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= 022096
(302 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 73/159 (45%), Gaps = 29/159 (18%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTM---GSINSAKN 156
C++++ L L E F +GTV +++ ++P TG SRG G+L+ S++
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 157 AIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH--KLYVGNLSWAV 214
LDG +I P + I E K++VG + V
Sbjct: 64 TQHILDGK------------------------VIDPKRAIPRDEQDKTGKIFVGGIGPDV 99
Query: 215 KPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS 253
+P++ F ++GT++ A+++ D+ +R FGF+++ S
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSL 263
K+++G L+W ++LR +FG++GTV +++ D +R FGF+SF + D +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 264 NGTVESHTV 272
++ +
Sbjct: 65 QHILDGKVI 73
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 114 SELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSA 154
E E F +GT++ ++ + +TG SRG G++T S ++
Sbjct: 102 KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
>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 = 1e-09, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 76/165 (46%), Gaps = 18/165 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V LP++ E +F G + S ++ R+ TG S G G++ N A AI L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
+G + + ++V ++ ++ R+A LYV L + +++
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMSQKEMEQ 109
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNG 265
F ++G ++++R+L D+ +R GFI F E + A+ LNG
Sbjct: 110 LFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 98 RPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
R LYV LP++ E+ ++F +G +++ + + TG+SRG G++ A+ A
Sbjct: 89 RDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 148
Query: 158 IIALDGSD-VGGRE-MRVRFS 176
I L+G +G E + V+F+
Sbjct: 149 IKGLNGQKPLGAAEPITVKFA 169
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
+S L V L + ++ ++ FG G + S +++ D+ + +GF+++S + D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 260 AL-SLNG-TVESHTV 272
A+ +LNG +++ T+
Sbjct: 62 AINTLNGLKLQTKTI 76
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 77/167 (46%), Gaps = 18/167 (10%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
L V LP++ EL +F G V S ++ R+ G S G G++ + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 160 ALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDL 219
L+G + + ++V ++ + ++A LY+ L + +D+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDA-----------------NLYISGLPRTMTQKDV 105
Query: 220 RNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL-SLNG 265
+ F RFG ++++RVL D+ +R FI F +E + A+ S NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 98 RPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+ LY+ LPR+ ++ +MF FG +++ V + TG+SRG ++ + A+ A
Sbjct: 87 KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEA 146
Query: 158 IIALDG 163
I + +G
Sbjct: 147 ITSFNG 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 77/167 (46%), Gaps = 18/167 (10%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
L V LP++ EL +F G V S ++ R+ G S G G++ + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 160 ALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDL 219
L+G + + ++V ++ + ++A LY+ L + +D+
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDA-----------------NLYISGLPRTMTQKDV 105
Query: 220 RNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL-SLNG 265
+ F RFG ++++RVL D+ +R FI F +E + A+ S NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 98 RPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+ LY+ LPR+ ++ +MF FG +++ V + TG+SRG ++ + A+ A
Sbjct: 87 KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEA 146
Query: 158 IIALDG 163
I + +G
Sbjct: 147 ITSFNG 152
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 76/165 (46%), Gaps = 18/165 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V LP++ E +F G + S ++ R+ TG S G G++ A+ AI L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
+G + + ++V ++ ++ R+A LYV L + ++L
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMTQKELEQ 107
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNG 265
F ++G ++++R+L D+ +R GFI F E + A+ LNG
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 98 RPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
R LYV LP++ EL ++F +G +++ + + TG+SRG G++ A+ A
Sbjct: 87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146
Query: 158 IIALDGSDVGG 168
I L+G G
Sbjct: 147 IKGLNGQKPSG 157
Score = 30.8 bits (68), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF--SSDAERD 258
S L V L + E+ R+ FG G + S +++ D+ + +GF+++ DAE+
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK- 59
Query: 259 AALSLNG 265
A +LNG
Sbjct: 60 AINTLNG 66
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 49/76 (64%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C L++ +LP+ F ++L F PFG V+S +V + +T +S+ G+++ + +SA+ AI
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 160 ALDGSDVGGREMRVRF 175
A++G VG + ++V+
Sbjct: 101 AMNGFQVGTKRLKVQL 116
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L++ +L DL + F FG V+SA+V D++ ++ FGF+SF + D+ + A ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 264 NG 265
NG
Sbjct: 103 NG 104
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/182 (23%), Positives = 78/182 (42%), Gaps = 20/182 (10%)
Query: 87 DSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYL 146
D + +PR A L V LP+ EL +F+ G + + + R+ +TG S G ++
Sbjct: 4 DDLMNDPR--ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFV 61
Query: 147 TMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLY 206
S ++ AI L+G V + ++V ++ ++ LY
Sbjct: 62 DFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDT-----------------NLY 104
Query: 207 VGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNG 265
V NL + + L FG++G++V +L D+ R F+ ++ E A+S LN
Sbjct: 105 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 164
Query: 266 TV 267
+
Sbjct: 165 VI 166
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 50/75 (66%), Gaps = 4/75 (5%)
Query: 101 ELYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
+L+V L SFD +E L ++F +G + V V ++ ET SRG G++T +I+ AK+A+
Sbjct: 14 KLFVGGL--SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 159 IALDGSDVGGREMRV 173
+A++G V GR++RV
Sbjct: 72 MAMNGKSVDGRQIRV 86
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALS 262
KL+VG LS+ + L F ++G + V+ DR+ Q +R FGF++F + D +DA ++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 263 LNG 265
+NG
Sbjct: 74 MNG 76
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 40/172 (23%), Positives = 73/172 (42%), Gaps = 18/172 (10%)
Query: 97 ARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKN 156
A L V LP+ EL +F+ G + + + R+ +TG S G ++ S ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 157 AIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKP 216
AI L+G V + ++V ++ ++ LYV NL +
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGGESIKDTN-----------------LYVTNLPRTITD 103
Query: 217 EDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNGTV 267
+ L FG++G++V +L D+ R F+ ++ E A+S LN +
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 50/82 (60%), Gaps = 4/82 (4%)
Query: 94 RSRARPCELYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
+ A P LYV +L F+I+E L +F+PFG + S+++ + ETG S+G G++T
Sbjct: 21 KGSAGPMRLYVGSL--HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
Query: 152 NSAKNAIIALDGSDVGGREMRV 173
AK A+ L+G ++ GR M+V
Sbjct: 79 ECAKKALEQLNGFELAGRPMKV 100
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 202 PHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS-SDAERDAA 260
P +LYVG+L + + + LR F FG + S +++ D + ++ +GFI+FS S+ + A
