ +L G + RI+ + + ++G F+ F A +AI
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 162 KLN 164
LN
Sbjct: 149 GLN 151
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 49/89 (55%)
Query: 176 STSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
S S RLFIG IP+ E++ + +++V GV V + + NRGFAF+EY +H
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 236 KCAEYSRQKMTNPNFKLGTNAPTVSWADP 264
+ A +R+K+ +L + V WA+P
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDWAEP 91
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTE-----VRIMKGKDSSENKGFAFVTFRNVELASK 158
++IGGIP ++ + I +VTE + D +N+GFAFV + + A+
Sbjct: 11 LFIGGIPKMKKREEI---LEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 159 AIDKL 163
A KL
Sbjct: 68 ARRKL 72
>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 = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 47/80 (58%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P VY+G IP+D +E + D C ++G V +++M + +KG+AF+ FR++E ++
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 159 AIDKLNNTEFKGKKIRCSTS 178
A+ LN + + ++C S
Sbjct: 62 AVRNLNGYQLGSRFLKCGYS 81
Score = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRIT--KVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+ VY+ ++P + T++Q+ L + G + K++ P + G+ K F+ F + S+ A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-QTGRSKG-YAFIEFRDLESSASA 62
Query: 334 LKNTEKYELDGQALEC 349
++N Y+L + L+C
Sbjct: 63 VRNLNGYQLGSRFLKC 78
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
+++G+IP + E + + S VGP V ++++ D + ++G+AFIE+ + E S
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFD-PQTGRSKGYAFIEFRD---LESSAS 61
Query: 244 KMTNPN-FKLGT 254
+ N N ++LG+
Sbjct: 62 AVRNLNGYQLGS 73
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
VY+G IP+D +E + D C ++G V +++M + +KG+AF+ FR++E ++ A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 164 NNTEFKGKKIRCSTS 178
N + + ++C S
Sbjct: 65 NGYQLGSRFLKCGYS 79
Score = 32.3 bits (72), Expect = 0.54, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 8/91 (8%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
+++G+IP + E + + S VGP V ++++ D + ++G+AFIE+ + E S
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFD-PQTGRSKGYAFIEFRD---LESSAS 59
Query: 244 KMTNPN-FKLGTNAPTVSWADPRNVDSSGAS 273
+ N N ++LG+ ++ N D SG S
Sbjct: 60 AVRNLNGYQLGSRFLKCGYSS--NSDISGVS 88
Score = 32.0 bits (71), Expect = 0.68, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRIT--KVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+ VY+ ++P + T++Q+ L + G + K++ P + G+ K F+ F + S+ A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-QTGRSKG-YAFIEFRDLESSASA 60
Query: 334 LKNTEKYELDGQALEC 349
++N Y+L + L+C
Sbjct: 61 VRNLNGYQLGSRFLKC 76
>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 = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
VY+G IP+D +E + D C ++G V +++M + +KG+AF+ FR++E ++ A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 164 NNTEFKGKKIRCSTS 178
N + + ++C S
Sbjct: 66 NGYQLGSRFLKCGYS 80
Score = 32.3 bits (72), Expect = 0.56, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 8/91 (8%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
+++G+IP + E + + S VGP V ++++ D + ++G+AFIE+ + E S
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGP-VINLKMMFD-PQTGRSKGYAFIEFRD---LESSAS 60
Query: 244 KMTNPN-FKLGTNAPTVSWADPRNVDSSGAS 273
+ N N ++LG+ ++ N D SG S
Sbjct: 61 AVRNLNGYQLGSRFLKCGYSS--NSDISGVS 89
Score = 32.0 bits (71), Expect = 0.70, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRIT--KVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+ VY+ ++P + T++Q+ L + G + K++ P + G+ K F+ F + S+ A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-QTGRSKG-YAFIEFRDLESSASA 61
Query: 334 LKNTEKYELDGQALEC 349
++N Y+L + L+C
Sbjct: 62 VRNLNGYQLGSRFLKC 77
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 68/144 (47%), Gaps = 8/144 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + +P + ++ +LR SIGEV ++++ K + + G+ FV + + A +AI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 162 KLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
LN + K I+ S ++ L+I +PR +D++ + S G + LV
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAE 239
S RG AFI + AE
Sbjct: 123 DQTTGLS--RGVAFIRFDKRSEAE 144
Score = 58.5 bits (140), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 42/151 (27%), Positives = 74/151 (49%), Gaps = 8/151 (5%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L + +P+N ++L+ + S +G V +L++D K + ++ G+ F+ Y K AE R
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYVTAKDAE--RA 60
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRIT 303
T +L + VS+A P SS + +Y+ LPR +TQ ++ +F GRI
Sbjct: 61 INTLNGLRLQSKTIKVSYARP----SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 304 KVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
V + + F+ F +RS A +A+
Sbjct: 117 NSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V LP+N+TQD+L+ LF G + + K GFV++ A +A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 338 EKYELDGQALECSLAKPQAD 357
L + ++ S A+P ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +YI G+P ++ D+ D G + R++ + + ++G AF+ F A +AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 162 KLN 164
N
Sbjct: 149 SFN 151
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 68/144 (47%), Gaps = 8/144 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + +P + ++ +LR SIGEV ++++ K + + G+ FV + + A +AI+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 162 KLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
LN + K I+ S ++ L+I +PR +D++ + S G + LV
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAE 239
S RG AFI + AE
Sbjct: 123 DQTTGLS--RGVAFIRFDKRSEAE 144
Score = 58.5 bits (140), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 42/151 (27%), Positives = 74/151 (49%), Gaps = 8/151 (5%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L + +P+N ++L+ + S +G V +L++D K + ++ G+ F+ Y K AE R
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRD-KVAGHSLGYGFVNYVTAKDAE--RA 60
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRIT 303
T +L + VS+A P SS + +Y+ LPR +TQ ++ +F GRI
Sbjct: 61 INTLNGLRLQSKTIKVSYARP----SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 304 KVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
V + + F+ F +RS A +A+
Sbjct: 117 NSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V LP+N+TQD+L+ LF G + + K GFV++ A +A+
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 338 EKYELDGQALECSLAKPQAD 357
L + ++ S A+P ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSE 84
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +YI G+P ++ D+ D G + R++ + + ++G AF+ F A +AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 162 KLN 164
N
Sbjct: 149 SFN 151
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 82/166 (49%), Gaps = 13/166 (7%)
Query: 180 AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAE 239
+K L + +P+N ++ + + +G + +LV+D K + + G+ F+ Y + A+
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGD-IESCKLVRD-KITGQSLGYGFVNYSDPNDAD 60
Query: 240 YSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHH 299
+ + KL T VS+A P SS + + +YV LP+ ++Q ++++LF +
Sbjct: 61 KAINTLNG--LKLQTKTIKVSYARP----SSASIRDANLYVSGLPKTMSQKEMEQLFSQY 114
Query: 300 GRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQ 345
GRI + + +GF+ F +R A +A+K L+GQ
Sbjct: 115 GRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG-----LNGQ 155
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/169 (23%), Positives = 84/169 (49%), Gaps = 10/169 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + +P + ++ + + SIG++ ++++ K + ++ G+ FV + + A KAI+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 162 KLNNTEFKGKKIRCST---SQAKYR---LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
LN + + K I+ S S A R L++ +P+ ++++++ S+ G +T L+
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILL 124
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAP-TVSWAD 263
S RG FI + AE + + + N LG P TV +A+
Sbjct: 125 DQATGVS--RGVGFIRFDKRIEAEEAIKGL-NGQKPLGAAEPITVKFAN 170
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V LP+N+TQD+ K LF G I + K + GFV++++ + A KA+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 338 EKYELDGQALECSLAKPQA 356
+L + ++ S A+P +
Sbjct: 67 NGLKLQTKTIKVSYARPSS 85
>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 = 1e-08, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 53/91 (58%), Gaps = 9/91 (9%)
Query: 269 SSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERS 328
SSG ++VK ++V+NL VT++ L+K F G++ +V ++ F+HF ER
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERD 56
Query: 329 SAMKALKNTEKYELDGQALECSLAKPQADQK 359
A+KA++ +L+G+ +E AKP DQK
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKP-PDQK 86
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 70/153 (45%), Gaps = 9/153 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S +++G +P D +E ++R + G+ EV I K +KGF F+ LA A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKV 76
Query: 162 KLNNTEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNS 221
+L+N +GK++R + L + N+P+ +E L++ S G V +V D
Sbjct: 77 ELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRP 136
Query: 222 SNNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGT 254
S G +E+ A + + + +F L T
Sbjct: 137 S---GKGIVEFSGKPAARKALDRCSEGSFLLTT 166
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/158 (24%), Positives = 73/158 (46%), Gaps = 21/158 (13%)
Query: 177 TSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHK 236
T + RLF+GN+P + E+++K+ + G V + KD +GF FI
Sbjct: 18 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKD-------KGFGFIRLETRT 69
Query: 237 CAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLF 296
AE ++ ++ N + + + A ++ V+NLP+ V+ + L++ F
Sbjct: 70 LAEIAKVELDNMPLR------------GKQLRVRFACHSASLTVRNLPQYVSNELLEEAF 117
Query: 297 EHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
G++ + VV G+ + G V F+ + +A KAL
Sbjct: 118 SVFGQVERAVVIVDDRGRPSGK-GIVEFSGKPAARKAL 154
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 11/117 (9%)
Query: 258 TVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKN 317
T+ + R +Q ++V NLP ++T+++++KLFE +G+ +V + K
Sbjct: 5 TIDLKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----- 59
Query: 318 RIGFVHFAERSSAMKALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLLQN 374
GF+ R+ A A K ELD L + + SA +V P + N
Sbjct: 60 -FGFIRLETRTLAEIA-----KVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSN 110
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V++G IP++A+E L+D +G V R++ +++ + KG+ F +++ E A A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 164 NNTEFKGKKIRCSTSQAK 181
N EF G+ +R + ++
Sbjct: 71 NGREFSGRALRVDNAASE 88
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 275 VKAVYVKNLPRNVTQDQLKKLFEHHGRITKV-VVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+++V+V N+P T++QLK +F G + +V + G+ K GF + ++ +A+ A
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG-YGFCEYQDQETALSA 66
Query: 334 LKNTEKYELDGQAL 347
++N E G+AL
Sbjct: 67 MRNLNGREFSGRAL 80
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
+F+GNIP E L+ + SEVGP V LV D + + +G+ F EY + + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGP-VVSFRLVYD-RETGKPKGYGFCEYQDQETALSAMR 68
Query: 244 KMTNPNF 250
+ F
Sbjct: 69 NLNGREF 75
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 34/152 (22%), Positives = 74/152 (48%), Gaps = 8/152 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + +P D ++ +L ++IG + RIM+ + + G+AFV F + + +AI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 162 KLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
LN + K+++ S ++ L++ N+PR + L + + G + ++
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG-SIVQKNIL 122
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTN 247
+D K + RG AF+ Y+ + A+ + + N
Sbjct: 123 RD-KLTGRPRGVAFVRYNKREEAQEAISALNN 153
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 72/153 (47%), Gaps = 12/153 (7%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L + +P++ +L + +GP + +++D K + + G+AF+++ + ++ + +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYK-TGYSYGYAFVDFTSEMDSQRAIK 63
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGASQVK--AVYVKNLPRNVTQDQLKKLFEHHGR 301
+ + VS+A P G +K +YV NLPR +T DQL +F +G
Sbjct: 64 VLNGITVR--NKRLKVSYARP------GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 302 ITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
I + + K + FV + +R A +A+
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 44/73 (60%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++GG+ D +E L G+++EV ++K +++ ++GF FVTF N++ A A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 163 LNNTEFKGKKIRC 175
+N G++IR
Sbjct: 74 MNGKSVDGRQIRV 86
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 41/90 (45%)
Query: 272 ASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAM 331
AS ++V L + + L+++F +G+I++VVV + Q GFV F A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 332 KALKNTEKYELDGQALECSLAKPQADQKSA 361
A+ +DG+ + A +D +S
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSSDNRSG 98
>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 = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 32/154 (20%), Positives = 74/154 (48%), Gaps = 5/154 (3%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDM-KNSSNNRGFAFIEYHNHKCAEYS 241
+ F+G +PR W +DL+++ + G V + +++D +N ++G F+ ++ K A +
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 242 RQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGR 301
+ + N G + P P + + + A + + +++ + + T++ ++ F G+
