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= 004788
(730 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
LFV N+ ++ + E+R LFE+YG ++ K +GF I A A L N PL
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 115 RRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVK 165
R ++L + F+ + +L V NL VSN+ L + F +G+V+
Sbjct: 84 RGKQLRVRFA----------CHSASLTVRNLPQYVSNELLEEAFSVFGQVE 124
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 9/115 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
L V + ++ D EL +LF G I T Y G+ + + ++ A++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 110 QNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
+R ++L + ++ P S KD N L V NL ++++D L IFG YG +
Sbjct: 66 NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSI 116
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 35/169 (20%), Positives = 73/169 (43%), Gaps = 17/169 (10%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 110 QNKPLRRRKLDI-------HFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYG 162
+ L R + + D +E+ + V ++ +S+DD++ +F A+G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 163 EVKE--IRETPHKRHHK---FIEFYDVXXXXXXXXXXNRSDINGKRIKL 206
++K + P HK FIE+ N D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 32/124 (25%), Positives = 58/124 (46%), Gaps = 13/124 (10%)
Query: 55 LFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 107
+FV + + +LR LFEQYG +I L ++ +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 108 ALQNKPLRRRKLDIHFSI---PKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
AL N + +H I P D+ V L + + + +D+R +F ++G++
Sbjct: 66 ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 165 KEIR 168
+E R
Sbjct: 123 EECR 126
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 34/136 (25%), Positives = 62/136 (45%), Gaps = 19/136 (13%)
Query: 49 EHPSR------TLFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKH----RGFVMIS 95
+HP + +FV + + +LR LFEQYG +I L ++ +G ++
Sbjct: 6 DHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT 65
Query: 96 YYDIRAARTAMRALQNKPLRRRKLDIHFSI---PKDNPSEKDVNQGTLVVFNLDASVSND 152
+Y +AA A AL N + +H I P D+ V L + + + +
Sbjct: 66 FYTRKAALEAQNALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEN 122
Query: 153 DLRQIFGAYGEVKEIR 168
D+R +F ++G+++E R
Sbjct: 123 DIRVMFSSFGQIEECR 138
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 128 DNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKEI-------RETPHKRHHKFIE 180
D+P + D++ + V + + S DLR++F YG V EI + P + F+
Sbjct: 6 DHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVT 65
Query: 181 FY 182
FY
Sbjct: 66 FY 67
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 13/124 (10%)
Query: 43 GEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAA 102
GE Y + LFV N+ +++ + + + LFE+YG+ ++ + RGF I A
Sbjct: 15 GEKTYTQRCR--LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLA 71
Query: 103 RTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYG 162
A L L+ R L I F+ + L V NL VSN+ L Q F +G
Sbjct: 72 EIAKAELDGTILKSRPLRIRFA----------THGAALTVKNLSPVVSNELLEQAFSQFG 121
Query: 163 EVKE 166
V++
Sbjct: 122 PVEK 125
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 44/170 (25%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 55 LFVRNINSNVEDLELRS----LFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 106
LFV N+N N EL++ +F + D+R T R F Y D +A
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 107 RALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKE 166
+AL+ L+ +I PK S+K+ + TL+ NL V+ D+L+++F E++
Sbjct: 63 KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 167 IRETPHKRHHKFIEFYDVXXXXXXXXXXNRSDINGKRIKL----EPSRPG 212
+ + + +IEF ++I+G+ I L EP G
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPKGEG 172
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 35/82 (42%)
Query: 43 GEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAA 102
G+ E +RTL +N+ V EL+ +FE +IR + K +G I + A
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADA 143
Query: 103 RTAMRALQNKPLRRRKLDIHFS 124
Q + R + ++++
Sbjct: 144 EKTFEEKQGTEIDGRSISLYYT 165
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 54/115 (46%), Gaps = 9/115 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
L V + + D EL +LF G I T ++ G+ + + ++ A++ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 110 QNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
+R ++L + ++ P S KD N L V NL ++++D L IFG YG +
Sbjct: 77 NGITVRNKRLKVSYARPG-GESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSI 127
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 35/169 (20%), Positives = 73/169 (43%), Gaps = 17/169 (10%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 110 QNKPLRRRKLDI-------HFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYG 162
+ L R + + D +E+ + V ++ +S+DD++ +F A+G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 163 EVKE--IRETPHKRHHK---FIEFYDVXXXXXXXXXXNRSDINGKRIKL 206
++K + P HK FIE+ N D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ ++F Q+G I + + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>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 = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 30/120 (25%), Positives = 53/120 (44%), Gaps = 7/120 (5%)