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Query: 261 LSLNG 265
LNG
Sbjct: 86 EQLNG 90
>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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 49/76 (64%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
L++ +LP+ F +LL+MF PFG V+S +V + +T +S+ G+++ + SA+ AI
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 160 ALDGSDVGGREMRVRF 175
+++G +G + ++V+
Sbjct: 86 SMNGFQIGMKRLKVQL 101
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL-SL 263
L++ +L +DL F FG VVSA+V D++ ++ FGF+S+ + AA+ S+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 264 NG 265
NG
Sbjct: 88 NG 89
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 48/166 (28%), Positives = 72/166 (43%), Gaps = 30/166 (18%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C L+V NLP + +F+ +G V ++R+ RG G++ + S A+ A
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA 76
Query: 160 ALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDL 219
LDG+ + R +R+RF+ T A L V NLS V E L
Sbjct: 77 ELDGTILKSRPLRIRFA------THGA-----------------ALTVKNLSPVVSNELL 113
Query: 220 RNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLNG 265
F +FG V A V+ D +G+ T GF+ F++ AL G
Sbjct: 114 EQAFSQFGPVEKAVVVVDDRGRATGK-GFVEFAAKPPARKALERCG 158
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 41/94 (43%), Gaps = 16/94 (17%)
Query: 175 FSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARV 234
F+ID+ S + P +K Y +L+VGNL + ED + F R+G +
Sbjct: 4 FTIDIKS-------FLKPGEK--TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI 54
Query: 235 LHDRKGQTTRVFGFISFSSDAERD-AALSLNGTV 267
DR FGFI S + A L+GT+
Sbjct: 55 NRDRG------FGFIRLESRTLAEIAKAELDGTI 82
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 38/175 (21%), Positives = 68/175 (38%), Gaps = 30/175 (17%)
Query: 88 SSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLT 147
S E P+ + +L++ L L F+ +GT+ V R+P T SRG G++T
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 148 MGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH---- 203
++ A MN+R + + PK+ E
Sbjct: 62 YATVEEVDAA---------------------MNARPHKVDGRVVEPKRAVSREDSQRPGA 100
Query: 204 -----KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS 253
K++VG + + LR++F ++G + ++ DR R F F++F
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 260 ALS 262
A++
Sbjct: 71 AMN 73
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 73/175 (41%), Gaps = 34/175 (19%)
Query: 88 SSVEEPRSRARPCELYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGY 145
S E P+ + +L++ L SF+ ++ L F+ +GT+ V R+P T SRG G+
Sbjct: 3 SKSESPKEPEQLRKLFIGGL--SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 146 LTMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH-- 203
+T ++ A MN+R + + PK+ E
Sbjct: 61 VTYATVEEVDAA---------------------MNARPHKVDGRVVEPKRAVSREDSQRP 99
Query: 204 -------KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF 251
K++VG + + LR++F ++G + ++ DR R F F++F
Sbjct: 100 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 12 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 71
Query: 260 ALS 262
A++
Sbjct: 72 AMN 74
>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 = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 73/175 (41%), Gaps = 34/175 (19%)
Query: 88 SSVEEPRSRARPCELYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGY 145
S E P+ + +L++ L SF+ ++ L F+ +GT+ V R+P T SRG G+
Sbjct: 1 SKSESPKEPEQLRKLFIGGL--SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 58
Query: 146 LTMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH-- 203
+T ++ A MN+R + + PK+ E
Sbjct: 59 VTYATVEEVDAA---------------------MNARPHKVDGRVVEPKRAVSREDSQRP 97
Query: 204 -------KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF 251
K++VG + + LR++F ++G + ++ DR R F F++F
Sbjct: 98 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 10 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 69
Query: 260 ALS 262
A++
Sbjct: 70 AMN 72
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 193 PKKIFVYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS 252
P+ + S K+++G LSW E LR +FG+FG V V+ D + +R FGF++F
Sbjct: 16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Query: 253 SDAERDAALSLN-GTVESHTVAFQPLFP 279
A D L+ + ++S T+ + FP
Sbjct: 76 DQAGVDKVLAQSRHELDSKTIDPKVAFP 103
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLT 147
C++++ L L E F FG V V R+P T SRG G++T
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LRN++ ++G + V+ D + +R FGF++FSS AE DA
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84
Query: 260 ALS 262
A++
Sbjct: 85 AMA 87
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 73/175 (41%), Gaps = 34/175 (19%)
Query: 88 SSVEEPRSRARPCELYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGY 145
S E P+ + +L++ L SF+ ++ L F+ +GT+ V R+P T SRG G+
Sbjct: 2 SKSESPKEPEQLRKLFIGGL--SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59
Query: 146 LTMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH-- 203
+T ++ A MN+R + + PK+ E
Sbjct: 60 VTYATVEEVDAA---------------------MNARPHKVDGRVVEPKRAVSREDSQRP 98
Query: 204 -------KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF 251
K++VG + + LR++F ++G + ++ DR R F F++F
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 260 ALS 262
A++
Sbjct: 71 AMN 73
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/172 (21%), Positives = 67/172 (38%), Gaps = 30/172 (17%)
Query: 91 EEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGS 150
E P+ + +L++ L L F+ +GT+ V R+P T SRG G++T +
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 62
Query: 151 INSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH------- 203
+ A MN+R + + PK+ E
Sbjct: 63 VEEVDAA---------------------MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT 101
Query: 204 --KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS 253
K++VG + + LR++F ++G + ++ DR R F F++F
Sbjct: 102 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 9 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 68
Query: 260 ALS 262
A++
Sbjct: 69 AMN 71
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 47/85 (55%)
Query: 92 EPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
+ S L+V +L + D L FK F + LS V + +TG SRG G+++ S
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 152 NSAKNAIIALDGSDVGGREMRVRFS 176
+ A+NA+ ++ G D+ GR +R+ ++
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 38/165 (23%), Positives = 77/165 (46%), Gaps = 17/165 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV NL ++ L + F+ G + ++++ + + ++ + A A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIALQTL 61
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
+G + +++ ++ ++ S F L+VG+L+ V E LRN
Sbjct: 62 NGKQIENNIVKINWAF---------QSQQSSSDDTF------NLFVGDLNVNVDDETLRN 106
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSLNG 265
F F + +S V+ D + ++R +GF+SF+S D ++A S+ G
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 151
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 34/59 (57%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS 262
K+++G LSW E LR +FG+FG V V+ D + +R FGF++F A D L+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Score = 30.8 bits (68), Expect = 0.93, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLT 147
C++++ L L E F FG V V R+P T SRG G++T
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 48
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P LY+ NLP S D EL M KPFG V+S + R+ +G SRG G+ M S + I
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
Query: 159 IALDG 163
+G
Sbjct: 84 GHFNG 88
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
+ P LY+ NL ++ ++L N FG V+S R+L D G T+R GF S + +A