Sbjct: 64 QNALHNXKVLPGXHHPI--QXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 302 ITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
I + + G + FV F R+ A A+K
Sbjct: 122 IEECRILRGPDGLSRG-CAFVTFTTRAXAQTAIK 154
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 77/173 (44%), Gaps = 18/173 (10%)
Query: 105 YIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSS--ENKGFAFVTFRNVELASKAIDK 162
++G +P SE DLR+ + G V E+ +++ + + ++KG FVTF + A +A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 163 LNN----------TEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGV 212
L+N + K + + +LFIG I + D++ S G +
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ----I 122
Query: 213 ELVKDMKNSSN-NRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAP-TVSWAD 263
E + ++ +RG AF+ + A+ + + G ++P V +AD
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
+++IG I +E+D+R S G++ E RI++G D ++G AFVTF A AI
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGL-SRGCAFVTFTTRAXAQTAI 153
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 54.7 bits (130), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 44/82 (53%)
Query: 97 LPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELA 156
L P S VY+ +P + +DL G+V +V IMK KD+ ++KG AF+ F + + A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 157 SKAIDKLNNTEFKGKKIRCSTS 178
+NN + G+ I+ S +
Sbjct: 72 QNCTRAINNKQLFGRVIKASIA 93
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 43/81 (53%)
Query: 272 ASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAM 331
A VYV NLP ++T + L ++F +G++ KV + K ++ + F+ F ++ SA
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 332 KALKNTEKYELDGQALECSLA 352
+ +L G+ ++ S+A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93
>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 = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 76/147 (51%), Gaps = 16/147 (10%)
Query: 99 PHGS--EVYIGGIPHDASEHDLRDFCQS---IGEVTEV--RIMKGKDSSENKGFAFVTFR 151
P GS +Y+G IP +E + DF + +G +T+ + +++K FAF+ FR
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 152 NVELASKAIDKLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEV 205
+V+ ++A+ + F+G+ ++ ++LFIG +P + ++++++
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSF 120
Query: 206 GPGVTGVELVKDMKNSSNNRGFAFIEY 232
GP + LVKD + ++G+AF EY
Sbjct: 121 GP-LKAFNLVKD-SATGLSKGYAFCEY 145
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 41/75 (54%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P +++IGG+P+ ++ +++ S G + ++K + +KG+AF + ++ + +
Sbjct: 94 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 153
Query: 159 AIDKLNNTEFKGKKI 173
AI LN + KK+
Sbjct: 154 AIAGLNGMQLGDKKL 168
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/152 (21%), Positives = 73/152 (48%), Gaps = 8/152 (5%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + +P D ++ +L ++IG + RI + + + G+AFV F + + +AI
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 162 KLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
LN + K+++ S ++ L++ N+PR + L + + G + ++
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG-SIVQKNIL 133
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTN 247
+D K + RG AF+ Y+ + A+ + + N
Sbjct: 134 RD-KLTGRPRGVAFVRYNKREEAQEAISALNN 164
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 71/153 (46%), Gaps = 12/153 (7%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L + +P++ +L + +GP + + +D K + + G+AF+++ + ++ + +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYK-TGYSFGYAFVDFTSEXDSQRAIK 74
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGASQVK--AVYVKNLPRNVTQDQLKKLFEHHGR 301
+ + VS+A P G +K +YV NLPR +T DQL +F +G
Sbjct: 75 VLNGITVR--NKRLKVSYARP------GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 126
Query: 302 ITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
I + + K + FV + +R A +A+
Sbjct: 127 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.9 bits (128), Expect = 2e-07, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 44/73 (60%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S +Y+G + + +E LR + G++ + +MK D+ +KG+ F+TF + E A +A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 162 KLNNTEFKGKKIR 174
+LN E G+ +R
Sbjct: 66 QLNGFELAGRPMR 78
Score = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 45/94 (47%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSA 330
G+S +YV +L N+T+D L+ +FE G+I +V+ GF+ F++ A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 331 MKALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
+AL+ +EL G+ + + D S S
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 36/137 (26%), Positives = 73/137 (53%), Gaps = 6/137 (4%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFR---NVELASK 158
+++IGG+ D +E +LR++ G VT+++IMK + ++GF F++F +V+ K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 159 AIDKLNNTEFKGKKIRCSTSQAKY-RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKD 217
L+ K+ Q K ++F+G I + ++ ++ S+ G + +L+ D
Sbjct: 64 TQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGT-IIDAQLMLD 122
Query: 218 MKNSSNNRGFAFIEYHN 234
K++ +RGF F+ Y +
Sbjct: 123 -KDTGQSRGFGFVTYDS 138
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 46/83 (55%), Gaps = 7/83 (8%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++GGI D + +F G + + ++M KD+ +++GF FVT+ + + A+D+
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----AVDR 144
Query: 163 LNN---TEFKGKKIRCSTSQAKY 182
+ +FK +KI ++ ++
Sbjct: 145 VCQNKFIDFKDRKIEIKRAEPRH 167
Score = 35.8 bits (81), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 6/87 (6%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRIT--KVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
+++ L + T+D L++ F +G +T K++ PA G+ + GF+ F + SS + +K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-TGRSRG-FGFLSFEKPSSVDEVVK 63
Query: 336 NTEKYELDGQALECSLAKPQADQKSAG 362
++ LDG+ ++ A P+ +Q G
Sbjct: 64 T--QHILDGKVIDPKRAIPRDEQDKTG 88
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 39/178 (21%), Positives = 88/178 (49%), Gaps = 13/178 (7%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
R+++G+I G + +++ + GP + +++ D + ++GFAF+EY + A+ +
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWD-SVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 243 QKMTNP-----NFKLGTNAPTVSWADPRNVDSSGASQVKA---VYVKNLPRNVTQDQLKK 294
++M + N K+G + + A P + A + +A +YV ++ ++++ D +K
Sbjct: 88 EQMNSVMLGGRNIKVGRPS-NIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 144
Query: 295 LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLA 352
+FE G+I + + GF+ + + S+ A+ + ++L GQ L A
Sbjct: 145 VFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 38/170 (22%), Positives = 79/170 (46%), Gaps = 23/170 (13%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S VY+G I ++ E +R G + + + + ++KGFAFV + E A A++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 162 KLNNTEFKGKKIRCST-----------------SQAKYRLFIGNIPRNWGSEDLQKVVSE 204
++N+ G+ I+ ++A R+++ ++ ++ +D++ V
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 205 VGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTNPN-FKLG 253
G + L +D + ++G+ FIEY A+ S+ +++ N F LG
Sbjct: 149 FGK-IKSATLARD-PTTGKHKGYGFIEYEK---AQSSQDAVSSMNLFDLG 193
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 12/72 (16%), Positives = 37/72 (51%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+ + D S+ D++ ++ G++ + + + ++KG+ F+ + + + A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 164 NNTEFKGKKIRC 175
N + G+ +R
Sbjct: 188 NLFDLGGQYLRV 199
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 46/176 (26%), Positives = 85/176 (48%), Gaps = 15/176 (8%)
Query: 173 IRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVEL-VKDMKNSSNNRGFAFIE 231
+ S S + LFIGN+ N +L+ +SE+ +L V D++ +N R F +++
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISEL---FAKNDLAVVDVRTGTN-RKFGYVD 60
Query: 232 YHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQ 291
+ AE + + K+ N + P+ DS + + KNL N+T+D+
Sbjct: 61 FE---SAEDLEKALELTGLKVFGN--EIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDE 115
Query: 292 LKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQAL 347
LK++FE I V ++ G+ K I ++ F + A K L+ + E+DG+++
Sbjct: 116 LKEVFEDALEIRLV----SQDGKSKG-IAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 35/140 (25%), Positives = 73/140 (52%), Gaps = 14/140 (10%)
Query: 104 VYIGGIPHDASEHDLRDFCQS---IGEVTEV--RIMKGKDSSENKGFAFVTFRNVELASK 158
+Y+G IP +E + DF + +G +T+ + +++K FAF+ FR+V+ ++
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 159 AIDKLNNTEFKGKKIRCSTSQ------AKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGV 212
A+ + F+G+ ++ ++LFIG +P + ++++++ GP +
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGP-LKAF 124
Query: 213 ELVKDMKNSSNNRGFAFIEY 232
LVKD + ++G+AF EY
Sbjct: 125 NLVKD-SATGLSKGYAFCEY 143
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 41/75 (54%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P +++IGG+P+ ++ +++ S G + ++K + +KG+AF + ++ + +
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 159 AIDKLNNTEFKGKKI 173
AI LN + KK+
Sbjct: 152 AIAGLNGMQLGDKKL 166
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 39/178 (21%), Positives = 88/178 (49%), Gaps = 13/178 (7%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
R+++G+I G + +++ + GP + +++ D + ++GFAF+EY + A+ +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDMSWD-SVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 243 QKMTNP-----NFKLGTNAPTVSWADPRNVDSSGASQVKA---VYVKNLPRNVTQDQLKK 294
++M + N K+G + + A P + A + +A +YV ++ ++++ D +K
Sbjct: 73 EQMNSVMLGGRNIKVGRPS-NIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 129
Query: 295 LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLA 352
+FE G+I + + GF+ + + S+ A+ + ++L GQ L A
Sbjct: 130 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 78/168 (46%), Gaps = 23/168 (13%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
VY+G I ++ E +R G + + + + ++KGFAFV + E A A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 164 NNTEFKGKKIRCST-----------------SQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
N+ G+ I+ ++A R+++ ++ ++ +D++ V G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTNPN-FKLG 253
+ L +D + ++G+ FIEY A+ S+ +++ N F LG
Sbjct: 136 K-IKSCTLARD-PTTGKHKGYGFIEYEK---AQSSQDAVSSMNLFDLG 178
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 12/72 (16%), Positives = 37/72 (51%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+ + D S+ D++ ++ G++ + + + ++KG+ F+ + + + A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 164 NNTEFKGKKIRC 175
N + G+ +R
Sbjct: 173 NLFDLGGQYLRV 184
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 47/179 (26%), Positives = 76/179 (42%), Gaps = 27/179 (15%)
Query: 177 TSQAKYRLFIGNIPRNWGSEDLQKVVSEVG-PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
T + RLF+GN+P + ED +++ G P + + +RGF FI +
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI---------NRDRGFGFIRLESR 68
Query: 236 KCAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKL 295
AE ++ ++ K R + A+ A+ VKNL V+ + L++
Sbjct: 69 TLAEIAKAELDGTILK------------SRPLRIRFATHGAALTVKNLSPVVSNELLEQA 116
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLAKP 354
F G + K VV G+ + GFV FA + A KAL+ DG L + +P
Sbjct: 117 FSQFGPVEKAVVVVDDRGRATGK-GFVEFAAKPPARKALERCG----DGAFLLTTTPRP 170
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 70/152 (46%), Gaps = 9/152 (5%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++G +P D +E D + + GE +EV I + ++GF F+ + LA A +L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAEL 78
Query: 164 NNTEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSN 223
+ T K + +R + L + N+ +E L++ S+ GP V +V D ++
Sbjct: 79 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT- 137
Query: 224 NRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTN 255
G F+E+ A + ++ + F L T
Sbjct: 138 --GKGFVEFAAKPPARKALERCGDGAFLLTTT 167
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 43/170 (25%), Positives = 77/170 (45%), Gaps = 21/170 (12%)
Query: 182 YRLFIGNIPRNWGSEDLQKVVSEVGP----GVTGVELVKDMKNSSNNRGFAFIEYHNHKC 237
+ LF+GN+ N + +L+ +S+V V V + R F ++++
Sbjct: 8 FNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRI-------GMTRKFGYVDFE---S 57
Query: 238 AEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFE 297
AE + + K+ N + P+ DS + + KNLP VTQD+LK++FE
Sbjct: 58 AEDLEKALELTGLKVFGNE--IKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFE 115
Query: 298 HHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQAL 347
I V +K G+ K I ++ F + A K + + E+DG+++
Sbjct: 116 DAAEIRLV----SKDGKSKG-IAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+G + D +E L + G + +R+ + + + G+A+V F+ A +A+D
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 162 KLNNTEFKGKKIRCSTSQAKYRL--------FIGNIPRNWGSEDLQKVVSEVGPGVTGVE 213
+N KGK +R SQ L FI N+ ++ ++ L S G + +
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCK 134
Query: 214 LVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKM 245
+V D S +G+ F+ + + AE + +KM
Sbjct: 135 VVCDENGS---KGYGFVHFETQEAAERAIEKM 163
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 83/184 (45%), Gaps = 14/184 (7%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L++G++ + L + S GP + + + +DM + + G+A++ + AE +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMI-TRRSLGYAYVNFQQPADAERALD 75
Query: 244 KMTNPNFKLGTNAPT-VSWA--DPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHG 300
M NF + P + W+ DP S S V +++KNL +++ L F G
Sbjct: 76 TM---NFDVIKGKPVRIMWSQRDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128
Query: 301 RITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLAKPQADQKS 360
I V + G + GFVHF + +A +A++ L+ + + K + ++++