Query: 56 FVRNINSNVEDLELRSLFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMRA 108
FV + + +LR LFEQYG +I L ++ +G +++Y +AA A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 109 LQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKEIR 168
L N + P D+ V L + + + +D+R F ++G+++E R
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
LFV N+ ++ + E+R LFE+YG ++ K +GF I A A L N PL
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 115 RRRKLDIHFSI 125
R ++L + F+
Sbjct: 77 RGKQLRVRFAC 87
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F Q+G I + + K RG + + ++ +A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>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 = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 39/160 (24%), Positives = 70/160 (43%), Gaps = 15/160 (9%)
Query: 55 LFVRNINSNVEDLELR----SLFEQYG----DIRTLYTACKHRGFVMISYYDIRAARTAM 106
LF+ N+N N EL+ LF + D+RT +R F Y D +A
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 107 RALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKE 166
+AL+ L+ +I PK S+K TL+ NL +++ D+L+++F E++
Sbjct: 69 KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 167 IRETPHKRHHKFIEFYDVXXXXXXXXXXNRSDINGKRIKL 206
+ + + +IEF ++I+G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
Score = 33.5 bits (75), Expect = 0.43, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 111
+RTL +N++ N+ + EL+ +FE +IR + K +G I + A + Q
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 112 KPLRRRKLDIHFS 124
+ R + ++++
Sbjct: 159 AEIDGRSVSLYYT 171
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F Q+G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMR 107
R L V I + V++++LR LFE+YG I ++ C + RG+ + + +A+ A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 108 ALQNKPLRRRKLDIHFS 124
L + ++L + +
Sbjct: 103 GLNGFNILNKRLKVALA 119
Score = 33.1 bits (74), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 122 HFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHH 176
H + NP E DV + +V + + +V LRQ+F YG ++ + RET R +
Sbjct: 29 HIPPTQMNP-EPDVLRNLMVNY-IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 177 KFIEFYDVXXXXXXXXXXNRSDINGKRIKLEPSRPGGAR 215
F++F N +I KR+K+ + G R
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 44 EHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMI 94
E P R LF+ ++ D LRS FEQ+G + T C + RGF +
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 58
Query: 95 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQ-------GTLVVFNLDA 147
+Y + AM A R K+D PK S +D + + V +
Sbjct: 59 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 112
Query: 148 SVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
LR F YG+++ I R + KR F+ F D
Sbjct: 113 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 44 EHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMI 94
E P R LF+ ++ D LRS FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 95 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQ-------GTLVVFNLDA 147
+Y + AM A R K+D PK S +D + + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 148 SVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
LR F YG+++ I R + KR F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 17/119 (14%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 105
L V + N+ E RSLF G+I +CK G+ ++Y D + A A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIE----SCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 106 MRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
+ L L+ + + + ++ PS + L V L +++ +L Q+F YG +
Sbjct: 61 INTLNGLRLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRI 115
>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 = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 41/186 (22%), Positives = 80/186 (43%), Gaps = 28/186 (15%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
++V +I + + +R F +G I+++ KH+GF + Y AA+ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 110 QNKPLRRRKLDIH--FSIPKDNP-----SEKDVNQGTLVVFNLDASVSNDDLRQIFGAYG 162
+ L R + + +I + P +E+ + V ++ +S+DD++ +F A+G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 163 EVKE--IRETPHKRHHK---FIEFYDVXXXXXXXXXXNRSDINGKRIK-----------L 206
++K + P HK FIE+ N D+ G+ ++ L
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 207 EPSRPG 212
P+ PG
Sbjct: 195 TPATPG 200
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
LF+ N+ + E+RSLFEQYG + K+ GFV I D AA A+R L + L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLEC-DIIKNYGFVHIE--DKTAAEDAIRNLHHYKL 67
Query: 115 RRRKLDIHFSIPKDNPS 131
+++ S K S
Sbjct: 68 HGVNINVEASKNKSKAS 84
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 44 EHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMI 94
E P R LF+ ++ D LRS FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 95 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQ-------GTLVVFNLDA 147
+Y + AM A R K+D PK S +D + + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 148 SVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