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG-TSRGVGFARMESTEKCEA 81
Query: 260 AL 261
+
Sbjct: 82 VI 83
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/162 (21%), Positives = 63/162 (38%), Gaps = 30/162 (18%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ L L F+ +GT+ V R+P T SRG G++T ++ A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 161 LDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPH---------KLYVGNLS 211
MN+R + + PK+ E K++VG +
Sbjct: 65 ------------------MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIK 106
Query: 212 WAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS 253
+ LR++F ++G + ++ DR R F F++F
Sbjct: 107 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 40/63 (63%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E KL++G LS+ E LR+HF ++GT+ V+ D + +R FGF+++++ E DA
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 260 ALS 262
A++
Sbjct: 64 AMN 66
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 54/96 (56%), Gaps = 3/96 (3%)
Query: 78 NVGGNEVDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPET 137
N+G + D EE R+ R +YV ++ + ++ +F+ FG + S ++R+P T
Sbjct: 107 NIGQAQPIIDQLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTT 163
Query: 138 GISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRV 173
G +G G++ S+++A+ +++ D+GG+ +RV
Sbjct: 164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/186 (19%), Positives = 86/186 (46%), Gaps = 7/186 (3%)
Query: 80 GGNEVDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGI 139
GG ++ S+ + + A +YV ++ + + F PFG + S+++S + T
Sbjct: 9 GGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68
Query: 140 SRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVY 199
+G ++ +A+ A+ ++ +GGR ++V ++ + L +
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--- 125
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS-SDAERD 258
+++YV ++ + +D+++ F FG + SA + D + +GFI + + + +D
Sbjct: 126 ---NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182
Query: 259 AALSLN 264
A S+N
Sbjct: 183 AVSSMN 188
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 54/96 (56%), Gaps = 3/96 (3%)
Query: 78 NVGGNEVDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPET 137
N+G + D EE R+ R +YV ++ + ++ +F+ FG + S ++R+P T
Sbjct: 92 NIGQAQPIIDQLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTT 148
Query: 138 GISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRV 173
G +G G++ S+++A+ +++ D+GG+ +RV
Sbjct: 149 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 35/175 (20%), Positives = 81/175 (46%), Gaps = 7/175 (4%)
Query: 91 EEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGS 150
+ R+ A C +YV ++ + + F PFG + S+++S + T +G ++
Sbjct: 5 QRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 64
Query: 151 INSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNL 210
+A+ A+ ++ +GGR ++V ++ + L + +++YV ++
Sbjct: 65 PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF------NRIYVASV 118
Query: 211 SWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS-SDAERDAALSLN 264
+ +D+++ F FG + S + D + +GFI + + + +DA S+N
Sbjct: 119 HQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 44/174 (25%), Positives = 78/174 (44%), Gaps = 18/174 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV +L + L E F P G +LS+ V R+ T S G Y+ A+ A+ +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
+ + G+ +R+ +S R+ S IF + NL ++ + L +
Sbjct: 78 NFDVIKGKPVRIMWS------QRDPSLRKSGVGNIF---------IKNLDKSIDNKALYD 122
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISF-SSDAERDAALSLNGTVESHTVAF 274
F FG ++S +V+ D G ++ +GF+ F + +A A +NG + + F
Sbjct: 123 TFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 76/167 (45%), Gaps = 18/167 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV +L + L E F P G +LS+ V R+ T S G Y+ A+ A+ +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
+ + G+ +R+ +S R+ S IF + NL ++ + L +
Sbjct: 73 NFDVIKGKPVRIMWS------QRDPSLRKSGVGNIF---------IKNLDKSIDNKALYD 117
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISF-SSDAERDAALSLNGTV 267
F FG ++S +V+ D G ++ +GF+ F + +A A +NG +
Sbjct: 118 TFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGML 162
>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 = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 45/75 (60%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L+V +L + D L FK F + LS V + +TG SRG G+++ S + A+NA+ ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 162 DGSDVGGREMRVRFS 176
G D+ GR +R+ ++
Sbjct: 64 QGQDLNGRPLRINWA 78
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L+VG+L+ V E LRN F F + +S V+ D + ++R +GF+SF+S D ++A S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 264 NG 265
G
Sbjct: 64 QG 65
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 53/96 (55%), Gaps = 3/96 (3%)
Query: 78 NVGGNEVDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPET 137
N+G + D EE R+ R +YV ++ + ++ +F+ FG + S ++R+P T
Sbjct: 91 NIGQAQPIIDQLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTT 147
Query: 138 GISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRV 173
G +G G++ S+++A+ + + D+GG+ +RV
Sbjct: 148 GKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/177 (19%), Positives = 79/177 (44%), Gaps = 7/177 (3%)
Query: 89 SVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTM 148
+ + R+ A C +YV ++ + + F PFG + S++ S + T +G ++
Sbjct: 2 AAQRQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY 61
Query: 149 GSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVG 208
+A+ A+ + +GGR ++V ++ + L + +++YV
Sbjct: 62 EVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF------NRIYVA 115
Query: 209 NLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS-SDAERDAALSLN 264
++ + +D+++ F FG + S + D + +GFI + + + +DA S N
Sbjct: 116 SVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 44/75 (58%), Gaps = 7/75 (9%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
LYV NL + E LR F FGT+ SA+V+ + G ++ FGF+ FSS E A++ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 264 NGTVESHTVAFQPLF 278
NG + VA +PL+
Sbjct: 76 NGRI----VATKPLY 86
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 95 SRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSA 154
+R + LYV NL D L + F PFGT+ S +V E G S+G G++ S A
Sbjct: 11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEA 68
Query: 155 KNAIIALDGSDVGGREMRV 173
A+ ++G V + + V
Sbjct: 69 TKAVTEMNGRIVATKPLYV 87
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF 251
KL+VG L W+ E LR++F ++G VV ++ D+ +R FGF+ F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAA 260
+P +L+V N+ + + DLR FG+FG ++ ++ + +G ++ FGF++F + A+ D A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 71
Query: 261 LS-LNGTV 267
L+GTV
Sbjct: 72 REKLHGTV 79
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P L+V N+P F +L +MF FG +L VE+ N E G S+G G++T + A A
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRAR 72
Query: 159 IALDGSDVGGREMRV 173
L G+ V GR++ V
Sbjct: 73 EKLHGTVVEGRKIEV 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAA 260
P +L+V N+ + + DLR FG+FG ++ ++ + +G ++ FGF++F + A+ D A
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 85
Query: 261 LS-LNGTV 267
L+GTV
Sbjct: 86 REKLHGTV 93
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 95 SRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSA 154
++++P L+V N+P F +L +MF FG +L VE+ N E G S+G G++T + A
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADA 82
Query: 155 KNAIIALDGSDVGGREMRV 173
A L G+ V GR++ V
Sbjct: 83 DRAREKLHGTVVEGRKIEV 101
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LY+ NLP E+ ++F +G + + V PET RG Y+ I AKNA+ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 162 DGSDVGGREMRVRF 175