Sbjct: 129 NILSCKVVCDENGSKG--YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186
Query: 361 AGGS 364
G+
Sbjct: 187 ELGA 190
Score = 33.1 bits (74), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
++I + L D + G + +++ D + +KG+ FV F E A +AI+K+
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 163
Query: 164 NNTEFKGKKI 173
N +K+
Sbjct: 164 NGMLLNDRKV 173
>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 = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 130 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 156
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 81/194 (41%), Gaps = 22/194 (11%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 69
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 70 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE-LDGQALECSLAKP 354
FE +G+I + + + +K FV F + S K + +KY ++G C + K
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 180
Query: 355 QADQKSAGGSVSEK 368
+ Q+ A S S++
Sbjct: 181 LSKQEMASASSSQR 194
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 71 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 109
>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 = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 9 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 69 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 128
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 129 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 155
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 81/194 (41%), Gaps = 22/194 (11%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 68
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 69 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 123
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE-LDGQALECSLAKP 354
FE +G+I + + + +K FV F + S K + +KY ++G C + K
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 179
Query: 355 QADQKSAGGSVSEK 368
+ Q+ A S S++
Sbjct: 180 LSKQEMASASSSQR 193
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 69
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 70 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 108
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 11 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 71 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 131 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 157
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 81/194 (41%), Gaps = 22/194 (11%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 70
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 71 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 125
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE-LDGQALECSLAKP 354
FE +G+I + + + +K FV F + S K + +KY ++G C + K
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 181
Query: 355 QADQKSAGGSVSEK 368
+ Q+ A S S++
Sbjct: 182 LSKQEMASASSSQR 195
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 71
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 72 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 110
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 70 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 130 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 156
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 35.8 bits (81), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 36/159 (22%), Positives = 64/159 (40%), Gaps = 17/159 (10%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 69
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 70 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
FE +G+I + + + +K FV F + S K +
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 35.4 bits (80), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 71 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 109
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 8 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 68 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 127
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 128 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 154
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 35.8 bits (81), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 36/159 (22%), Positives = 64/159 (40%), Gaps = 17/159 (10%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 67
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 68 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 122
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
FE +G+I + + + +K FV F + S K +
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 35.4 bits (80), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 68
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 69 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 107
>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 = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/149 (22%), Positives = 71/149 (47%), Gaps = 13/149 (8%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P +++IGG+ + ++ LR + G +T+ +M+ ++ ++GF FVT+ VE
Sbjct: 3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 158 KAID----KLNNTEFKGKKI-------RCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
A++ K++ + K+ R ++F+G I + L+ + G
Sbjct: 63 AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 122
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNH 235
+ +E++ D + S RGFAF+ + +H
Sbjct: 123 K-IEVIEIMTD-RGSGKKRGFAFVTFDDH 149
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
++++GGI D EH LRD+ + G++ + IM + S + +GFAFVTF + + K +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 22/190 (11%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + E L+ + G +T +++D N+ +RGF F+ Y E
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGT-LTDCVVMRD-PNTKRSRGFGFVTY---ATVEEVD 62
Query: 243 QKMTNPNFKLGTNAPTVSWADPRNVDSSGASQ-------VKAVYVKNLPRNVTQDQLKKL 295
M K+ +P+ S SQ VK ++V + + + L+
Sbjct: 63 AAMNARPHKVDGRV-----VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 117
Query: 296 FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE-LDGQALECSLAKP 354
FE +G+I + + + +K FV F + S K + +KY ++G C + K
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV--IQKYHTVNGH--NCEVRKA 173
Query: 355 QADQKSAGGS 364
+ Q+ A S
Sbjct: 174 LSKQEMASAS 183
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 48/100 (48%), Gaps = 3/100 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMK 332
Q++ +++ L T + L+ FE G +T VV P +++R GFV +A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-MRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVSEKPSLL 372
A+ N +++DG+ +E A + D + G ++ K +
Sbjct: 64 AM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 102
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G + + A+ +++ G+V V+++ +++ + KGF FV + E S+AI KL
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 164 NNTEFKGKKIRCSTSQAKYRL 184
+NT+F G+ IR + + K L
Sbjct: 63 DNTDFMGRTIRVTEANPKKSL 83
Score = 36.2 bits (82), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 275 VKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAER--SSAMK 332
++ +YV NL + T +Q+K+LF G++ V + + ++ GFV E S A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 333 ALKNTEKYELDGQALECSLAKPQ 355
L NT + G+ + + A P+
Sbjct: 61 KLDNT---DFMGRTIRVTEANPK 80
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+++++GGIPH+ E +LR++ + G VTEV ++ + +GF F+TF + + +A++
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 162 KLNNTEFKGKKIRCSTSQAK 181
++ + GKK+ ++ +
Sbjct: 71 -MHFHDIMGKKVEVKRAEPR 89
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V +P N + +L++ F+ G +T+VV+ Q GF+ F + S +A+ N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 338 EKYELDGQALECSLAKPQADQKSAGGS 364
+++ G+ +E A+P+ D KS+G S
Sbjct: 72 HFHDIMGKKVEVKRAEPR-DSKSSGPS 97
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 7/92 (7%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
++F+G IP N G +L++ + G VT V ++ D + RGF FI + + E S
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGV-VTEVVMIYDAEK-QRPRGFGFITFED----EQSV 65
Query: 243 QKMTNPNFK-LGTNAPTVSWADPRNVDSSGAS 273
+ N +F + V A+PR+ SSG S
Sbjct: 66 DQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPS 97
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 41/175 (23%), Positives = 81/175 (46%), Gaps = 18/175 (10%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSS--ENKGFAFVTFRNVELASKAI 160
++++G +P SE DLR+ + G V E+ +++ + + ++KG FVTF + A +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 161 DKLNN----------TEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVT 210
+ L+N + K + + +LFIG I + D++ + S G
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ--- 133
Query: 211 GVELVKDMKNSSN-NRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAP-TVSWAD 263
+E + ++ +RG AF+ + A+ + + M G ++P V +AD
Sbjct: 134 -IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 187
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVV-------PPAKPGQEKNRIGFVHFAERSSA 330
++V +PR ++ L++LFE +G + ++ V PP G FV F R +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-----CCFVTFYTRKAA 72
Query: 331 MKA 333
++A
Sbjct: 73 LEA 75
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+G + D +E L + G + +R+ + + + G+A+V F+ A +A+D
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 162 KLNNTEFKGKKIRCSTSQAKYRL--------FIGNIPRNWGSEDLQKVVSEVGPGVTGVE 213
+N KGK +R SQ L FI N+ ++ ++ L S G + +
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCK 129
Query: 214 LVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKM 245
+V D S +G+ F+ + + AE + +KM
Sbjct: 130 VVCDENGS---KGYGFVHFETQEAAERAIEKM 158
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 83/184 (45%), Gaps = 14/184 (7%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L++G++ + L + S GP + + + +DM + + G+A++ + AE +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMI-TRRSLGYAYVNFQQPADAERALD 70
Query: 244 KMTNPNFKLGTNAPT-VSWA--DPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHG 300
M NF + P + W+ DP S S V +++KNL +++ L F G
Sbjct: 71 TM---NFDVIKGKPVRIMWSQRDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 301 RITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLAKPQADQKS 360
I V + G + GFVHF + +A +A++ L+ + + K + ++++
Sbjct: 124 NILSCKVVCDENGSKG--YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181
Query: 361 AGGS 364
G+
Sbjct: 182 ELGA 185
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
++I + L D + G + +++ D + +KG+ FV F E A +AI+K+
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 158
Query: 164 NNTEFKGKKI 173
N +K+
Sbjct: 159 NGMLLNDRKV 168
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 52/93 (55%), Gaps = 8/93 (8%)
Query: 269 SSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERS 328
SSG+S + +++ NLPR T+ +++ LFE +G++ + + KN GFVH +++
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KN-YGFVHIEDKT 53
Query: 329 SAMKALKNTEKYELDGQALECSLAKPQADQKSA 361
+A A++N Y+L G + +K ++ S
Sbjct: 54 AAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86
Score = 36.2 bits (82), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
+++IG +P +A+E ++R + G+V E I+ K + FV + A AI
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 163 LNNTEFKGKKIRCSTSQAK 181
L++ + G I S+ K
Sbjct: 62 LHHYKLHGVNINVEASKNK 80
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%)
Query: 106 IGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNN 165
+ G+ +E DLR+ G + +V I+ + S ++GFAFV F NV+ A +A ++ N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 166 TEFKGKKIRCSTSQAK 181
E G++IR S K
Sbjct: 77 MELDGRRIRVDFSITK 92
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 197 DLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHN 234
DL++V S+ GP + V +V D + S +RGFAF+ + N
Sbjct: 28 DLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFEN 63
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 31/73 (42%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V L T+ L+++F +G I V + + + FV+F A +A +
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 340 YELDGQALECSLA 352
ELDG+ + +
Sbjct: 77 MELDGRRIRVDFS 89
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/175 (23%), Positives = 81/175 (46%), Gaps = 18/175 (10%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSS--ENKGFAFVTFRNVELASKAI 160
++++G +P SE DLR+ + G V E+ +++ + + ++KG FVTF + A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 DKLNN----------TEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVT 210
+ L+N + K + + +LFIG I + D++ + S G
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ--- 121
Query: 211 GVELVKDMKNSSN-NRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAP-TVSWAD 263
+E + ++ +RG AF+ + A+ + + M G ++P V +AD
Sbjct: 122 -IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVV-------PPAKPGQEKNRIGFVHFAERSSA 330
++V +PR ++ L++LFE +G + ++ V PP G FV F R +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-----CCFVTFYTRKAA 60
Query: 331 MKA 333
++A
Sbjct: 61 LEA 63
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 108 GIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTE 167
G+ +E DLR+ G + +V I+ + S ++GFAFV F NV+ A +A ++ N E
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 168 FKGKKIRCSTSQAK 181
G++IR S K
Sbjct: 113 LDGRRIRVDFSITK 126
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 196 EDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHN 234
DL++V S+ GP + V +V D + S +RGFAF+ + N
Sbjct: 61 RDLREVFSKYGP-IADVSIVYD-QQSRRSRGFAFVYFEN 97
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 31/73 (42%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V L T+ L+++F +G I V + + + FV+F A +A +