LR F YG+++ I R + KR F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 42/161 (26%), Positives = 61/161 (37%), Gaps = 31/161 (19%)
Query: 44 EHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMI 94
E P R LF+ ++ D LRS FEQ+G + T C + RGF +
Sbjct: 4 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 59
Query: 95 SYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQ-------GTLVVFNLDA 147
+Y + AM A R K+D PK S +D + + V +
Sbjct: 60 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 113
Query: 148 SVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
LR F YG+++ I R + KR F+ F D
Sbjct: 114 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 48 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMR 107
G S +FV ++ + ELR F QYGD+ ++ R F +++ D + A++
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS--- 57
Query: 108 ALQNKPLRRRKLDIHFS 124
L + L + + +H S
Sbjct: 58 -LCGEDLIIKGISVHIS 73
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 40/152 (26%), Positives = 59/152 (38%), Gaps = 31/152 (20%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAAR 103
R LF+ ++ D LRS FEQ+G + T C + RGF ++Y +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 104 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQ-------GTLVVFNLDASVSNDDLRQ 156
AM A R K+D PK S +D + + V + LR
Sbjct: 63 AAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 116
Query: 157 IFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
F YG+++ I R + KR F+ F D
Sbjct: 117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYG---DIRTLYTACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ +LF Q+G DI L T K RG + + ++ ++
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTM-KMRGQAFVIFKELGSST 63
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R LQ P + + I ++
Sbjct: 64 NALRQLQGFPFYGKPMRIQYA 84
>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 = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 68 ALRSMQGFPFYDKPMRIQYA 87
>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 = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 64 ALRSMQGFPFYDKPMRIQYA 83
>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 = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 55 LFVRNINS-NVEDLELRSLFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 112
+F+ N+N+ V+ ++ ++F +YG I C H+GF + Y + R AR A+ +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 73
Query: 113 PLRRRKLDIHFSI-PKDNPS 131
+ + LDI+ + PK N S
Sbjct: 74 MIAGQVLDINLAAEPKVNRS 93
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 29/119 (24%), Positives = 50/119 (42%), Gaps = 17/119 (14%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACK---------HRGFVMISYYDIRAARTA 105
L V + N+ E +SLF GDI + CK G+ ++Y D A A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 106 MRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
+ L L+ + + + ++ PS + L V L ++S ++ Q+F YG +
Sbjct: 63 INTLNGLKLQTKTIKVSYA----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRI 117
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 136 NQGTLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXX 190
++G L V L + L Q+F YG++ E+ RET R F+ F ++
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 191 XXXXNRSDINGKRIKLEPS 209
N ++G++I+++ +
Sbjct: 71 MMAMNGKSVDGRQIRVDQA 89
Score = 34.7 bits (78), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTA-----CKHRGFVMISYYDIRAARTAMRAL 109
LFV ++ + + L +F +YG I + + RGF +++ +I A+ AM A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 110 QNKPLRRRKLDIH 122
K + R++ +
Sbjct: 75 NGKSVDGRQIRVD 87
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 59/152 (38%), Gaps = 31/152 (20%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC---------KHRGFVMISYYDIRAAR 103
R LF+ ++ D LRS FEQ+G + T C + RGF ++Y +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 104 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKD-------VNQGTLVVFNLDASVSNDDLRQ 156
AM A R K+D PK S +D + + V + LR
Sbjct: 71 AAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 124
Query: 157 IFGAYGEVKEI-----RETPHKRHHKFIEFYD 183
F YG+++ I R + KR F+ F D
Sbjct: 125 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR 107
+TLFV +N + + +LR FE YG I+ ++ + K RG+ I Y R +A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 108 ALQNKPLRRRKL 119
K + R++
Sbjct: 163 HADGKKIDGRRV 174
>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 = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 54 TLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA 108
+L V N+ LR +FE+YG + +Y + RGF + ++D R A AM A
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 109 LQNKPLRRRKLDIHFS 124
+ L R+L + +
Sbjct: 109 MDGAVLDGRELRVQMA 124
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
++V N+ +N EL F YG +R+++ A GF + + D R A A+R L + L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 48 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR--------GFVMISYYDI 99
G S LF++N+N + + L+ +F + G I++ + K GF + Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 100 RAARTAMRALQNKPLRRRKLDIHFSIPKDNPS 131
A+ A++ LQ + KL++ S P+
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.4 bits (85), Expect = 0.031, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