G +V R + V +
Sbjct: 68 SGFNVSNRYLVVLY 81
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 78/165 (47%), Gaps = 20/165 (12%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEV----SRNPETGISRGCGYLTMGSINSAKN 156
+++V +PR++ +L E+F+ +G V + V S+NP S+GC ++T + +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ--SKGCCFVTFYTRKAALE 74
Query: 157 AIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKP 216
A AL M+V + + + A++ +K E KL++G +S
Sbjct: 75 AQNAL-------HNMKVLPGMHHPIQMKPADS-----EKNNAVED-RKLFIGMISKKCTE 121
Query: 217 EDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
D+R F FG + R+L G +R F++F++ A A+
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAI 165
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ + + +++ MF FG + + R P+ G+SRGC ++T + A+ AI A
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 167
Query: 161 L 161
+
Sbjct: 168 M 168
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFG--FISFSSDAERDAAL 261
K++VG + +DLR F ++G V VL DR + G F++F + R AAL
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT---RKAAL 73
Query: 262 SLNGTVESHTV 272
+ + V
Sbjct: 74 EAQNALHNMKV 84
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 42/76 (55%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
++V +L ++ F PFG + V ++ TG S+G G+++ + A+NAI+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 161 LDGSDVGGREMRVRFS 176
+ G +GGR++R ++
Sbjct: 77 MGGQWLGGRQIRTNWA 92
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
++VG+LS + ED+++ F FG + ARV+ D ++ +GF+SF + + + A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 69/163 (42%), Gaps = 20/163 (12%)
Query: 103 YVCNLPRSFDISELLEMFKPFGTVLSVEV----SRNPETGISRGCGYLTMGSINSAKNAI 158
+V +PR++ +L E+F+ +G V + V S+NP S+GC ++T + +A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ--SKGCCFVTFYTRKAALEAQ 64
Query: 159 IALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPED 218
AL V +S NA KL++G +S D
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKNNAV-------------EDRKLFIGXISKKCTEND 111
Query: 219 LRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
+R F FG + R+L G +R F++F++ A A+
Sbjct: 112 IRVXFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAXAQTAI 153
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ + + +++ F FG + + R P+ G+SRGC ++T + A+ AI A
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKA 155
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFG--FISFSSDAERDAAL 261
K +VG + +DLR F ++G V VL DR + G F++F + R AAL
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT---RKAAL 61
Query: 262 SLNGTVESHTV 272
+ + V
Sbjct: 62 EAQNALHNXKV 72
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 78/165 (47%), Gaps = 20/165 (12%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEV----SRNPETGISRGCGYLTMGSINSAKN 156
+++V +PR++ +L E+F+ +G V + V S+NP S+GC ++T + +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ--SKGCCFVTFYTRKAALE 62
Query: 157 AIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKP 216
A AL M+V + + + A++ +K E KL++G +S
Sbjct: 63 AQNAL-------HNMKVLPGMHHPIQMKPADS-----EKNNAVED-RKLFIGMISKKCTE 109
Query: 217 EDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
D+R F FG + R+L G +R F++F++ A A+
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAI 153
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ + + +++ MF FG + + R P+ G+SRGC ++T + A+ AI A
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 155
Query: 161 L 161
+
Sbjct: 156 M 156
Score = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFG--FISFSSDAERDAAL 261
K++VG + +DLR F ++G V VL DR + G F++F + R AAL
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT---RKAAL 61
Query: 262 SLNGTVESHTV 272
+ + V
Sbjct: 62 EAQNALHNMKV 72
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 47/74 (63%), Gaps = 4/74 (5%)
Query: 102 LYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
LYV +L F+I+E L +F+PFG + ++ + ++ +TG S+G G++T A+ A+
Sbjct: 8 LYVGSL--HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 160 ALDGSDVGGREMRV 173
L+G ++ GR MRV
Sbjct: 66 QLNGFELAGRPMRV 79
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS-SDAERDAALSL 263
LYVG+L + + + LR F FG + + ++ D ++ +GFI+FS S+ R A L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 264 NG 265
NG
Sbjct: 68 NG 69
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 32/62 (51%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E K +VG LSW +DL+++F +FG VV + D +R FGFI F A +
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 260 AL 261
L
Sbjct: 69 VL 70
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 110 SFDIS--ELLEMFKPFGTVLSVEVSRNPETGISRGCGYL 146
S+D S +L + F FG V+ + +P TG SRG G++
Sbjct: 20 SWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFI 58
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 47/104 (45%), Gaps = 12/104 (11%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
++V +L ++ F PFG + V ++ TG S+G G+++ + A+NAI
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 161 LDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHK 204
+ G +GGR++R + A PP YES K
Sbjct: 77 MGGQWLGGRQIRTNW------------ATRKPPAPKSTYESNTK 108
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
++VG+LS + ED++ F FG + ARV+ D ++ +GF+SF + + + A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 265 G 265
G
Sbjct: 78 G 78
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C+++V NLP F L + F G VL ++ E G S+GCG + S A+ A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACR 66
Query: 160 ALDGSDVGGREMRVRFSIDMNS 181
++G + GRE+ VR ID N+
Sbjct: 67 MMNGMKLSGREIDVR--IDRNA 86
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 37/62 (59%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
+YVGNL ++ E ++ F +FG V + ++++DR+ + + FGF+ ++ +A L+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 265 GT 266
T
Sbjct: 64 NT 65
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+YV NL S ++ E+F FG V +V++ + ET +G G++ M S AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 162 DGSDVGGREMRV 173
D +D GR +RV
Sbjct: 63 DNTDFMGRTIRV 74
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LY+ NLP E+ ++F +G + + V PET RG Y+ I AKNA L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 162 DGSDVGGREMRVRF 175
G +V R + V +
Sbjct: 78 SGFNVCNRYLVVLY 91
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 50/88 (56%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V +P + D +L ++F+ +G + SV++ + ET SRG G++ S +SA+ AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEAL 189
+G ++ + ++V + + R A A+
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGIAGAV 132
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
L V + V LR F R+G + S +++ DR+ + +R +GF+ F S + A++ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 264 NG 265
NG
Sbjct: 105 NG 106
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 36/61 (59%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L+V +PR D +L +F+ FG + + V ++ TG+ +GC +LT + +SA A A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 161 L 161
L
Sbjct: 77 L 77
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
KL+VG + + +DL+ F FG + VL DR + F+++ + RD+AL
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCA---RDSAL 71
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%)
Query: 203 HKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS 262
+K++VG + +LR +F +FG V +++D + Q R FGFI+F + D A++
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 263 LN 264
++
Sbjct: 71 MH 72
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+++V +P + +EL E FK FG V V + + E RG G++T S A +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VN 70
Query: 161 LDGSDVGGREMRVR 174
+ D+ G+++ V+
Sbjct: 71 MHFHDIMGKKVEVK 84