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 340 YELDGQALECSLA 352
ELDG+ + +
Sbjct: 111 MELDGRRIRVDFS 123
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 40/69 (57%)
Query: 108 GIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTE 167
G+ +E DLR+ G + +V I+ + S ++GFAFV F NV+ A +A ++ N E
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 168 FKGKKIRCS 176
G++IR S
Sbjct: 82 LDGRRIRVS 90
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 31/71 (43%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V L T+ L+++F +G I V + + + FV+F A +A +
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 340 YELDGQALECS 350
ELDG+ + S
Sbjct: 80 MELDGRRIRVS 90
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 197 DLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQK 244
DL++V S+ GP + V +V D + S +RGFAF+ + N A+ ++++
Sbjct: 31 DLREVFSKYGP-IADVSIVYDQQ-SRRSRGFAFVYFENVDDAKEAKER 76
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%)
Query: 106 IGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNN 165
+ G+ +E DLR+ G + +V I+ + S ++GFAFV F NV+ A +A ++ N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 166 TEFKGKKIRCSTSQAK 181
E G++IR S K
Sbjct: 80 MELDGRRIRVDFSITK 95
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 197 DLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHN 234
DL++V S+ GP + V +V D + S +RGFAF+ + N
Sbjct: 31 DLREVFSKYGP-IADVSIVYDQQ-SRRSRGFAFVYFEN 66
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 31/73 (42%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V L T+ L+++F +G I V + + + FV+F A +A +
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 340 YELDGQALECSLA 352
ELDG+ + +
Sbjct: 80 MELDGRRIRVDFS 92
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 45/76 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+GG+ + + L G++T+++I ++ +++GFAFV F E A+ AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 164 NNTEFKGKKIRCSTSQ 179
N +E G+ IR + ++
Sbjct: 75 NESELFGRTIRVNLAK 90
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 42/71 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G + + +E LR + G + +++M ++ +KG+ F+TF + E A KA+++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 164 NNTEFKGKKIR 174
N E G+ ++
Sbjct: 89 NGFELAGRPMK 99
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 49/88 (55%), Gaps = 2/88 (2%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKV-VVPPAKPGQEKNRIGFVHFAERSS 329
G++ +YV +L N+T+D L+ +FE GRI + ++ ++ G+ K GF+ F++
Sbjct: 22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG-YGFITFSDSEC 80
Query: 330 AMKALKNTEKYELDGQALECSLAKPQAD 357
A KAL+ +EL G+ ++ + D
Sbjct: 81 AKKALEQLNGFELAGRPMKVGHVTERTD 108
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 38/178 (21%), Positives = 86/178 (48%), Gaps = 13/178 (7%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
R+++G+I G + +++ + GP + ++ D + ++GFAF+EY + A+ +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGP-IKSIDXSWD-SVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 243 QK-----MTNPNFKLGTNAPTVSWADPRNVDSSGASQVKA---VYVKNLPRNVTQDQLKK 294
++ + N K+G + + A P + A + +A +YV ++ ++++ D +K
Sbjct: 72 EQXNSVXLGGRNIKVGRPS-NIGQAQP--IIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 295 LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLA 352
+FE G+I + + GF+ + + S+ A+ + ++L GQ L A
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 76/168 (45%), Gaps = 23/168 (13%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
VY+G I ++ E +R G + + + ++KGFAFV + E A A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 164 NNTEFKGKKIRCST-----------------SQAKYRLFIGNIPRNWGSEDLQKVVSEVG 206
N+ G+ I+ ++A R+++ ++ ++ +D++ V G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 207 PGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTNPN-FKLG 253
+ L +D + ++G+ FIEY A+ S+ +++ N F LG
Sbjct: 135 K-IKSCTLARD-PTTGKHKGYGFIEYEK---AQSSQDAVSSXNLFDLG 177
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 12/72 (16%), Positives = 36/72 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+ + D S+ D++ ++ G++ + + + ++KG+ F+ + + + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 164 NNTEFKGKKIRC 175
N + G+ +R
Sbjct: 172 NLFDLGGQYLRV 183
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 80/170 (47%), Gaps = 9/170 (5%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
L++GN+ + +ED+ K +VG + ++++ D N N +AF+EYH A + Q
Sbjct: 3 LYVGNLDKA-ITEDILKQYFQVGGPIANIKIMIDKNNK--NVNYAFVEYHQSHDANIALQ 59
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHH-GRI 302
+ ++ N ++WA S + ++V +L NV + L+ F+ +
Sbjct: 60 TLNGK--QIENNIVKINWAFQS--QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
Query: 303 TKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYELDGQALECSLA 352
+ V+ + G + GFV F + A A+ + + +L+G+ L + A
Sbjct: 116 SGHVMWDMQTGSSRGY-GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/150 (22%), Positives = 73/150 (48%), Gaps = 11/150 (7%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G + +E L+ + Q G + ++IM K+ ++N +AFV + A+ A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61
Query: 164 NNTEFKGKKIRC--------STSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELV 215
N + + ++ S+S + LF+G++ N E L+ + ++G ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG-HVM 120
Query: 216 KDMKNSSNNRGFAFIEYHNHKCAEYSRQKM 245
DM+ S +RG+ F+ + + A+ + M
Sbjct: 121 WDMQTGS-SRGYGFVSFTSQDDAQNAMDSM 149
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
+ +YV NL + +T+D LK+ F+ G I + + K + N FV + + A AL+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNY-AFVEYHQSHDANIALQ 59
Query: 336 NTEKYELDGQALECSLAK 353
L+G+ +E ++ K
Sbjct: 60 -----TLNGKQIENNIVK 72
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/73 (17%), Positives = 35/73 (47%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++G + + + LR+ + +M + ++G+ FV+F + + A A+D +
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 164 NNTEFKGKKIRCS 176
+ G+ +R +
Sbjct: 150 QGQDLNGRPLRIN 162
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 42/71 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+GG+ + + L G++T+++I ++ +++GFAFV F E A+ AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 164 NNTEFKGKKIR 174
N +E G+ IR
Sbjct: 126 NESELFGRTIR 136
>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 = 49.7 bits (117), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 45/76 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+GG+ + + L G++T+++I ++ +++GFAFV F E A+ AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 164 NNTEFKGKKIRCSTSQ 179
N +E G+ IR + ++
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 52/96 (54%), Gaps = 9/96 (9%)
Query: 268 DSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAE 326
D S VK +YV+NL + +++ ++K F + + P A +K R FVHF+
Sbjct: 8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNN-------IKPGAVERVKKIRDYAFVHFSN 60
Query: 327 RSSAMKALKNTEKYELDGQALECSLAKPQADQKSAG 362
R A++A+K LDG +E +LAKP D+ S+G
Sbjct: 61 REDAVEAMKALNGKVLDGSPIEVTLAKP-VDKDSSG 95
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 45/76 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+GG+ + + L G++T+++I ++ +++GFAFV F E A+ AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 164 NNTEFKGKKIRCSTSQ 179
N +E G+ IR + ++
Sbjct: 68 NESELFGRTIRVNLAK 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 = 49.3 bits (116), Expect = 5e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 42/71 (59%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+GG+ + + L G++T+++I ++ +++GFAFV F E A+ AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 164 NNTEFKGKKIR 174
N +E G+ IR
Sbjct: 65 NESELFGRTIR 75
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 44/81 (54%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P + + + +P + ++ +LR SIGEV ++++ K + + G+ FV + + A +
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 159 AIDKLNNTEFKGKKIRCSTSQ 179
AI+ LN + K I+ S ++
Sbjct: 62 AINTLNGLRLQSKTIKVSYAR 82
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V LP+N+TQD+L+ LF G + + K GFV++ A +A+
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 338 EKYELDGQALECSLAKP 354
L + ++ S A+P
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>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 = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 44/80 (55%)
Query: 100 HGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKA 159
G+ + + +P + ++ +LR SIGEV ++++ K + + G+ FV + + A +A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 160 IDKLNNTEFKGKKIRCSTSQ 179
I+ LN + K I+ S ++
Sbjct: 78 INTLNGLRLQSKTIKVSYAR 97
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V LP+N TQD+L+ LF G + + K GFV++ A +A+
Sbjct: 24 VNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
Query: 340 YELDGQALECSLAKP 354
L + ++ S A+P
Sbjct: 84 LRLQSKTIKVSYARP 98
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 268 DSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAER 327
D G + +K V NL + D L+++FE +GR+ V +P + +E FV F ++
Sbjct: 43 DVEGMTSLK---VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 328 SSAMKALKNTEKYELDGQALECSLAK 353
A A+ + LDG+ L +A+
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMAR 125
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 109 IPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEF 168
+ + S LR + G V +V I + + + E++GFAFV F + A A+D ++
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 169 KGKKIRCSTSQ 179
G+++R ++
Sbjct: 115 DGRELRVQMAR 125
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/160 (23%), Positives = 75/160 (46%), Gaps = 34/160 (21%)
Query: 104 VYIGGIPHDASEHDLRDFCQS---IGEVTEV--RIMKGKDSSENKGFAFVTFRNVELASK 158
+Y+G IP +E + DF + +G +T+ + +++K FAF+ FR+V+ ++
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 159 AIDKLNNTEFKGK--KIR------------------------CSTSQAKYRLFIGNIPRN 192
A+ + F+G+ KIR + ++LFIG +P
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 193 WGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEY 232
+ ++++++ GP + LVKD + ++G+AF EY
Sbjct: 126 LNDDQVKELLTSFGP-LKAFNLVKD-SATGLSKGYAFCEY 163
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 42/78 (53%)
Query: 96 ALPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVEL 155
+P +++IGG+P+ ++ +++ S G + ++K + +KG+AF + ++ +
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168
Query: 156 ASKAIDKLNNTEFKGKKI 173
+AI LN + KK+
Sbjct: 169 TDQAIAGLNGMQLGDKKL 186
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 100 HGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKA 159
H +++IGG+ + +E L+ G ++EV ++K + +S+++GFAF+TF N A A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64
Query: 160 IDKLNNTEFKGKKIRCSTSQ 179
+N GK I+ ++
Sbjct: 65 AKDMNGKSLHGKAIKVEQAK 84
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG + R + L+ V + GP ++ V L+KD +S +RGFAFI + N A+ +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGP-ISEVLLIKD--RTSKSRGFAFITFENPADAKNAA 65
Query: 243 QKM 245
+ M
Sbjct: 66 KDM 68
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ IP + DLR G++ +V I+ + S KGF FVTF N A +A +KL
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 89
Query: 164 NNTEFKGKKIRCSTSQAK 181
+ T +G+KI + + A+
Sbjct: 90 HGTVVEGRKIEVNNATAR 107
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 169 KGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFA 228
+G + RL + NIP + DL+++ + G + VE++ + + S +GF
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIFNERGS---KGFG 72
Query: 229 FIEYHNHKCAEYSRQKM 245
F+ + N A+ +R+K+
Sbjct: 73 FVTFENSADADRAREKL 89
Score = 31.6 bits (70), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 2/91 (2%)
Query: 266 NVDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFA 325
++++ SQ K ++V N+P L+++F G+I V + + G + GFV F
Sbjct: 20 HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFE 77
Query: 326 ERSSAMKALKNTEKYELDGQALECSLAKPQA 356
+ A +A + ++G+ +E + A +
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVNNATARV 108
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ IP + DLR G++ +V I+ + S KGF FVTF N A +A +KL
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 75
Query: 164 NNTEFKGKKIRCSTSQAK 181
+ T +G+KI + + A+
Sbjct: 76 HGTVVEGRKIEVNNATAR 93
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
RL + NIP + DL+++ + G + VE++ + + S +GF F+ + N A+ +R
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGK-ILDVEIIFNERGS---KGFGFVTFENSADADRAR 72
Query: 243 QKM 245
+K+
Sbjct: 73 EKL 75
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
K ++V N+P L+++F G+I V + + G + GFV F + A +A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADADRARE 73
Query: 336 NTEKYELDGQALECSLAKPQADQKSA 361
++G+ +E + A + S
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNSG 99
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIG-EVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
V + +P A+E D+R QS G + EVR+M+ K S +++GFAFV F +++ A++ ++
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V NL + D L+++FE +GR+ V +P + FV F +R A A +
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 340 YELDGQALECSLAK 353
ELDG+ L +A+
Sbjct: 78 AELDGRELRVQVAR 91
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 35/79 (44%)
Query: 109 IPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEF 168
+ + S LR + G V +V I + + +GFAFV F + A A ++ E
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL 80
Query: 169 KGKKIRCSTSQAKYRLFIG 187
G+++R ++ R G
Sbjct: 81 DGRELRVQVARYGRRDLSG 99
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%)
Query: 105 YIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++GG+ D S+ DL+D+ GEV + I ++ ++GF F+ F++ K +D+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 267 VDSSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAE 326