++V N+ +N EL F YG +R+++ A GF + + D R A A+R L + L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.4 bits (85), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 42 AGEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACK------HRGFVMIS 95
+G+ P + S+ L VRNI E+R LF +G+++T+ K HRGF +
Sbjct: 6 SGQVPKKQTTSKIL-VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 96 YYDIRAARTAMRAL 109
+ + A+ A AL
Sbjct: 65 FITKQDAKKAFNAL 78
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.0 bits (84), Expect = 0.035, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
++V N+ + EL F YG +RT++ A GF + + D R A A+R L K +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 115 --RRRKLDIHFSIPK 127
R ++++ +P+
Sbjct: 63 CGSRVRVELSTGMPR 77
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 36.6 bits (83), Expect = 0.049, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 54 TLFVRNINSNVEDLELRSLFEQYGDI------RTLYTACKHRGFVMISYYDIRAARTAMR 107
+L V N+ LR +FE+YG + R YT + RGF + ++D R A AM
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK-ESRGFAFVRFHDKRDAEDAMD 130
Query: 108 ALQNKPLRRRKLDIHFS 124
A+ L R+L + +
Sbjct: 131 AMDGAVLDGRELRVQMA 147
>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 = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>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 = 36.6 bits (83), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 109
LFV ++N NV+D LR+ F+ + G + RG+ +S+ A+ AM ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 110 QNKPLRRRKLDIHFS 124
Q + L R L I+++
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 36.2 bits (82), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXXXXX 193
L VF L + DLR++F YG + ++ +++ R F+ F +V
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 194 XNRSDINGKRIKLEPS 209
N +++G+RI+++ S
Sbjct: 108 ANGMELDGRRIRVDFS 123
Score = 32.7 bits (73), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 51 PSRTLFVRNINSNVEDLELRSLFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 105
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 106 MRALQNKPLRRRKLDIHFSIPK 127
L R++ + FSI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126
>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 = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 65 ALRSMQGFPFYDKPMRIQYA 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.2 bits (82), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 107
R L+V + V+D L + F +GDI + Y KHRGF + + A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 108 ALQNKPLRRRKLDIHFSIP 126
+ L R + ++ + P
Sbjct: 73 NMNESELFGRTIRVNLAKP 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXXXXX 193
L VF L + DLR++F YG + ++ +++ R F+ F +V
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 194 XNRSDINGKRIKL 206
N +++G+RI++
Sbjct: 77 ANGMELDGRRIRV 89
>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 = 36.2 bits (82), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 36.2 bits (82), Expect = 0.074, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 51 PSRTLFVRNIN----SNVEDLELRSLFEQYG---DIRTLYTACKHRGFVMISYYDIRAAR 103
P++T+++ N+N L ++F Q+G DI L T K RG + + +I +A
Sbjct: 5 PNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKT-LKMRGQAFVIFKEIGSAS 63
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R +Q P + + I +S
Sbjct: 64 NALRTMQGFPFYDKPMQIAYS 84
>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 = 35.8 bits (81), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R++Q P + + I ++
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 35.8 bits (81), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH----RGFVMISYYDIRAARTA 105
PS+TLFV+ ++ + + L+ F+ G +R + +GF + + A+ A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 106 MRALQNKPLRRRKLDIHFSIPK 127
A+++ + K+ + ++ PK
Sbjct: 71 KEAMEDGEIDGNKVTLDWAKPK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.8 bits (81), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXXXXX 193
L VF L + DLR++F YG + ++ +++ R F+ F +V
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 194 XNRSDINGKRIKLEPS 209
N +++G+RI+++ S
Sbjct: 77 ANGMELDGRRIRVDFS 92
Score = 32.3 bits (72), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 51 PSRTLFVRNINSNVEDLELRSLFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 105
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 106 MRALQNKPLRRRKLDIHFSIPK 127
L R++ + FSI K
Sbjct: 74 KERANGMELDGRRIRVDFSITK 95
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.8 bits (81), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 54 TLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRA 108
TL V N+ LR +FE+YG + +Y RGF + ++D R A+ A A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 109 LQNKPLRRRKLDIHFS 124
+ L R+L + +
Sbjct: 75 MDGAELDGRELRVQVA 90
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXXXXX 193
L VF L + DLR++F YG + ++ +++ R F+ F +V
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 194 XNRSDINGKRIKLEPS 209
N +++G+RI+++ S
Sbjct: 74 ANGMELDGRRIRVDFS 89
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 51 PSRTLFVRNINSNVEDLELRSLFEQYG---DIRTLY--TACKHRGFVMISYYDIRAARTA 105