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSV-EVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+++ NL D L + F FG +L ++ R+P+TG S+G ++ S +++ AI A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 161 LDGSDVGGREMRVRFSIDMNSR 182
++G + R + V ++ +S+
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NL L +F+ +G V V + R P T RG ++ A++A A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 162 DGSDVGGREMRVRFS 176
DG+++ GRE+RV+ +
Sbjct: 76 DGAELDGRELRVQVA 90
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS--DAERDAALS 262
L V NL++ P+ LR F ++G V + + + R F F+ F DA+ DA +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ-DAEAA 74
Query: 263 LNGT 266
++G
Sbjct: 75 MDGA 78
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 65/151 (43%), Gaps = 30/151 (19%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L+V NLP E+ ++F+ +G V + ++ +G G++ + + A+ A + L
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 78
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRN 221
D + G+++RVRF+ S L V NL V E L
Sbjct: 79 DNMPLRGKQLRVRFACHSAS-----------------------LTVRNLPQYVSNELLEE 115
Query: 222 HFGRFGTVVSARVLHDRKGQTTRVFGFISFS 252
F FG V A V+ D +G+ + G + FS
Sbjct: 116 AFSVFGQVERAVVIVDDRGRPSGK-GIVEFS 145
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 179 MNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDR 238
M T + + P +K F S +L+VGNL + E++R F ++G +H
Sbjct: 1 MEGLTIDLKNFRKPGEKTFTQRS--RLFVGNLPPDITEEEMRKLFEKYGKAGEV-FIHKD 57
Query: 239 KGQTTRVFGFISFSS 253
KG FGFI +
Sbjct: 58 KG-----FGFIRLET 67
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LY+ NLP E+ ++F +G + + V PET RG Y+ I AKNA L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 162 DGSDVGGREMRVRF 175
G +V R + V +
Sbjct: 72 SGFNVCNRYLVVLY 85
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ +PR+ D +L +F+ FG + + V ++ TG+ +GC +LT SA A A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 161 L 161
L
Sbjct: 75 L 75
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSL 263
KL++G + + +DL+ F FG + VL DR + F+++ ER++AL
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY---CERESALKA 71
Query: 264 NGTVESH 270
+
Sbjct: 72 QSALHEQ 78
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL--- 261
+++G LSW +DL+++F +FG VV + D +R FGF+ F D +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 262 --SLNGTV 267
LNG V
Sbjct: 62 EHKLNGKV 69
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L+V L + ++L +F+PFG + V R P+ G S+GC ++ S A+ AI A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 161 LDGS 164
L GS
Sbjct: 76 LHGS 79
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL-S 262
KL+VG L+ ED+ F FG + VL G +++ F+ FSS E AA+ +
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIHA 75
Query: 263 LNGT 266
L+G+
Sbjct: 76 LHGS 79
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 42/76 (55%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+YV NLP S ++L +F +G V+ V + ++ +T S+G ++ +SA+N A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 162 DGSDVGGREMRVRFSI 177
+ + GR ++ +I
Sbjct: 79 NNKQLFGRVIKASIAI 94
Score = 33.9 bits (76), Expect = 0.10, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF-SSDAERDA 259
S +YV NL +++ DL F ++G VV ++ D+ + ++ FI F D+ ++
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 260 ALSLN 264
++N
Sbjct: 75 TRAIN 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV LP++ E+ ++F +G +++ + + TG+SRG G++ A+ AI L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 162 DG 163
+G
Sbjct: 64 NG 65
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
LYV L + +++ F ++G ++++R+L D+ +R GFI F E + A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 264 NG 265
NG
Sbjct: 64 NG 65
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NL L +F+ +G V V + R+ T SRG ++ A++A+ A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 162 DGSDVGGREMRVRFS 176
DG+ + GRE+RV+ +
Sbjct: 133 DGAVLDGRELRVQMA 147
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS--DAERDAALS 262
L V NL++ P+ LR F ++G V + DR + +R F F+ F DAE DA +
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE-DAMDA 131
Query: 263 LNGTV 267
++G V
Sbjct: 132 MDGAV 136
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSD 254
++VG LS ED++++F +FG V A ++ D+ R FGF++F S+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L + NLP E+ ++F +G + + V PET RG Y+ I AKNA L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 162 DGSDVGGREMRVRF 175
G +V R + V +
Sbjct: 78 SGFNVCNRYLVVLY 91
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
++V NLP F L + F G VL ++ E G S+GCG + S A+ A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMM 65
Query: 162 DGSDVGGREMRVRFSIDMNS 181
+G + GRE+ VR ID N+
Sbjct: 66 NGMKLSGREIDVR--IDRNA 83
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 95 SRARP---CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
SRA P C L V L +L E+F +G + V + + ++ SRG ++ ++
Sbjct: 5 SRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 152 NSAKNAIIALDGSDVGGREMRVRFSI 177
+ AK A +G ++ GR +RV FSI
Sbjct: 65 DDAKEAKERANGMELDGRRIRVDFSI 90
Score = 34.3 bits (77), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L V LS DLR F ++G + +++D++ + +R F F+ F + D ++A
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 264 NG 265
NG
Sbjct: 75 NG 76
>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 = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ LP + ++ E+ FG + + + ++ TG+S+G + IN AI
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 161 LDGSDVGGREMRVR 174
L+G +G +++ V+
Sbjct: 158 LNGMQLGDKKLLVQ 171
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 37/185 (20%), Positives = 74/185 (40%), Gaps = 38/185 (20%)
Query: 93 PRSRARPCELYVCNLPRSFDISELLEMFK-----------PFGTVLSVEVSRNPETGISR 141
P AR LYV N+P +++ F P VL+V+++++ +
Sbjct: 2 PLGSAR--RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------K 53
Query: 142 GCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYES 201
+L S++ A+ A DG G+ +++R R + + L
Sbjct: 54 NFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR-------RPHDYQPL----------PG 95
Query: 202 PHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
HKL++G L + + ++ FG + + ++ D ++ + F + D A+
Sbjct: 96 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 262 S-LNG 265
+ LNG
Sbjct: 156 AGLNG 160
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
+YVGN+ + +DL HF G++ +L D+ + + +I F+ DAA++++
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 265 GTV 267
TV
Sbjct: 99 ETV 101
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ LP + ++ E+ FG + + + ++ TG+S+G + IN AI
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 161 LDGSDVGGREMRVR 174
L+G +G +++ V+
Sbjct: 156 LNGMQLGDKKLLVQ 169
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 34/176 (19%), Positives = 71/176 (40%), Gaps = 36/176 (20%)
Query: 102 LYVCNLPRSFDISELLEMFK-----------PFGTVLSVEVSRNPETGISRGCGYLTMGS 150
LYV N+P +++ F P VL+V+++++ + +L S
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRS 60
Query: 151 INSAKNAIIALDGSDVGGREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNL 210
++ A+ A DG G+ +++R R + + L HKL++G L
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIR-------RPHDYQPL----------PGAHKLFIGGL 102
Query: 211 SWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNG 265
+ + ++ FG + + ++ D ++ + F + D A++ LNG
Sbjct: 103 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 158
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NL L +F+ +G V V + R+ T SRG ++ A++A+ A+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 162 DGSDVGGREMRVRFS 176
DG+ + GRE+RV+ +
Sbjct: 110 DGAVLDGRELRVQMA 124
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 184 RNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTT 243