+D G + +K V NL + D L+++FE +GR+ V +P + +E FV F +
Sbjct: 65 MDVEGMTSLK---VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
Query: 327 RSSAMKALKNTEKYELDGQALECSLAK 353
+ A A+ + LDG+ L +A+
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMAR 148
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 40/78 (51%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ + + + + S LR + G V +V I + + + E++GFAFV F + A A+D
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 162 KLNNTEFKGKKIRCSTSQ 179
++ G+++R ++
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 33/50 (66%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV 153
++IGG+ + +E LR++ + G++T+ +M+ S ++GF FVTF ++
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSS--ENKGFAFVTFRNVELASKAI 160
++++G +P SE DLR+ + G V E+ +++ + + ++KG FVTF + A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 DKLNNTE 167
+ L+N +
Sbjct: 65 NALHNMK 71
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDM-KNSSNNRGFAFIEYHNHKCAEYS 241
++F+G +PR W +DL+++ + G V + +++D +N ++G F+ ++ K A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYG-AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 242 RQKMTNPNFKLGTNAPT 258
+ + N G + P
Sbjct: 64 QNALHNMKVLPGMHHPI 80
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 12/63 (19%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVV-------PPAKPGQEKNRIGFVHFAERSSA 330
++V +PR ++ L++LFE +G + ++ V PP G FV F R +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-----CCFVTFYTRKAA 60
Query: 331 MKA 333
++A
Sbjct: 61 LEA 63
>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 = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 42/78 (53%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V++G + + + D++ G +++ R++K + ++KG+ FV+F N A AI ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 164 NNTEFKGKKIRCSTSQAK 181
G++IR + + K
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKV-VVPPAKPGQEKNRIGFVHFAERSSAMKALKN 336
V+V +L +T + +K F GRI+ VV G+ K GFV F + A A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQ 76
Query: 337 TEKYELDGQALECSLA--KPQA 356
L G+ + + A KP A
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPA 98
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 54/92 (58%), Gaps = 9/92 (9%)
Query: 273 SQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
++VK ++V+NL VT++ L+K F G++ +V ++ FVHF +R +A+K
Sbjct: 13 AKVKVLFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDRGAAVK 64
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
A+ E++G+ +E LAKP D+K +G S
Sbjct: 65 AMDEMNGKEIEGEEIEIVLAKP-PDKKRSGPS 95
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
+++I G+P ++ +L + C++ G V ++R++ + + + KG A+V + N AS+A+ K
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77
Query: 163 LNNTEFKGKKIRCSTSQA 180
++ K I+ + S +
Sbjct: 78 MDGMTIKENIIKVAISNS 95
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 44/96 (45%), Gaps = 11/96 (11%)
Query: 173 IRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNN----RGFA 228
R STS K++LFI +P + E+L+++ G VKD++ +N +G A
Sbjct: 9 FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGT-------VKDLRLVTNRAGKPKGLA 61
Query: 229 FIEYHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADP 264
++EY N A + KM K +S + P
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP 97
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/76 (19%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+++ LP + T+++L+++ + HG + + + + G+ K + +V + S A +A+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG-LAYVEYENESQASQAV--- 75
Query: 338 EKYELDGQALECSLAK 353
++DG ++ ++ K
Sbjct: 76 --MKMDGMTIKENIIK 89
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P VY GGI ++ +R G++ E+R+ KG++FV F E A+
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHESAAH 76
Query: 159 AIDKLNNTEFKGKKIRC 175
AI +N T +G ++C
Sbjct: 77 AIVSVNGTTIEGHVVKC 93
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S +++G +P D +E ++R + G+ EV I K +KGF F+ LA A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKV 69
Query: 162 KLNNTEFKGKKIR 174
+L+N +GK++R
Sbjct: 70 ELDNMPLRGKQLR 82
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 6/92 (6%)
Query: 273 SQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Q ++V NLP ++T+++++KLFE +G+ +V + + GF+ R+ A
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEI 66
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
A + L G+ L A A S S
Sbjct: 67 AKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 177 TSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHK 236
T + RLF+GN+P + E+++K+ + G V + KD +GF FI
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKD-------KGFGFIRLETRT 62
Query: 237 CAEYSRQKMTN 247
AE ++ ++ N
Sbjct: 63 LAEIAKVELDN 73
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 46/93 (49%)
Query: 275 VKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
++ + V +P V + QL++LFE +G I V + + ++ GFV F SSA +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 335 KNTEKYELDGQALECSLAKPQADQKSAGGSVSE 367
+ + + L+ +LA + G+V +
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQRPGIAGAVGD 134
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ VY+GG+ SE L + G V + K + + +++G+ FV F + E A AI
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 162 KLNNTEFKGKKIRCSTSQA 180
++ + GK IR + + A
Sbjct: 76 IMDMIKLYGKPIRVNKASA 94
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 2/94 (2%)
Query: 273 SQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Q VYV L V++ L +LF G + +P + + GFV F A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGSVS 366
A+K + +L G+ + + K A K+ G S
Sbjct: 73 AIKIMDMIKLYGKPIRVN--KASAHNKNLSGPSS 104
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
PP + YIG IPH A+E DL Q+ G + + + KG F+ + E A+
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK------HYPEKGCCFIKYDTHEQAA 77
Query: 158 KAIDKLNNTEFKGKKIR 174
I L N F+G+ +R
Sbjct: 78 VCIVALANFPFQGRNLR 94
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++IGG+ D ++ DL+D+ GEV + + + ++GF FV F+ E K +D+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 42/79 (53%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
V++G + + + D++ G++++ R++K + ++KG+ FV+F N A AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 163 LNNTEFKGKKIRCSTSQAK 181
+ G++IR + + K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKV-VVPPAKPGQEKNRIGFVHFAERSSAMKALKN 336
V+V +L +T + +K F G+I+ VV G+ K GFV F + A A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKG-YGFVSFYNKLDAENAIVH 76
Query: 337 TEKYELDGQALECSLA--KPQA 356
L G+ + + A KP A
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPA 98
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
+++IG IP + E DL+ + G++ E+ ++K + + +KG AF+T+ E A KA
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 163 LN 164
L+
Sbjct: 75 LH 76
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 269 SSGASQVK-----AVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVH 323
SSG+S +K +++ +PRN+ + LK LFE G+I ++ V + F+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 324 FAERSSAMKA 333
+ ER SA+KA
Sbjct: 62 YCERESALKA 71
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LFIG IPRN +DL+ + E G + + ++KD + + ++G AF+ Y + A ++
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGK-IYELTVLKD-RFTGMHKGCAFLTYCERESALKAQ 72
Query: 243 QKMTNPNFKLGTNAP 257
+ G N P
Sbjct: 73 SALHEQKTLPGMNRP 87
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 50/253 (19%), Positives = 93/253 (36%), Gaps = 14/253 (5%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++ I G+P D + ++ D +K + KG AFVT N E A AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 163 LNNTEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSS 222
+ + + +++ L + N+P + + +++V G + LV + +
Sbjct: 77 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-ERTG 134
Query: 223 NNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKN 282
++G+ F EY A ++ + LG V W D + + + + V
Sbjct: 135 QSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQL-TPALLHSRCLCVDR 191
Query: 283 LPRNVTQ-DQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE 341
LP D L + T + + GQ K + + A +A + +
Sbjct: 192 LPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG-FAVLEYETAEMAEEAQQQADGLS 250
Query: 342 LDGQALECSLAKP 354
L G L S P
Sbjct: 251 LGGSHLRVSFCAP 263
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/182 (20%), Positives = 72/182 (39%), Gaps = 12/182 (6%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++ I G+P D + ++ D +K + KG AFVT N E A AI+
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 163 LNNTEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSS 222
+ + + +++ L + N+P + + +++V G + LV + +
Sbjct: 77 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-ERTG 134
Query: 223 NNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKN 282
++G+ F EY A ++ + LG V W D + + + + V
Sbjct: 135 QSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQL-TPALLHSRCLCVDR 191
Query: 283 LP 284
LP
Sbjct: 192 LP 193
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKV-VVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+ V NLP ++TQ Q ++L G + + +V + GQ K GF + ++ SA +A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG-YGFAEYMKKDSAARA 153
>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 = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 50/253 (19%), Positives = 93/253 (36%), Gaps = 14/253 (5%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++ I G+P D + ++ D +K + KG AFVT N E A AI+
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINA 74
Query: 163 LNNTEFKGKKIRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSS 222
+ + + +++ L + N+P + + +++V G + LV + +
Sbjct: 75 FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFG-SLERCFLVYS-ERTG 132
Query: 223 NNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGASQVKAVYVKN 282
++G+ F EY A ++ + LG V W D + + + + V
Sbjct: 133 QSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQL-TPALLHSRCLCVDR 189
Query: 283 LPRNVTQ-DQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEKYE 341
LP D L + T + + GQ K + + A +A + +
Sbjct: 190 LPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG-FAVLEYETAEMAEEAQQQADGLS 248
Query: 342 LDGQALECSLAKP 354
L G L S P
Sbjct: 249 LGGSHLRVSFCAP 261
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V NL V+ +++LF G + K V + G+ VHF R+ A+KA+K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQY 149
Query: 338 EKYELDGQALECSLAKPQAD 357
+ LDG+ ++ L Q D
Sbjct: 150 KGVPLDGRPMDIQLVASQID 169
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++GG+ + + D++ + + G+V + +M K ++ ++GF FVTF + ++ K + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 164 NNTEFKGKKIRCSTS 178
+ E K + C +
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V L N T + +K FE G++ ++ K GFV F E ++ +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 338 EKYELDGQALECSLA 352
+E++ + +EC A
Sbjct: 61 HFHEINNKMVECKKA 75
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 94 LLALPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV 153
L PP ++++G + SE D+R ++ G + E I++G D + +KG AFV + +
Sbjct: 8 CLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSH 66
Query: 154 ELASKAIDKLNNTE 167
A AI+ L+ ++
Sbjct: 67 AEAQAAINALHGSQ 80
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
K ++VK L + T++ LK+ F+ G + +V + G K GFV F A A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKG-FGFVDFNSEEDAKAAKE 72
Query: 336 NTEKYELDGQALECSLAKPQ 355
E E+DG + AKP+
Sbjct: 73 AMEDGEIDGNKVTLDWAKPK 92
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ D +E L+ +S RI+ +++ +KGF FV F + E A A + +
Sbjct: 18 LFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 164 NNTEFKGKKI 173
+ E G K+
Sbjct: 75 EDGEIDGNKV 84
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 9/89 (10%)
Query: 178 SQAKYRLFIGNIPRNWGSEDL-QKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHK 236
SQ LF+ + SED ++ + E G +V D + S+ +GF F+++++ +
Sbjct: 12 SQPSKTLFVKGL-----SEDTTEETLKESFDGSVRARIVTDRETGSS-KGFGFVDFNSEE 65
Query: 237 CAEYSRQKMTNPNFKLGTNAPTVSWADPR 265
A+ +++ M + ++ N T+ WA P+
Sbjct: 66 DAKAAKEAMEDG--EIDGNKVTLDWAKPK 92
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%)
Query: 109 IPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEF 168
+P D ++ +L ++IG + RIM+ + + G+AFV F + + +AI LN
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 169 KGKKIRCSTSQ 179
+ K+++ S ++
Sbjct: 71 RNKRLKVSYAR 81
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S++ + G+P +E DL+++ + GEV V++ K + +KGF FV F E K +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 162 K 162
+
Sbjct: 76 Q 76
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 11/104 (10%)
Query: 269 SSGASQVKAVYVKN-------LPRNVTQDQLKKLFEHHGRITKVVVPP-AKPGQEKNRIG 320
SSG+S VK K LP T+ LK+ F G + V V K G K G
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG-FG 60
Query: 321 FVHFAERSSAMKALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
FV F E + +K + ++++ +DG+ +C L + Q S S
Sbjct: 61 FVRFTEYETQVKVM--SQRHMIDGRWCDCKLPNSKQSQDSGPSS 102
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+++++G I + +LR + G V E I+K +AFV E A +AI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 62
Query: 162 KLNNTEFKGKKIRCSTSQAKYRLFIG 187
L+NTEF+GK++ S ++ R G
Sbjct: 63 GLDNTEFQGKRMHVQLSTSRLRTASG 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 32/50 (64%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRN 152
++++GG+ ++ LR + GEV + IMK K +++++GF FV F++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 35.4 bits (80), Expect = 0.078, Method: Composition-based stats.