P+ L V ++ + +LR +F +YG D+ +Y + + RGF + + ++ A+ A
Sbjct: 11 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 106 MRALQNKPLRRRKLDIHFSIPK 127
L R++ + FSI K
Sbjct: 71 KERANGMELDGRRIRVDFSITK 92
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQY-----GDIRTLYTACKHRGFVMISYYDIRAARTAMRAL 109
LFV ++N NV+D LR+ F+ + G + RG+ +S+ A+ AM ++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 110 QNKPLRRRKLDIHFS 124
Q + L R L I+++
Sbjct: 150 QGQDLNGRPLRINWA 164
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 46 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACK------HRGFVMISYYDI 99
P +H + LFV I +++ +L+ LFE++G I L T K H+G ++Y
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYEL-TVLKDRLTGLHKGCAFLTYCAR 67
Query: 100 RAARTAMRALQNK 112
+A A AL +
Sbjct: 68 DSALKAQSALHEQ 80
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 55 LFVRNINSN-VEDLELRSLFEQYGDIRTLYTACK-HRGFVMISYYDIRAARTAMRALQNK 112
+F+ N+N+ V+ ++ ++F +YG + C H+G+ + Y + R AR A+ +
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRV----AGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 113 PLRRRKLDIHFS 124
L + LDI+ +
Sbjct: 86 VLAGQTLDINMA 97
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 136 NQGTLVVFNLDASVSNDDLRQIFGAYGEVKEI-----RETPHKRHHKFIEFYDVXXXXXX 190
++ T+ V NL S++N+DL +IF YG+V ++ ++T + FI F D
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 191 XXXXNRSDINGKRIK 205
N + G+ IK
Sbjct: 75 TRAINNKQLFGRVIK 89
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 51 PSR-TLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAART 104
PS+ T++V N+ ++ + +L +F +YG + + K +G I + D +A+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 105 AMRALQNKPLRRRKLDIHFSI 125
RA+ NK L R + +I
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
>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 = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 29/141 (20%), Positives = 64/141 (45%), Gaps = 12/141 (8%)
Query: 50 HPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 103
+P +L+V +++ +V + L F G I ++ C+ G+ +++ A
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 104 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGE 163
A+ + ++ + + I +S + +PS + G + + NLD S+ N L F A+G
Sbjct: 72 RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 164 V---KEIRETPHKRHHKFIEF 181
+ K + + + + F+ F
Sbjct: 130 ILSCKVVCDENGSKGYGFVHF 150
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH---RGFVMISYYDIRAARTAMRALQN 111
+F++N++ ++++ L F +G+I + C +G+ + + AA A+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 112 KPLRRRKL 119
L RK+
Sbjct: 166 MLLNDRKV 173
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 15/93 (16%)
Query: 42 AGEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACK------HRGFVMIS 95
+G +H + LF+ I N+++ +L+ LFE++G I L T K H+G ++
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYEL-TVLKDRFTGMHKGCAFLT 61
Query: 96 YYDIRAARTAMRALQ--------NKPLRRRKLD 120
Y + +A A AL N+P++ + D
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEIRETPHK-RHHKFIEFYDVXXXXXXXXXXNRS 197
TLV+ NL S + + L+++F +K + K + + FIEF N+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 198 DINGKRIKLEPSRPGGA 214
+I G+ I+LE P G+
Sbjct: 77 EIEGRAIRLELQGPRGS 93
>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 = 34.7 bits (78), Expect = 0.21, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLY-------TACKHRGFVMISYYDIRAART 104
S TL+V N++ + ++ LF + GDI+ + TAC GF + YY A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC---GFCFVEYYSRADAEN 74
Query: 105 AMRALQNKPLRRR 117
AMR + L R
Sbjct: 75 AMRYINGTRLDDR 87
>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 = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMR 107
+TLFV +N + + +LR FE YG I+ ++ + K RG+ I Y R +A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 108 ALQNKPLRRRKL 119
K + R++
Sbjct: 163 HADGKKIDGRRV 174
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/115 (20%), Positives = 50/115 (43%), Gaps = 9/115 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
L V + N+ ELRSLF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 110 QNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
L+ + + + ++ PS + + L + L +++ D+ +F +G +
Sbjct: 65 NGLRLQSKTIKVSYA----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRI 115
>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 = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/115 (20%), Positives = 50/115 (43%), Gaps = 9/115 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMRAL 109
L V + N+ ELRSLF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 110 QNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEV 164
L+ + + + ++ PS + + L + L +++ D+ +F +G +
Sbjct: 65 NGLRLQSKTIKVSYA----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRI 115
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 51 PSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAART 104
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 105 AMRALQNKPLRRRKLDIHFS 124
A+R+ Q P + I ++