R + + PP + E L V NL++ P+ LR F ++G V + DR + +
Sbjct: 32 RGSMSYGRPPPDV---EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES 88
Query: 244 RVFGFISFSS--DAERDAALSLNGTV 267
R F F+ F DAE DA +++G V
Sbjct: 89 RGFAFVRFHDKRDAE-DAMDAMDGAV 113
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 39/74 (52%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ LP + ++ E+ FG + + + ++ TG+S+G + IN AI
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 161 LDGSDVGGREMRVR 174
L+G +G +++ V+
Sbjct: 176 LNGMQLGDKKLLVQ 189
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 36/179 (20%), Positives = 75/179 (41%), Gaps = 22/179 (12%)
Query: 102 LYVCNLPRSFDISELLEMFK-----------PFGTVLSVEVSRNPETGISRGCGYLTMGS 150
LYV N+P +++ F P VL+V+++++ + +L S
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRS 60
Query: 151 INSAKNAIIALDGSDVGGREMRVRFSID---MNSRTRNAEALISPPKKIFVYESPHKLYV 207
++ A+ A DG G+ +++R D + + N + V +S HKL++
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 208 GNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-LNG 265
G L + + ++ FG + + ++ D ++ + F + D A++ LNG
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 202 PHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAE 256
P+ ++VG + + ++R+ F R+G+V +++ DR G ++ +GF+SF +D +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVD 62
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 9/91 (9%)
Query: 95 SRARP-------CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLT 147
S ARP LYV NLPR+ +L +F +G+++ + R+ TG RG ++
Sbjct: 2 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 148 MGSINSAKNAIIALDG--SDVGGREMRVRFS 176
A+ AI AL+ + G + + VR +
Sbjct: 62 YNKREEAQEAISALNNVIPEGGSQPLSVRLA 92
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
LYV NL + + L FG++G++V +L D+ R F+ ++ E A+S L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 264 NGTV 267
N +
Sbjct: 76 NNVI 79
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 202 PHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAE 256
P+ ++VG + + ++R+ F R+G+V +++ DR G ++ +GF+SF +D +
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVD 63
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 202 PHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAE 256
P+ ++VG + + ++R+ F R+G+V +++ DR G ++ +GF+SF +D +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVD 62
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
++V N+P +L ++F G V+S + + ETG +G G+ +A +A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 162 DGSDVGGREMRVRFSIDMNSRTRNAEALIS 191
+G + GR +RV D + +N E L S
Sbjct: 71 NGREFSGRALRV----DNAASEKNKEELKS 96
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 198 VYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAER 257
V S ++VGN+ + E L++ F G VVS R+++DR+ + +GF +
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 258 DAAL-SLNG 265
+A+ +LNG
Sbjct: 64 LSAMRNLNG 72
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 95 SRARP---CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
+RA P C L V L +L E+F +G + V + + ++ SRG ++ ++
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 152 NSAKNAIIALDGSDVGGREMRVRFSI 177
+ AK A +G ++ GR +RV FSI
Sbjct: 68 DDAKEAKERANGMELDGRRIRVDFSI 93
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L V LS DLR F ++G + +++D++ + +R F F+ F + D ++A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 264 NG 265
NG
Sbjct: 78 NG 79
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 39/74 (52%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ LP + ++ E+ FG + + + ++ TG+S+G + IN AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 161 LDGSDVGGREMRVR 174
L+G +G +++ V+
Sbjct: 63 LNGMQLGDKKLLVQ 76
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
++YV NL EL F +G + +V ++RNP G ++ A++A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 161 LDGSDVGGREMRVRFSIDMNSRTR 184
LDG + G +RV S M R+R
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSR 80
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS--DAERDAAL 261
K+YVGNL +L F +G + + + + G F F+ F DAE DA
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG-----FAFVEFEDPRDAE-DAVR 55
Query: 262 SLNGTV 267
L+G V
Sbjct: 56 GLDGKV 61
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 95 SRARP---CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
+RA P C L V L +L E+F +G + V + + ++ SRG ++ ++
Sbjct: 39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 152 NSAKNAIIALDGSDVGGREMRVRFSI 177
+ AK A +G ++ GR +RV FSI
Sbjct: 99 DDAKEAKERANGMELDGRRIRVDFSI 124
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L V LS DLR F ++G + +++D++ + +R F F+ F + D ++A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 264 NG 265
NG
Sbjct: 109 NG 110
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 96 RARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAK 155
R +L+V L + ++ +MF+PFGT+ V R P+ G S+GC ++ + A+
Sbjct: 9 RGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQ 67
Query: 156 NAIIALDGS 164
AI L S
Sbjct: 68 AAINTLHSS 76
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS 262
KL+VG L ED+R F FGT+ VL G T++ F+ F + AE AA++
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDG-TSKGCAFVKFQTHAEAQAAIN 71
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
+ V NL ++L E+F+PFG++ + ++++ TG S+G +++ A AI
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 160 ALDG 163
+ G
Sbjct: 76 GVSG 79
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 12/93 (12%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
+ V NLS + DL+ F FG++ + D+ ++ F FISF DAA ++
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR--REDAARAIA 75
Query: 265 GTVESHTVAFQPLFPFNYVLFVSFTYSKPSCRT 297
G F +++ L ++ ++KPS +
Sbjct: 76 GVSG---------FGYDH-LILNVEWAKPSTNS 98
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAE-RD 258
+ P KL++G L+ + L+ FG+ G + ++ DR + +R F FI+F + A+ ++
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK-SRGFAFITFENPADAKN 63
Query: 259 AALSLNG 265
AA +NG
Sbjct: 64 AAKDMNG 70
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P +L++ L R + L +F G + V + ++ T SRG ++T + AKNA
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAA 65
Query: 159 IALDGSDVGGREMRV 173
++G + G+ ++V
Sbjct: 66 KDMNGKSLHGKAIKV 80
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L+V NLP E+ ++F+ +G V + ++ +G G++ + + A+ A + L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 162 DGSDVGGREMRVRFSIDMNSRT 183
D + G+++RVRF+ S T
Sbjct: 72 DNMPLRGKQLRVRFACHSASLT 93
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAA 260
K++VG L + LR +F FG + A V+ DR+ +R +GF++ + A + A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+++V LP + L + F+ FG + V + +TG SRG G++TM +A+ A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSD 254
K++VG LS E +R +FG FG V S + D K R F FI+F +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 53
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C++YV NL + + +EL F +G + SV V+RNP G ++ A +A+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVR 128
Query: 160 ALDGSDVGGREMRVRFS 176
LDG + G +RV S
Sbjct: 129 ELDGRTLCGCRVRVELS 145
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 94 RSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYL 146
R+ + +L V LP +L E F FG VL V+V ++ +TG S+G G++
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFS 252
L V L W +DL+ +F FG V+ +V D K ++ FGF+ F+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C++YV NL + + +EL F +G + SV V+RNP G ++ A +A+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVR 128
Query: 160 ALDGSDVGGREMRVRFS 176
LDG + G +RV S
Sbjct: 129 DLDGRTLCGCRVRVELS 145
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV L D L F PFG + +++ + ET RG ++ A AI +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 162 DGSDVGGREMRVRFSIDM 179