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 1/93 (1%)
Query: 272 ASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAM 331
A ++ ++V L + TQ+ L+ F +G + V+ K + GFV F + +
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72
Query: 332 KALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
L + + LDG+ ++ P+ Q S S
Sbjct: 73 TVLA-SRPHTLDGRNIDPKPCTPRGMQPSGPSS 104
Score = 29.6 bits (65), Expect = 4.3, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKC 237
+LF+G + + E L+ S+ G V V ++KD K ++ +RGF F+++ + C
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCV-IMKD-KTTNQSRGFGFVKFKDPNC 70
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 12/73 (16%)
Query: 101 GSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV------- 153
G +++IGG+ ++ LR++ GEV E +M+ + ++GF FVTF +
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 154 -----ELASKAID 161
EL SK ID
Sbjct: 85 AQSRHELDSKTID 97
Score = 32.7 bits (73), Expect = 0.47, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSA 330
G+S K +++ L TQ+ L++ F G + + +V + GFV F +++
Sbjct: 22 GSSGCK-MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 331 MKALKNTEKYELDGQALECSLAKPQADQ 358
K L + ++ELD + ++ +A P+ Q
Sbjct: 81 DKVLAQS-RHELDSKTIDPKVAFPRRAQ 107
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 41/71 (57%)
Query: 109 IPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEF 168
+P + ++ + + SIG++ ++++ K + ++ G+ FV + + A KAI+ LN +
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 169 KGKKIRCSTSQ 179
+ K I+ S ++
Sbjct: 72 QTKTIKVSYAR 82
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 40/77 (51%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V LP+N+TQD+ K LF G I + K + GFV++++ + A KA+
Sbjct: 9 VNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Query: 340 YELDGQALECSLAKPQA 356
+L + ++ S A+P +
Sbjct: 69 LKLQTKTIKVSYARPSS 85
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++GG+ D E +R++ GEV + + +++ +GF F+TF+ E K ++K
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 37/63 (58%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+++++GG+P+ ++ LR + + G++ E ++ + + +++G+ FVT + A +A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 162 KLN 164
N
Sbjct: 78 DPN 80
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 5/93 (5%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V LP + T L+K FE G I + VV + + GFV A+R++A +A K+
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 338 EKYELDGQALECSL----AKPQADQKSAGGSVS 366
+DG+ +L AKP++ Q VS
Sbjct: 80 NPI-IDGRKANVNLAYLGAKPRSLQTGFAIGVS 111
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 40/71 (56%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
+++IGG+P+ ++ +++ S G + ++K + +KG+AF + ++ + +AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 163 LNNTEFKGKKI 173
LN + KK+
Sbjct: 63 LNGMQLGDKKL 73
Score = 32.7 bits (73), Expect = 0.48, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 182 YRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEY 232
++LFIG +P + ++++++ GP + LVKD + ++G+AF EY
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKD-SATGLSKGYAFCEY 50
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ + + +SE DL + G ++E+ + + KGFAFVTF E A KA ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 164 NNTEFKGKKIRCSTSQAK 181
+ F+G+ + S K
Sbjct: 71 DGQVFQGRMLHVLPSTIK 88
Score = 32.0 bits (71), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V+NL +++ L+KLF +G ++++ P ++ FV F A+KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA-- 68
Query: 338 EKYELDGQALE 348
E+DGQ +
Sbjct: 69 ---EVDGQVFQ 76
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V++GGI E ++R F G V EV+I+ + + +KG+ FV+F N K ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 164 NNTEFKGKKIRCSTSQAKYRL 184
N F GKK++ + K L
Sbjct: 71 IN--FHGKKLKLGPAIRKQNL 89
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 12/71 (16%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV--------- 153
+++IGG+ ++ LR++ GEV E +M+ + ++GF FVTF +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 154 ---ELASKAID 161
EL SK ID
Sbjct: 62 SRHELDSKTID 72
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+++ L TQ+ L++ F G + + +V + GFV F +++ K L +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 338 EKYELDGQALECSLA 352
++ELD + ++ +A
Sbjct: 63 -RHELDSKTIDPKVA 76
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 33/59 (55%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
+++GG+ D E +R++ GEV + + +++ +GF F+TF+ E K ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 35/59 (59%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
+ + + + D E DL++ + G ++ + + K K + ++KGFAF++F E A++AI
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P G ++I +P + ++ DL G V ++ K +S +K F FV+F N + A
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 159 AIDKLNNTEFKGKKIR 174
AI +N + K+++
Sbjct: 98 AIKAMNGFQVGTKRLK 113
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMKALKN 336
V++ L RNVT+D + ++F +G+I + +P + ++ +V F A KALK+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 337 TEKYELDGQALECS 350
+ ++DGQ + +
Sbjct: 67 MDGGQIDGQEITAT 80
Score = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/82 (19%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRI-MKGKDSSENKGFAFVTFRNVELASKAI 160
++V+IG + + ++ + + + G++ + + ++ +KG+A+V F N + A KA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 161 DKLNNTEFKGKKIRCSTSQAKY 182
++ + G++I + A +
Sbjct: 65 KHMDGGQIDGQEITATAVLAPW 86
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 13/90 (14%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR--------IGFV 322
G+S +++KNL + T++ LK +F G I + ++KN+ GFV
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTIS-----KKKNKAGVLLSMGFGFV 55
Query: 323 HFAERSSAMKALKNTEKYELDGQALECSLA 352
+ + A KALK + + +DG LE ++
Sbjct: 56 EYKKPEQAQKALKQLQGHTVDGHKLEVRIS 85
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSE---NKGFAFVTFRNVELASK 158
S ++I + +E L+ +G + I K K+ + + GF FV ++ E A K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 159 AIDKLNNTEFKGKKIRCSTSQ 179
A+ +L G K+ S+
Sbjct: 66 ALKQLQGHTVDGHKLEVRISE 86
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V++GGI E ++R F G V EV+I+ + + +KG+ FV+F N K ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 164 NNTEFKGKKIRC 175
N F GKK++
Sbjct: 71 IN--FHGKKLKL 80
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKAL 334
+YV NLPR +T DQL +F +G I + + K + FV + +R A +A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+ +P ++ L G + + I++ K + +G AFV + E A +AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 162 KLNNT 166
LNN
Sbjct: 74 ALNNV 78
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+YV LP+ ++Q ++++LF +GRI + + +GF+ F +R A +A+K
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG- 62
Query: 338 EKYELDGQ 345
L+GQ
Sbjct: 63 ----LNGQ 66
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 30/63 (47%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+ G+P S+ ++ G + RI+ + + ++G F+ F A +AI
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 162 KLN 164
LN
Sbjct: 62 GLN 64
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V NL V+ +++LF G + K V + G+ VHF R+ A+KA+K +
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD-VHFERRADALKAMKQYKG 98
Query: 340 YELDGQALECSLAKPQAD 357
LDG+ ++ L Q D
Sbjct: 99 VPLDGRPMDIQLVASQID 116
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V++GGI E ++R F G V EV+I+ + + +KG+ FV+F N K ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 164 NNTEFKGKKIRC 175
N F GKK++
Sbjct: 72 IN--FHGKKLKL 81
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 280 VKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNTEK 339
V NL V+ +++LF G + K V + G+ VHF R+ A+KA+K +
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD-VHFERRADALKAMKQYKG 98
Query: 340 YELDGQALECSLAKPQAD 357
LDG+ ++ L Q D
Sbjct: 99 VPLDGRPMDIQLVASQID 116
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRI-MKGKDSSENKGFAFVTFRNVELASKAI 160
S++ + IP A++ ++R+ + GE+ VR+ K + ++GF FV F + A KA
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 161 DKL-NNTEFKGKKI 173
+ L ++T G+++
Sbjct: 76 NALCHSTHLYGRRL 89
Score = 35.8 bits (81), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNR-IGFVHFAERSSAMKAL 334
+ V+N+P Q ++++LF G + V +P G +R GFV F + A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 2/95 (2%)
Query: 179 QAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCA 238
Q ++ + NIP +++++ S G T V L K M + +RGF F+++ + A
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKT-VRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 239 EYSRQKMTNPNFKLGTNAPTVSWADPRNVDSSGAS 273
+ + + + G + WAD SG S
Sbjct: 72 KKAFNALCHSTHLYGRRL-VLEWADSEVTVQSGPS 105
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G + + A+ +L G V V I+ K S KGFA++ F + E ++ L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 164 NNTEFKGKKIR 174
+ + F+G++I+
Sbjct: 67 DESLFRGRQIK 77
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++G IP E DL+ + G + E+ ++K + + +KG AF+T+ + A KA
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 163 LN 164
L+
Sbjct: 77 LH 78
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
++V +PR + + LK LFE GRI ++ V + F+ + R SA+KA
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Score = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSR 242
+LF+G IPR +DL+ + E G + + ++KD + + ++G AF+ Y A ++
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGR-IYELTVLKD-RLTGLHKGCAFLTYCARDSALKAQ 74
Query: 243 QKMTNPNFKLGTNAP 257
+ G N P
Sbjct: 75 SALHEQKTLPGMNRP 89
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 11/85 (12%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +++ P D E +L + G + EV+I+ G FAFV F E A+KAI+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEAESAAKAIE 83
Query: 162 KLNNTEFKGKKIRCSTSQA---KYR 183
+++ F + + S+ +YR
Sbjct: 84 EVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V+ P +V + +L ++F G P K + N FV F E SA KA++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFG--------PMKEVKILNGFAFVEFEEAESAAKAIEEV 85
Query: 338 EKYELDGQALECSLAK 353
Q LE +K
Sbjct: 86 HGKSFANQPLEVVYSK 101
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSA 330
GA VYV NLPR+ LK+ G VP Q R F+H+ + ++A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGS-----VPLRLTWQGPRRRAFLHYPDSAAA 69
Query: 331 MKALKNTEKYELDGQALECSLAKPQADQ 358
+A+ + L L +LA+ Q D+
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQQRDK 97
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 117 DLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNNTEFKGKKIRCS 176
DL DF ++G+V +VRI+ ++S +KG A+V F ++ AI L G I
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQ 99
Query: 177 TSQAK 181
SQA+
Sbjct: 100 ASQAE 104
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G + + A+ +L G V V I+ K S KGFA++ F + E ++ L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 164 NNTEFKGKKIR 174
+ + F+G++I+
Sbjct: 68 DESLFRGRQIK 78
>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 = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 99 PHGSE--VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELA 156
P GS V++G + + + + G +++ R++K + ++KG+ FV+F N A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 157 SKAIDKLNNTEFKGKKIRCSTSQAK 181
AI ++ G++IR + + K
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +++ P D E +L + G + EV+I+ G FAFV F E A+KAI+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEAESAAKAIE 56
Query: 162 KLNNTEFKGKKIRCSTSQ 179
+++ F + + S+
Sbjct: 57 EVHGKSFANQPLEVVYSK 74
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
++V+ P +V + +L ++F G P K + N FV F E SA KA++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFG--------PMKEVKILNGFAFVEFEEAESAAKAIEEV 58
Query: 338 EKYELDGQALECSLAK 353
Q LE +K
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
+ + KNL N+T+D+LK++FE I V ++ G+ K I ++ F + A K L+
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKG-IAYIEFKSEADAEKNLE 71
Query: 336 NTEKYELDGQAL 347
+ E+DG+++
Sbjct: 72 EKQGAEIDGRSV 83
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S +YI G+ ++ DL CQ G++ + + K +++ KG+ FV F + A KA+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 162 KL 163
L
Sbjct: 66 AL 67
Score = 28.9 bits (63), Expect = 6.6, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 29/64 (45%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSA 330
G+S +Y++ L T L KL + +G+I K + GFV F S+A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 331 MKAL 334
KA+
Sbjct: 61 QKAV 64
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 101 GSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAI 160
G V+I + D+ E L + Q G++ VR++ D+ +KG AF F E A K +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 161 DKLNNTEFKGKKIRCSTSQAKYRLFI 186
+ E +G ++ Q K L +
Sbjct: 75 -AAASLEAEGGGLKLDGRQLKVDLAV 99
>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 = 37.4 bits (85), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
++ V VKNLP++ Q+++ K F+H G I V V A ++ R + FA A+ A
Sbjct: 40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV--ADSLKKNFRFARIEFARYDGALAA 97
Query: 334 LKNTEK 339
+ T K
Sbjct: 98 ITKTHK 103
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 37/175 (21%), Positives = 69/175 (39%), Gaps = 16/175 (9%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
++ P ++ ++RD Q I V + + ++ FA++ + E A ++KL