Sbjct: 65 ALRSXQGFPFYDKPXRIQYA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.9 bits (76), Expect = 0.34, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 48 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAA 102
G R L+V + V+D L + F +GDI + Y KHRGF + + A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 103 RTAMRALQNKPLRRRKLDIHFS 124
A+ + L R + ++ +
Sbjct: 61 AAAIDNMNESELFGRTIRVNLA 82
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSAT 65
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R+ Q P + I ++
Sbjct: 66 NALRSXQGFPFYDKPXRIQYA 86
>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 = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELR----SLFEQYGDIRTLYT--ACKHRGFVMISYYDIRAAR 103
P+ T+++ N+N ++ EL+ ++F ++G I + + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSAT 66
Query: 104 TAMRALQNKPLRRRKLDIHFS 124
A+R+ Q P + I ++
Sbjct: 67 NALRSXQGFPFYDKPXRIQYA 87
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQN 111
+RTL +N++ N+ + EL+ +FE +IR + K +G I + A + Q
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 112 KPLRRRKLDIHFS 124
+ R + ++++
Sbjct: 76 AEIDGRSVSLYYT 88
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.9 bits (76), Expect = 0.37, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNK 112
+ LFVRN+ + V + L F Q+G + + K + + I + + A AM + K
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 113 PLRRRKLDIHFSIPKD 128
L ++I F+ P D
Sbjct: 69 DLEGENIEIVFAKPPD 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 46 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDI---RTLY--TACKHRGFVMISYYDIR 100
P + R++FV NI + +L+ +F + G + R +Y K +G+ Y D
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 101 AARTAMRALQNKPLRRRKLDIHFSIPKDNPSE-KDVNQGTLVV 142
A +AMR L + R L + + + N E K + G V+
Sbjct: 62 TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 140 LVVFNLDASVSNDDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDV 184
L++ NL ++ +++ IFG YG +++IR TP R ++ + D+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 67
>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 = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLY--------TACKHRGFVMISYYDIRAAR 103
S TL+V N++ + ++ LF + GDI+ + TAC GF + YY A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC---GFCFVEYYSRADAE 95
Query: 104 TAMRALQNKPLRRR 117
AMR + L R
Sbjct: 96 NAMRYINGTRLDDR 109
>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 = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 26/121 (21%), Positives = 56/121 (46%), Gaps = 9/121 (7%)
Query: 50 HPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR------GFVMISYYDIRAAR 103
+P +L+V +++ +V + L F G I ++ C+ G+ +++ A
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 66
Query: 104 TAMRALQNKPLRRRKLDIHFSIPKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGE 163
A+ + ++ + + I +S + +PS + G + + NLD S+ N L F A+G
Sbjct: 67 RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124
Query: 164 V 164
+
Sbjct: 125 I 125
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH---RGFVMISYYDIRAARTAMRALQN 111
+F++N++ ++++ L F +G+I + C +G+ + + AA A+ +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 112 KPLRRRKLDI-HFSIPKDNPSE 132
L RK+ + F K+ +E
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAE 182
>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 = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 132 EKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFY-DVXX 186
E + T+ V +D + ++R F YG VKE++ T + + F+ FY DV
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 187 XXXXXXXXNRSDINGKRIKLEPS 209
N +GK++KL P+
Sbjct: 64 QKIVESQIN---FHGKKLKLGPA 83
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 46 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH----RGFVMISYYD 98
P G+ T+FV I+ +++ E+RS F +YG ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 48 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAA 102
G S L+V +++ N+ + LR +FE +G I + + +G+ I++ D A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 103 RTAMRALQNKPLRRRKLDI 121
R A+ L L R + +
Sbjct: 61 RRALEQLNGFELAGRPMRV 79
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.1 bits (74), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFY-DVXXXXXXXXX 193
T+ V +D + ++R F YG VKE++ T + + F+ FY DV
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 194 XNRSDINGKRIKLEPS 209
N +GK++KL P+
Sbjct: 72 IN---FHGKKLKLGPA 84
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 54 TLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH----RGFVMISYYD 98
T+FV I+ +++ E+RS F +YG ++ + +G+ +S+Y+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 32.7 bits (73), Expect = 0.66, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 107
R L+V + V+D L + F +GDI + Y KHRGF + + A A+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 108 ALQNKPLRRRKLDIHFS 124
+ L R + ++ +
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.7 bits (73), Expect = 0.66, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 107
R L+V + V+D L + F +GDI + Y KHRGF + + A A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 108 ALQNKPLRRRKLDIHFS 124
+ L R + ++ +