+ S++ GR +RV + M
Sbjct: 75 NESELFGRTIRVNLAKPM 92
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
LYVG L+ V + L F FG + ++ D + + R F F+ F + DAA +++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAAAAID 72
Query: 265 GTVESH 270
ES
Sbjct: 73 NMNESE 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 = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 122 PFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFS 176
PFG + V ++ TG S+G G+++ + A+NAI + G +GGR++R ++
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV L D L F PFG + +++ + ET RG ++ A AI +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 162 DGSDVGGREMRVRFS 176
+ S++ GR +RV +
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 32.0 bits (71), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
LYVG L+ V + L F FG + ++ D + + R F F+ F + DAA +++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAAAAID 123
Query: 265 GTVES 269
ES
Sbjct: 124 NMNES 128
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 44/75 (58%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+Y+ ++P ++L++ G V+++++ +P+TG S+G ++ + S+ +A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 162 DGSDVGGREMRVRFS 176
+G +G R ++ +S
Sbjct: 67 NGYQLGSRFLKCGYS 81
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NLP S + E+ +PFG++ + + TG S+G G+ +SA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 162 DGSDVGGREMRVRFS 176
G +G R + V ++
Sbjct: 158 LGKPLGPRTLYVHWT 172
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NLP S + E+ +PFG++ + + TG S+G G+ +SA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 162 DGSDVGGREMRVRFS 176
G +G R + V ++
Sbjct: 158 LGKPLGPRTLYVHWT 172
>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 = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV L D L F PFG + +++ + ET RG ++ A AI +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 162 DGSDVGGREMRVRFS 176
+ S++ GR +RV +
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 31.6 bits (70), Expect = 0.58, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAA 260
S LYVG L+ V + L F FG + ++ D + + R F F+ F + DAA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAA 58
Query: 261 LSLNGTVES 269
+++ ES
Sbjct: 59 AAIDNMNES 67
>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 = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV L D L F PFG + +++ + ET RG ++ A AI +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 162 DGSDVGGREMRVRFS 176
+ S++ GR +RV +
Sbjct: 70 NESELFGRTIRVNLA 84
Score = 31.2 bits (69), Expect = 0.65, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
LYVG L+ V + L F FG + ++ D + + R F F+ F + DAA +++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAAAAID 67
Query: 265 GTVES 269
ES
Sbjct: 68 NMNES 72
>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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L V NLP S + E+ +PFG++ + + TG S+G G+ +SA A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 162 DGSDVGGREMRVRFS 176
G +G R + V ++
Sbjct: 156 LGKPLGPRTLYVHWT 170
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 37.0 bits (84), Expect = 0.014, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LYV L D L F PFG + +++ + ET RG ++ A AI +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 162 DGSDVGGREMRVRFS 176
+ S++ GR +RV +
Sbjct: 68 NESELFGRTIRVNLA 82
Score = 31.2 bits (69), Expect = 0.67, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
LYVG L+ V + L F FG + ++ D + + R F F+ F + DAA +++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF--ELAEDAAAAID 65
Query: 265 GTVES 269
ES
Sbjct: 66 NMNES 70
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 44/75 (58%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+Y+ ++P ++L++ G V+++++ +P+TG S+G ++ + S+ +A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 162 DGSDVGGREMRVRFS 176
+G +G R ++ +S
Sbjct: 66 NGYQLGSRFLKCGYS 80
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 44/75 (58%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+Y+ ++P ++L++ G V+++++ +P+TG S+G ++ + S+ +A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 162 DGSDVGGREMRVRFS 176
+G +G R ++ +S
Sbjct: 65 NGYQLGSRFLKCGYS 79
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 203 HKLYVGNLSWAVKPEDLR-------NHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDA 255
H +Y+ NL+ +K ++L+ + FG+ ++ +R L R GQ +F +S +++A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIFKEVSSATNA 67
Query: 256 ER 257
R
Sbjct: 68 LR 69
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 44/91 (48%)
Query: 85 DDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCG 144
DDD P+ L+V ++ E+ E F +G + ++ ++ + TG S+G
Sbjct: 12 DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71
Query: 145 YLTMGSINSAKNAIIALDGSDVGGREMRVRF 175
+ + A A AL+G+++ G+ ++V +
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>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 = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
+YVGN+ + E+L HF G+V +L D+ + F +I FS +L+L+
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 265 GTV 267
++
Sbjct: 68 ESL 70
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSD 254
++VG LS E +R +FG FG V S + D K R F FI+F +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE 51
>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 = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
+YVGN+ + E+L HF G+V +L D+ + F +I FS +L+L+
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
++V PR D ++L E F FG V SV + ++ G+ + MG + A+ A+++
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD--KGV---FAIVEMGDVG-AREAVLSQ 64
Query: 162 DGSDVGGREMRVR 174
+GG +RVR
Sbjct: 65 SQHSLGGHRLRVR 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 = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 257 R 257
R
Sbjct: 69 R 69
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 39/80 (48%)
Query: 97 ARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKN 156
A L V LP+ EL +F+ G + + + R+ +TG S G ++ S ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 157 AIIALDGSDVGGREMRVRFS 176
AI L+G V + ++V ++
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
>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 = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 68
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 203 HKLYVGNLSWAVKPEDLR-------NHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDA 255
H +Y+ NL+ +K ++L+ + FG+ ++ +R L R GQ +F +S +++A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIFKEVSSATNA 68
Query: 256 ER 257
R
Sbjct: 69 LR 70
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
C +YV NLP ++ ++F +G + +++ +N G ++ A++A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAVY 79
Query: 160 ALDGSDVGGREMRVRF 175
DG D G +RV F
Sbjct: 80 GRDGYDYDGYRLRVEF 95
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS--DAERDAAL 261
++YVGNL ++ +D+ + F ++G + + + R G F F+ F DAE DA
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP---FAFVEFEDPRDAE-DAVY 79
Query: 262 SLNG 265
+G
Sbjct: 80 GRDG 83
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQT 242
E+ KL V NL + V D++ F FGT+ A V +DR G++
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 75
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQT 242
E+ KL V NL + V D++ F FGT+ A V +DR G++
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 75
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L+V L + ++ +F+ FG + + R P+ G S+GC ++ S A+ AI A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
Query: 161 LDGSDV 166
L GS
Sbjct: 76 LHGSQT 81
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 201 SPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAA 260
S KL+VG L+ +D+R F FG + +L G ++ F+ +SS AE AA