Sbjct: 120 LWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 164 NNTEFKG------------KKIRCSTSQAKYR-LFIGNIPRNWGSEDLQKVVSEVGPGVT 210
N + +G K R ++ + R + I N+ E+L + E +
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIE 239
Query: 211 GVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQKMTNPNFKLGTNAPTVSWADPR 265
+ + K S N AF + N AE + Q + LG +VS AD +
Sbjct: 240 KINIPAGQKEHSFNNCCAFXVFENKDSAERALQXNRSL---LGNREISVSLADKK 291
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 11/87 (12%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPA--KPGQEKNRIGFVHFAERSSA 330
+Y+ NL + +D+LKK +F G+I ++V + GQ FV F E SSA
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ-----AFVIFKEVSSA 64
Query: 331 MKALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + + AK +D
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
QV +YVKNL + ++L+K F G IT V G GFV F+ A KA
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSSPEEATKA 71
Query: 334 LKNTEKYELDGQALECSLAKPQADQKSA 361
+ + + L +LA+ + +++S
Sbjct: 72 VTEMNGRIVATKPLYVALAQRKEERQSG 99
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+ + + LR G +T ++M + +KGF FV F + E A+KA+ ++
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 164 NNTEFKGKKIRCSTSQAK 181
N K + + +Q K
Sbjct: 76 NGRIVATKPLYVALAQRK 93
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 269 SSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERS 328
SSG+S + +Y+ NL VT D L++LF +P A K+ FV + +++
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQN 55
Query: 329 SAMKALKN-TEKYELDGQALEC 349
A++A++ + K EL G+ +E
Sbjct: 56 WAIRAIETLSGKVELHGKIMEV 77
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATN 66
Query: 333 ALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + + AK +D
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
VYI G P DA+ D++++ + G+V ++ M+ KG FV F ++E A K ++
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVE 168
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 274 QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
++ V VKNLP++ Q+++ K F+H G I V V A ++ R + FA A+ A
Sbjct: 3 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV--ADSLKKNFRFARIEFARYDGALAA 60
Query: 334 LKNTEKYE-----LDGQALECSL 351
+ T K + EC+L
Sbjct: 61 ITKTHKVVGQNEIIVSHLTECTL 83
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 36.6 bits (83), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVT--------EVRIMKGKDSSENKGFAFVTFRNV 153
S +Y+ G+ + DL DF + G V + I K++ + KG A V++ +
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 154 ELASKAIDKLNNTEFKGKKIRCSTSQAK 181
A A++ + +F+G K++ S ++ K
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 36.2 bits (82), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 93 ELLALPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRN 152
EL PP+ Y+G +P + + D+ + + + VR+++ KD+ + KGF +V F
Sbjct: 9 ELPTEPPY--TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDE 65
Query: 153 VELASKAI 160
V+ +A+
Sbjct: 66 VDSLKEAL 73
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEV-RIMKGKDSSENKGFAFVTFRNVELASKAI 160
S ++IG + + E L D + G + + +IM+ D+ +KG+AF+ F + + + AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 161 DKLNNTEFKGKKIRCSTSQAK 181
+ +N + I S + K
Sbjct: 66 EAMNGQYLCNRPITVSYAFKK 86
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 35.8 bits (81), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++G + ++ D+R + G + E +++G D + +KG AFV F+ A AI+
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGT-SKGCAFVKFQTHAEAQAAINT 72
Query: 163 LNNT 166
L+++
Sbjct: 73 LHSS 76
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 35.8 bits (81), Expect = 0.053, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 70 NGQDLMGQPI 79
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++G + SE D+ Q G + E +++G D S +KG AFV F + A AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSHTEAQAAIHA 75
Query: 163 LNNTE 167
L+ ++
Sbjct: 76 LHGSQ 80
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 35.4 bits (80), Expect = 0.065, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 70 NGQDLMGQPI 79
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 35.4 bits (80), Expect = 0.066, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 68
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 35.4 bits (80), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ---AFVIFKEVSSATN 64
Query: 333 ALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + AK +D
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSD 89
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 35.4 bits (80), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Y+ NL + +D+LKK +F G+I ++V ++ + + + FV F E SSA
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMRGQ-AFVIFKEVSSATN 67
Query: 333 ALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + + AK +D
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 35.4 bits (80), Expect = 0.074, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 70 NGQDLMGQPI 79
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 35.4 bits (80), Expect = 0.075, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 72 NGQDLMGQPI 81
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.4 bits (80), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V NL V+ +++LF G + K V + G+ VHF ++ A+KA+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD-VHFERKADALKAMKQY 89
Query: 338 EKYELDGQALECSLA 352
LDG+ + L
Sbjct: 90 NGVPLDGRPMNIQLV 104
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 35.4 bits (80), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ---AFVIFKEVSSATN 66
Query: 333 ALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + AK +D
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSD 91
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 35.4 bits (80), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 277 AVYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMK 332
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ---AFVIFKEVSSATN 67
Query: 333 ALKNTEKYELDGQALECSLAKPQAD 357
AL++ + + + AK +D
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 35.0 bits (79), Expect = 0.081, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 63
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 64 LRSMQGFPFYDKPMRIQYAKTDSD 87
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.081, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 67
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 62
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 63 LRSMQGFPFYDKPMRIQYAKTDSD 86
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.0 bits (79), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 271 GASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSA 330
G+S V+V ++T+D+L++ F +G + V +P KP + FV FA+ A
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP--KPFRA---FAFVTFADDQIA 55
Query: 331 MKALKNTEKYELDGQALECSLAKPQADQKSA 361
E + G ++ S A+P+ + S
Sbjct: 56 QSLCG--EDLIIKGISVHISNAEPKHNSNSG 84
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S V++G D +E +LR+F G+V +V I K + FAFVTF + ++A
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60
Query: 162 KLNNTEFKGKKIRCSTSQAKY 182
+ + KG + S ++ K+
Sbjct: 61 E--DLIIKGISVHISNAEPKH 79
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 35.0 bits (79), Expect = 0.088, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 68
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 35.0 bits (79), Expect = 0.092, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 68
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 35.0 bits (79), Expect = 0.093, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 67
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 35.0 bits (79), Expect = 0.093, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 64
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 65 LRSMQGFPFYDKPMRIQYAKTDSD 88
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 35.0 bits (79), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
VYI G P DA+ D++++ + G+V ++ + + KG FV F ++E A K ++
Sbjct: 113 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 169
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 35.0 bits (79), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
VYI G P DA+ D++++ + G+V ++ + + KG FV F ++E A K ++
Sbjct: 114 VYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 170
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 35.0 bits (79), Expect = 0.100, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 85 NGQDLMGQPI 94
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 4/90 (4%)
Query: 184 LFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAEYSRQ 243
LFI ++P+ +G +DL ++ G V+ + N S + F F+ Y N A+ + Q
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS--KCFGFVSYDNPVSAQAAIQ 85
Query: 244 KMTNPNFKLGTNAPTVSWADPRNVDSSGAS 273
M F++G V +N SG S
Sbjct: 86 SMN--GFQIGMKRLKVQLKRSKNDSKSGPS 113
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+++ +LP+ L ++F G + V K GFV + SA A+++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 338 EKYELDGQALECSLAKPQADQKSA 361
+++ + L+ L + + D KS
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKSG 111
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 278 VYVKNLPRNVTQDQLKK----LFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKA 333
+Y+ NL + +D+LKK +F G+I ++V + + + FV F E SSA A
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ---AFVIFKEVSSATNA 65
Query: 334 LKNTEKYELDGQALECSLAKPQAD 357
L++ + + + + AK +D
Sbjct: 66 LRSMQGFPFYDKPMRIQYAKTDSD 89
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ G+ +A+E D+ D GE+ + + + + KG+ V + + A A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 164 NNTEFKGKKI 173
N + G+ I
Sbjct: 86 NGQDLMGQPI 95
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
++++G + + +LR + G V E ++K +AFV A AI +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 163 LNNTEFKGKKI 173
LN E KGK+I
Sbjct: 63 LNGKEVKGKRI 73
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 269 SSGAS-QVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAER 327
SSG+S ++V N+ T +L+ LFE GR+ + V FVH +
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKE 53
Query: 328 SSAMKALKNTEKYELDGQALECSLA 352
+ A A+ E+ G+ + L+
Sbjct: 54 ADAKAAIAQLNGKEVKGKRINVELS 78
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
VYI G P DA+ D++++ + G+V ++ M+ KG FV F ++E A K ++
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVE 70
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 33/71 (46%)
Query: 103 EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDK 162
EV + + E L+D C+ GEV EV I+ + ++ G A V F + A + +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 163 LNNTEFKGKKI 173
L+ T G I
Sbjct: 68 LHLTSVMGNII 78
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 41/92 (44%), Gaps = 7/92 (7%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRI---GFVHFAERSSAMK 332
K +Y+KNL VT+ L LF R + PP + R+ F+ F + A +
Sbjct: 26 KVLYLKNLSPRVTERDLVSLF---ARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 333 ALKNTEKYELDGQALECSLAKPQADQKSAGGS 364
AL Y+L G+ L K Q+S+G S
Sbjct: 83 ALHLVNGYKLYGKILVIEFGK-NKKQRSSGPS 113
Score = 32.3 bits (72), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 104 VYIGGIPHDASEHDLRD----FCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKA 159
+Y+ + +E DL F + G + R+M G+ +G AF+TF N E+A +A
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR----MRGQAFITFPNKEIAWQA 83
Query: 160 IDKLNNTEFKGK 171
+ +N + GK
Sbjct: 84 LHLVNGYKLYGK 95
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ V + G+P S DL+D + G+V + + G V F E + A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 69
Query: 162 KLNNTEFK 169
KL+NT+F+
Sbjct: 70 KLDNTKFR 77
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+ + + + A+E L++ + + T +++ + ++ ++KG+AF+ F + E A +A++
Sbjct: 18 LVLSNLSYSATEETLQEVFE---KATFIKVPQNQNG-KSKGYAFIEFASFEDAKEALNSC 73
Query: 164 NNTEFKGKKIR 174
N E +G+ IR
Sbjct: 74 NKREIEGRAIR 84
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 101 GSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELA 156
GS+V++G D + +L+ F GEV +V I K + FAFVTF + ++A
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVA 61
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 33.1 bits (74), Expect = 0.35, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 95 LALPPHGSEV-YIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV 153
+ LPP + + YI +P+ + ++ D G + ++R+ ++ E +G A+V + ++
Sbjct: 5 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDI 61
Query: 154 ELASKAIDKLN 164
A A D L+
Sbjct: 62 FDAKNACDHLS 72
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 10/76 (13%)
Query: 277 AVYVKNLPRNVTQDQLKKL-------FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSS 329
+ V N+P+ V D+L+KL F G+IT P + G+ K I F+ +A +
Sbjct: 17 VIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYI-FLEYASPAH 73
Query: 330 AMKALKNTEKYELDGQ 345
A+ A+KN + Y+LD Q
Sbjct: 74 AVDAVKNADGYKLDKQ 89
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ V + G+P S DL+D + G+V + + G V F E + A+
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 68
Query: 162 KLNNTEFK 169
KL+NT+F+
Sbjct: 69 KLDNTKFR 76
>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 = 33.1 bits (74), Expect = 0.39, Method: Composition-based stats.
Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 13/107 (12%)
Query: 99 PHGS-EVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P GS ++I + L D + G + +++ D + +KG+ FV F E A
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAE 59
Query: 158 KAIDKLNNT----------EFKGKKIRCSTSQAKYRLFIGNIPRNWG 194
+AI+K+N FK +K R + A+ + F +N+G
Sbjct: 60 RAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFG 106
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.7 bits (73), Expect = 0.47, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 95 LALPPHGSEV-YIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV 153
+ LPP + + YI +P+ + ++ D G + ++R+ ++ E +G A+V + ++
Sbjct: 1 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDI 57
Query: 154 ELASKAIDKLN 164
A A+D L+
Sbjct: 58 FDAKNAVDHLS 68
>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 = 0.50, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 1/75 (1%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+ V NL V+ +++LF G + K V + G+ VHF ++ A+KA K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD-VHFERKADALKAXKQY 90
Query: 338 EKYELDGQALECSLA 352
LDG+ L
Sbjct: 91 NGVPLDGRPXNIQLV 105
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 10/76 (13%)
Query: 277 AVYVKNLPRNVTQDQLKKL-------FEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSS 329
+ V N+P+ V D+L+KL F G+IT P + G+ K I F+ +A +
Sbjct: 3 VIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYI-FLEYASPAH 59
Query: 330 AMKALKNTEKYELDGQ 345
A+ A+KN + Y+LD Q
Sbjct: 60 AVDAVKNADGYKLDKQ 75
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.3 bits (72), Expect = 0.56, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
VYV NL N + +L++ F ++G + V V PG FV F + A A++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG-----FAFVEFEDPRDAADAVR-- 128
Query: 338 EKYELDGQAL 347
ELDG+ L
Sbjct: 129 ---ELDGRTL 135
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P +VY+G + ++ ++ +L G + V + + GFAFV F + A+
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAAD 125
Query: 159 AIDKLNNTEFKGKKIRCSTSQAKYR 183
A+ +L+ G ++R S + R
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEKR 150
>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 = 32.3 bits (72), Expect = 0.62, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+YV NL T++Q+ +LF G I K+++ K + FV + R+ A A++
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 338 EKYELD 343
LD
Sbjct: 102 NGTRLD 107
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 32.3 bits (72), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V + G+P S DL+D + G+V + + G V F E + A+ KL
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKL 70
Query: 164 NNTEFK 169
+NT+F+
Sbjct: 71 DNTKFR 76
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 32.3 bits (72), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 269 SSGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERS 328
SSG+S ++V+NLP + T LK F G + + + G+ K G V F
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKG-CGVVKFESPE 59
Query: 329 SAMKALKNTEKYELDGQALE 348
A +A + +L G+ ++
Sbjct: 60 VAERACRMMNGMKLSGREID 79
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.3 bits (72), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +YI +P E +L + + G+V RI++ S ++G F + E I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEKCEAVIG 84
Query: 162 KLNNTEFK 169
N K
Sbjct: 85 HFNGKFIK 92
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 101 GSEVYIGGIPHDASEHDLRD-FCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKA 159
G +++ I +A E ++++ FC GE+ + + + + +KG+A V + + A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 160 IDKLNNTEFKGKKIR 174
+ LN E G+ I+
Sbjct: 85 KEALNGAEIMGQTIQ 99
>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 = 32.0 bits (71), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 12/78 (15%), Positives = 36/78 (46%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ + +D +E LR + G + + ++ K S + +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 164 NNTEFKGKKIRCSTSQAK 181
+ + G+++ + +
Sbjct: 165 DGKKIDGRRVLVDVERGR 182
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 32.0 bits (71), Expect = 0.77, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 276 KAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALK 335
+ V+V NL V ++ L +LF G +TKV + + G+ K+ GFV F S A+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS-FGFVCFKHPESVSYAIA 75
Query: 336 NTEKYELDGQALECS 350
L G+ + S
Sbjct: 76 LLNGIRLYGRPINVS 90
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 32.0 bits (71), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
V + G+P S DL+D + G+V + K G V + E A+ KL
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKL 70
Query: 164 NNTEFK 169
++T+F+
Sbjct: 71 DDTKFR 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 = 31.6 bits (70), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 12/78 (15%), Positives = 36/78 (46%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++ + +D +E LR + G + + ++ K S + +G+AF+ + + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 164 NNTEFKGKKIRCSTSQAK 181
+ + G+++ + +
Sbjct: 165 DGKKIDGRRVLVDVERGR 182
>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 = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 95 LALPPHGSEV-YIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNV 153
+ LPP + + YI +P+ + ++ D G + ++R+ ++ E +G A+V + ++
Sbjct: 11 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDI 67
Query: 154 ELASKAIDKLN 164
A A D L+
Sbjct: 68 FDAKNACDHLS 78
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 8/83 (9%)
Query: 99 PHGS--EVYIGGIPHDASEHDLRDFCQS---IGEVTEV--RIMKGKDSSENKGFAFVTFR 151
P GS +Y+G IP +E + DF + +G +T+ + +++K FAF+ FR
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 152 NVELASKAIDKLNNTEFKGKKIR 174
+V+ ++A+ + F+G+ ++
Sbjct: 62 SVDETTQAM-AFDGIIFQGQSLK 83
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
++I + L D + G + +++ D + +KG+ FV F E A +AI+K+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 71
Query: 164 NNTEFKGKKI 173
N +K+
Sbjct: 72 NGMLLNDRKV 81
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
VYV NL N + +L++ F ++G + V V PG FV F + A A++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG-----FAFVEFEDPRDAADAVR-- 128
Query: 338 EKYELDGQAL 347
+LDG+ L
Sbjct: 129 ---DLDGRTL 135
Score = 28.9 bits (63), Expect = 5.8, Method: Composition-based stats.
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 99 PHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASK 158
P +VY+G + ++ ++ +L G + V + + GFAFV F + A+
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAAD 125
Query: 159 AIDKLNNTEFKGKKIRCSTSQAKYR 183
A+ L+ G ++R S + R
Sbjct: 126 AVRDLDGRTLCGCRVRVELSNGEKR 150
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSEN-KGFAFVTF 150
PP+ + ++G +P+D +E +++F + + ++ VR+ + + E KGF + F
Sbjct: 18 PPYTA--FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>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 = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIG----FVHFAERSSAMKA 333
+YV NL T++Q+ +LF G I K+++ G +K + FV + R+ A A
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIM-----GLDKMKTACGFCFVEYYSRADAENA 75
Query: 334 LKNTEKYELD 343
++ LD
Sbjct: 76 MRYINGTRLD 85
>pdb|2L9W|A Chain A, Solution Structure Of The C-Terminal Domain Of Prp24
Length = 117
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 146 AFVTFRNVELASKAIDKLNNTEFKGKKIRCSTSQAKYRLF 185
A + FR+ + A+K + LN ++F+GK IR T R +
Sbjct: 65 AIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTINDMKRYY 104
>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 = 30.8 bits (68), Expect = 1.8, Method: Composition-based stats.
Identities = 13/71 (18%), Positives = 34/71 (47%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+++G + + + LR+ + +M + ++G+ FV+F + + A A+D +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 164 NNTEFKGKKIR 174
+ G+ +R
Sbjct: 64 QGQDLNGRPLR 74
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSEN-KGFAFVTF 150
PP+ + ++G +P+D +E +++F + + ++ VR+ + + E KGF + F
Sbjct: 14 PPYTA--FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>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 = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 101 GSEVYIGGIPHDASEHDLRD-FCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKA 159
G +++ I +A E ++++ FC GE+ + + + + +KG+A V + + A A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFC-DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 160 IDKLNNTEFKGKKIR 174
+ LN E G+ I+
Sbjct: 131 KEALNGAEIMGQTIQ 145
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 11/58 (18%)
Query: 178 SQAKYRLFIGNIP-RNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHN 234
S K RLFIGN+P +N EDL ++ S G + ++KN+ F FI++ N
Sbjct: 19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-----INIKNA-----FGFIQFDN 66
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 11/58 (18%)
Query: 178 SQAKYRLFIGNIP-RNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHN 234
S K RLFIGN+P +N EDL ++ S G + ++KN+ F FI++ N
Sbjct: 19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-----INIKNA-----FGFIQFDN 66
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 8/88 (9%)
Query: 173 IRCSTSQAKYRLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEY 232
IR R+++GN+P + ++D++ V + G + + D+KN FAF+E+
Sbjct: 14 IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYG-AIRDI----DLKNRRGGPPFAFVEF 68
Query: 233 HNHKCAE---YSRQKMTNPNFKLGTNAP 257
+ + AE Y R ++L P
Sbjct: 69 EDPRDAEDAVYGRDGYDYDGYRLRVEFP 96
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKL 163
+Y+G +P D D+ D G + ++ + K+ FAFV F + A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 164 NNTEFKGKKIR 174
+ ++ G ++R
Sbjct: 82 DGYDYDGYRLR 92
Score = 29.3 bits (64), Expect = 5.0, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 278 VYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSSAMKALKNT 337
+YV NLP ++ ++ +F +G I + + + G FV F + A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP---FAFVEFEDPRDAEDAVYGR 81
Query: 338 EKYELDGQALECSLAKPQADQKSAGGSVS 366
+ Y+ DG L P++ + + G S
Sbjct: 82 DGYDYDGYRLRVEF--PRSGRGTGSGPSS 108
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 128 VTEVRIMKGKDSSENKGFAFVTFRNVELASKAIDKLNN 165
V +R++K K + +N+GFAFV + AS+ + L +
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQS 75
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 104 VYIGGIPHDASEHDLRDFCQS---IGEVTEV--RIMKGKDSSENKGFAFVTFRNVELASK 158
+Y+G IP +E + DF + +G +T+ + +++K FAF+ FR+V+ ++
Sbjct: 4 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63
Query: 159 AIDKLNNTEFKGKKIR 174
A+ + F+G+ ++
Sbjct: 64 AM-AFDGIIFQGQSLK 78
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIG--EVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
VY+G ++ L +SIG +V E++ + + + ++KG+A V + K ++
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 162 KLNNTEFKGKK--IRCSTSQ 179
L G+K +R +T Q
Sbjct: 118 LLPGKVLNGEKVDVRPATRQ 137
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 3/77 (3%)
Query: 97 LPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELA 156
LP + + +P S DL+D + T + +D G + F + E+
Sbjct: 24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD---GTGALEFPSEEIL 80
Query: 157 SKAIDKLNNTEFKGKKI 173
+A+++LNN EF+G I
Sbjct: 81 VEALERLNNIEFRGSVI 97
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 3/77 (3%)
Query: 97 LPPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELA 156
LP + + +P S DL+D + T + +D G + F + E+
Sbjct: 2 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD---GTGALEFPSEEIL 58
Query: 157 SKAIDKLNNTEFKGKKI 173
+A+++LNN EF+G I
Sbjct: 59 VEALERLNNIEFRGSVI 75
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
S + + +P D++ CQ + ++ + +K NK AFVT N E A AI
Sbjct: 6 SGILVKNLPQDSN-------CQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 162 KLNNTEFKGKKI 173
+ F+GK +
Sbjct: 59 MFHQYSFRGKDL 70
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 12/85 (14%)
Query: 270 SGASQVKAVYVKNLPRNVTQDQLKKLFEHHGRITKVVVPPAKPGQEKNRIGFVHFAERSS 329
+G S V + V+NL VT D L ++F G + K++ K Q + + +A+ S
Sbjct: 41 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT-FTKNNQFQ---ALLQYADPVS 96
Query: 330 AMKALKNTEKYELDGQALE---CSL 351
A A K LDGQ + C+L
Sbjct: 97 AQHA-----KLSLDGQNIYNACCTL 116
>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 = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P G+ +Y+ G D + LR G + ++ + D N AFVT+ +E A
Sbjct: 36 PRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSM----DPPRN--CAFVTYEKMESAD 87
Query: 158 KAIDKLNNTEFKGKKIRCSTSQ 179
+A+ +LN T+ + +++ + ++
Sbjct: 88 QAVAELNGTQVESVQLKVNIAR 109
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTE--------VRIMKGKDSSENKGFAFVTFRNVEL 155
+++ G+ + + + D+ + IG + + + +++ + KG A V+F +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 156 ASKAIDKLNNTEFKGKKIRCS 176
A AID + EF G I+ S
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVS 90
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 98 PPHGSEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELAS 157
P G+ +Y+ G D + LR G + ++ + D N AFVT+ +E A
Sbjct: 12 PRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSM----DPPRN--CAFVTYEKMESAD 63
Query: 158 KAIDKLNNTEFKGKKIRCSTSQ 179
+A+ +LN T+ + +++ + ++
Sbjct: 64 QAVAELNGTQVESVQLKVNIAR 85
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 28.9 bits (63), Expect = 7.1, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 104 VYIGGIPHDASEHDLRDFCQSIGEVTE--------VRIMKGKDSSENKGFAFVTFRNVEL 155
+++ G+ + + + D+ + IG + + + +++ + KG A V+F +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 156 ASKAIDKLNNTEFKGKKIRCS 176
A AID + EF G I+ S
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVS 96
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 144 GFAFVTFRNVELASKAIDKLNNTEFKGKKIRCSTS 178
G +V FR E A KA+ LNN F G+ I S
Sbjct: 69 GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 28.5 bits (62), Expect = 8.0, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 129 TEVRIMKGKDSSENKGFAFVTFRNVELA 156
+ VR++K K + N+GFAF+ +E A
Sbjct: 53 SNVRVIKDKQTQLNRGFAFIQLSTIEAA 80
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.5 bits (62), Expect = 8.4, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 102 SEVYIGGIPHDASEHDLRDFCQSIGEVTEVRIMKGKDSSENKGFAFVTFRNVELASKAID 161
+ +Y+GG+ +E DLR+ GE+ + +++ + AF+ F + A A +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
Query: 162 K-LNNTEFKGKKI 173
K N G+++
Sbjct: 67 KSFNKLIVNGRRL 79
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 28.5 bits (62), Expect = 8.9, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 183 RLFIGNIPRNWGSEDLQKVVSEVGPGVTGVELVKDMKNSSNNRGFAFIEYHNHKCAE 239
++++GN+ G +L++ S GP ++ + + N GFAF+E+ + + AE
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGP-------LRTVWIARNPPGFAFVEFEDPRDAE 51
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.312 0.131 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,708,209
Number of Sequences: 62578
Number of extensions: 421920
Number of successful extensions: 1263
Number of sequences better than 100.0: 211
Number of HSP's better than 100.0 without gapping: 142
Number of HSP's successfully gapped in prelim test: 69
Number of HSP's that attempted gapping in prelim test: 870
Number of HSP's gapped (non-prelim): 410
length of query: 479
length of database: 14,973,337
effective HSP length: 103
effective length of query: 376
effective length of database: 8,527,803
effective search space: 3206453928
effective search space used: 3206453928
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)