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 32.7 bits (73), Expect = 0.66, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGFVMISYYDIRAARTAMR 107
R L+V + V+D L + F +GDI + Y KHRGF + + A A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 108 ALQNKPLRRRKLDIHFS 124
+ L R + ++ +
Sbjct: 68 NMNESELFGRTIRVNLA 84
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.7 bits (73), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKH--RGFVMISYYDIRAARTAMRAL 109
+FV I N + ELR F+++G ++ +Y A K RGF I++ D ++ A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 110 QNKPLRRRKLDIHFSIPKDNPS 131
+ +K+++ + P+D+ S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKS 93
>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 = 32.7 bits (73), Expect = 0.71, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 110 QNKPLRRRKLDIHFSIPKDNP 130
+ L + + + + + P
Sbjct: 70 NGQDLMGQPISVDWCFVRGPP 90
>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 = 32.7 bits (73), Expect = 0.82, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 140 LVVFNLDASVSNDDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDV 184
L + NL ++ +++ IFG YG +++IR TP R ++ + D+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 67
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTA 105
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 32.7 bits (73), Expect = 0.82, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 140 LVVFNLDASVSNDDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDV 184
L + NL ++ +++ IFG YG +++IR TP R ++ + D+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 61
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTA 105
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
>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 = 32.3 bits (72), Expect = 0.89, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 110 QNKPLRRRKLDIHFSIPKDNP 130
+ L + + + + + P
Sbjct: 86 NGQDLMGQPISVDWCFVRGPP 106
>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 = 32.3 bits (72), Expect = 0.96, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 110 QNKPLRRRKLDI 121
+ L + + +
Sbjct: 70 NGQDLMGQPISV 81
>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 = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 139 TLVVFNLDASVSNDDLRQIFGAYGEVKEIR----ETPHKRHHKFIEFY-DVXXXXXXXXX 193
T+ V +D + ++R F YG VKE++ T + + F+ FY DV
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 194 XNRSDINGKRIKLEPS 209
N +GK++KL P+
Sbjct: 71 IN---FHGKKLKLGPA 83
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 46 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH----RGFVMISYYD 98
P G+ T+FV I+ +++ E+RS F +YG ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 140 LVVFNLDASVSNDDLRQIFGAYGEVKEIR--ETPHKRHHKFIEFYDV 184
L + NL ++ +++ IFG YG +++IR TP R ++ + D+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 57
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC--KHRGFVMISYYDIRAARTAMRAL 109
+R L++RN+ + E+ +F +YG IR + + RG + Y DI A+ A+ L
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 110 QNKPLRRRKL 119
+ R L
Sbjct: 68 SGFNVSNRYL 77
>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 = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 110 QNKPLRRRKLDI 121
+ L + + +
Sbjct: 85 NGQDLMGQPISV 96
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 110 QNKPLRRRKLDI 121
+ L + + +
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRG---FVMISYYDIRAARTAMRAL 109
RTL+V N++ +V ++ + LF Q G ++ +H + + +Y+ R A A+ A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 110 QNKPLRRRKLDIHFS 124
+ + +++ ++++
Sbjct: 76 NGRKILGKEVKVNWA 90
>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 = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV ++ + ++ F +YG+I+ ++ R G+ ++ Y + A+ AM L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 110 QNKPLRRRKLDI 121
+ L + + +
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 54 TLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKP 113
TL+V + + + +LR+ F Q+G+IRT+ T + + I + +AA A NK
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 114 L-RRRKLDIHF 123
+ R+L++ +
Sbjct: 73 IVNGRRLNVKW 83
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 43 GEHPYGEHPS--RTLFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKHRGFVMISYY 97
G H E+ S + L V NI D +LR +F Q+G D+ ++ +GF +++
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 98 DIRAARTAMRALQNKPLRRRKLDIH 122
+ A A L + RK++++
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVN 102
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 53 RTLFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKHRGFVMISYYDIRAARTAMRAL 109
+ L V NI D +LR +F Q+G D+ ++ +GF +++ + A A L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 110 QNKPLRRRKLDIH 122
+ RK++++
Sbjct: 76 HGTVVEGRKIEVN 88
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 109
L+V +++ N+ + LR +FE +G I ++ + +G+ I++ D A+ A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 110 QNKPLRRRKLDI 121
L R + +
Sbjct: 89 NGFELAGRPMKV 100
>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 = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 55 LFVRNINSNVEDLELRSLFEQYG---DIRTLYTACKH----RGFVMISYYDIRAARTAMR 107
+FV + + +LR LFEQYG +I L ++ +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 108 ALQN 111
AL N
Sbjct: 66 ALHN 69
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 139 TLVVFNLD-ASVSNDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVXXXXXXXXXXNRS 197
L+V NL+ V+ L +FG YG+V+ ++ +K+ + ++ D N
Sbjct: 36 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 95
Query: 198 DINGKRIKLEPSR 210
++GK I++ S+
Sbjct: 96 KLHGKPIRITLSK 108
>pdb|1ZXX|A Chain A, The Crystal Structure Of Phosphofructokinase From
Lactobacillus Delbrueckii
Length = 319
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 581 KYTSKMLLAAIDENHRGTYDFLYLPIDF 608
K TS +L DE+HRG YD L L D
Sbjct: 290 KVTSHDILDLFDESHRGDYDLLKLNADL 317
>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 = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 137 QGT-LVVFNLDASVSNDDLRQIFGAYGEV---KEIRETP--HKRHHKFIEFYDVXXXXXX 190
QGT L+V L + + D+LR +F + GEV K IR+ H + F+ +
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 191 XXXXNRSDINGKRIKLEPSRP 211
N + K IK+ +RP
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
>pdb|2JRA|A Chain A, A Novel Domain-Swapped Solution Nmr Structure Of Protein
Rpa2121 From Rhodopseudomonas Palustris. Northeast
Structural Genomics Target Rpt6
pdb|2JRA|B Chain B, A Novel Domain-Swapped Solution Nmr Structure Of Protein
Rpa2121 From Rhodopseudomonas Palustris. Northeast
Structural Genomics Target Rpt6
Length = 67
Score = 29.6 bits (65), Expect = 5.7, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 526 LGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTTLMI 575
LG +A + G R V G+Q+DS++ + +D + +I+ D R L +
Sbjct: 8 LGADPTQAASSPGGARAVSIVGNQIDSRELFTVDREIVIAHGDDRYRLRL 57
>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 = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 140 LVVFNLDASVSNDDLRQIFGAYGEV---KEIRETP--HKRHHKFIEFYDVXXXXXXXXXX 194
L+V L +++ D+LR +F + GEV K IR+ H + F+ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 195 NRSDINGKRIKLEPSRP 211
N + K IK+ +RP
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 602 LYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWE 640
L+ PID K G+AF+ + P H + Y +G+ ++
Sbjct: 38 LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ 76
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTAC-----KHRGFVMISYYDIRAARTAMRAL 109
LFVRN++ + +L LF YG + L+ K +GF +++ A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 110 QNKPLRRRKLDIHFSIPKDNPSE 132
+ + R L + S K S+
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 139 TLVVFNLD-ASVSNDDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVXXXXXXXXXXNRS 197
L+V NL+ V+ L +FG YG+V+ ++ +K+ + ++ D N
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 198 DINGKRIKLEPSR 210
++GK I++ S+
Sbjct: 65 KLHGKPIRITLSK 77
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 29.3 bits (64), Expect = 7.8, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV +I+ ++ E++ F YG+I+ ++ R G+ ++ Y + A A AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 110 QNKPLRRRKLDIHFSIPK 127
+ + + + + K
Sbjct: 89 NGAEIMGQTIQVDWCFVK 106
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 126 PKDNPSEKDVNQGTLVVFNLDASVSNDDLRQIFGAYGEVKEIR 168
P DN S ++ + T+ L A + DL F A G+V+++R
Sbjct: 14 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR 56
>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 = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 52 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKH---RGFVMISYYDIRAARTAMRA 108
S +F++N++ ++++ L F +G+I + C +G+ + + AA A+
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64
Query: 109 LQNKPLRRRKL 119
+ L RK+
Sbjct: 65 MNGMLLNDRKV 75
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.9 bits (63), Expect = 9.4, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPL 114
+FV ++ EL+ F QYG++ ++ R F +++ D + A++ L + L
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDL 69
Query: 115 RRRKLDIHFS--IPKDN 129
+ + +H S PK N
Sbjct: 70 IIKGISVHISNAEPKHN 86
>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 = 28.9 bits (63), Expect = 9.6, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 55 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR-----GFVMISYYDIRAARTAMRAL 109
LFV +I+ ++ E++ F YG+I+ ++ R G+ ++ Y + A A AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 110 QNKPLRRRKLDIHFSIPK 127
+ + + + + K
Sbjct: 135 NGAEIMGQTIQVDWCFVK 152
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
0.315 0.133 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,832,583
Number of Sequences: 62578
Number of extensions: 1001094
Number of successful extensions: 3313
Number of sequences better than 100.0: 125
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 98
Number of HSP's that attempted gapping in prelim test: 3190
Number of HSP's gapped (non-prelim): 200
length of query: 730
length of database: 14,973,337
effective HSP length: 106
effective length of query: 624
effective length of database: 8,340,069
effective search space: 5204203056
effective search space used: 5204203056
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)