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDG-NSKGCAFVKYSSHAEAQAA 72
Query: 261 L-SLNGT 266
+ +L+G+
Sbjct: 73 INALHGS 79
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 35.0 bits (79), Expect = 0.050, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS- 262
K++VGN+S A ++LR+ F R G V+ V+ D + F+ +A+ AA++
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 263 LNG 265
LNG
Sbjct: 63 LNG 65
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQT 242
E+ KL V NL + V D++ F FGT+ A V +DR G++
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 128
>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 = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 44/91 (48%)
Query: 85 DDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCG 144
DDD P+ L+V ++ E+ E F +G + ++ ++ + TG S+G
Sbjct: 58 DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 117
Query: 145 YLTMGSINSAKNAIIALDGSDVGGREMRVRF 175
+ + A A AL+G+++ G+ ++V +
Sbjct: 118 LVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 34.7 bits (78), Expect = 0.074, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 6/87 (6%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+++ NL +S D L + F FG +LS +V + E G S+G G++ + +A+ AI +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 162 DGSDVGGREMRV-RFSIDMNSRTRNAE 187
+G + R++ V RF + + R AE
Sbjct: 72 NGMLLNDRKVFVGRFK---SRKEREAE 95
Score = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF-SSDAERDAALSL 263
+++ NL ++ + L + F FG ++S +V+ D G ++ +GF+ F + +A A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 71
Query: 264 NGTV 267
NG +
Sbjct: 72 NGML 75
>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 = 34.3 bits (77), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
+++ NL +S D L + F FG +LS +V + E G S+G G++ + +A+ AI +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 162 DGSDVGGREMRV 173
+G + R++ V
Sbjct: 66 NGMLLNDRKVFV 77
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF-SSDAERDAALSL 263
+++ NL ++ + L + F FG ++S +V+ D G ++ +GF+ F + +A A +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 264 NGTVESHTVAFQPLFP 279
NG + + F F
Sbjct: 66 NGMLLNDRKVFVGRFK 81
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 34.3 bits (77), Expect = 0.100, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 68
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
Score = 27.7 bits (60), Expect = 7.8, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F +FG ++ V K GQ +F +S +++A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 257 R 257
R
Sbjct: 70 R 70
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQT 242
KL V NL + V D++ F FGT+ A V +DR G++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS 68
>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 = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEV----SRNPETGISRGCGYLTMGSINSAKN 156
+++V +PR++ +L E+F+ +G V + V S+NP S+GC ++T + +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ--SKGCCFVTFYTRKAALE 62
Query: 157 AIIALDGSDV 166
A AL V
Sbjct: 63 AQNALHNMKV 72
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFG--FISFSSDAERDAAL 261
K++VG + +DLR F ++G V VL DR + G F++F + R AAL
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT---RKAAL 61
Query: 262 SLNGTVESHTV 272
+ + V
Sbjct: 62 EAQNALHNMKV 72
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQT 242
KL V NL + V D++ F FGT+ A V +DR G++
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS 69
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSL- 263
L+V LS E L+ F V AR++ DR+ +++ FGF+ F+S+ + AA
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 264 -NGTVESHTVAFQPLFP 279
+G ++ + V P
Sbjct: 75 EDGEIDGNKVTLDWAKP 91
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 4/85 (4%)
Query: 93 PRSRARPCE-LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
P +R++P + L+V L L E F G+V + V+ + ETG S+G G++ S
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVT-DRETGSSKGFGFVDFNSE 64
Query: 152 NSAKNAIIALDGSDVGGREMRVRFS 176
AK A A++ ++ G ++ + ++
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVTLDWA 89
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 64
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 65 LRSMQGFPFYDKPMRIQYA 83
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 257 R 257
R
Sbjct: 66 R 66
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 62
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 63 LRSMQGFPFYDKPMRIQYA 81
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 257 R 257
R
Sbjct: 64 R 64
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 10/84 (11%)
Query: 102 LYVCNLPRSFDISE--LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
+++ NL SFD E L E+ + FG + V V +P+T S+GC + + +A+ +
Sbjct: 18 VFIRNL--SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 160 ALD------GSDVGGREMRVRFSI 177
A G + GR+++V ++
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAV 99
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
E+ ++VGNL V+ E L F + G + + DR+G+ + FGF+ F
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFVCFKHPESVSY 72
Query: 260 ALSL 263
A++L
Sbjct: 73 AIAL 76
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
L V LS DLR F ++G + +++D++ + +R F F+ F + D ++A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 264 NG 265
NG
Sbjct: 78 NG 79
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 95 SRARP---CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSI 151
+RA P C L V L +L E+F +G + V + + ++ SRG ++ ++
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 152 NSAKNAIIALDGSDVGGREMRV 173
+ AK A +G ++ GR +RV
Sbjct: 68 DDAKEAKERANGMELDGRRIRV 89
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 68
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
Score = 29.6 bits (65), Expect = 2.2, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 257 R 257
R
Sbjct: 70 R 70
>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 = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 63
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 64 LRSMQGFPFYDKPMRIQYA 82
Score = 29.6 bits (65), Expect = 2.2, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 257 R 257
R
Sbjct: 65 R 65
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 9/91 (9%)
Query: 94 RSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINS 153
+S + C +Y + + + F PFG ++ + V PE G S ++ + S
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF--PEKGYS----FVRFSTHES 73
Query: 154 AKNAIIALDGSDVGGREMRVRF---SIDMNS 181
A +AI++++G+ + G ++ + S DM S
Sbjct: 74 AAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSS-DAERDAALSL 263
+Y G ++ + + +R F FG ++ RV ++ + F+ FS+ ++ A +S+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVSV 81
Query: 264 NG-TVESHTV 272
NG T+E H V
Sbjct: 82 NGTTIEGHVV 91
>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 = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 257 R 257
R
Sbjct: 69 R 69
>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 = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 67
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 68 LRSMQGFPFYDKPMRIQYA 86
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 68
Query: 257 R 257
R
Sbjct: 69 R 69
>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 = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 68
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 69 LRSMQGFPFYDKPMRIQYA 87
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 257 R 257
R
Sbjct: 70 R 70
>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 = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 102 LYVCNLPRSFDISELLE----MFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNA 157
+Y+ NL EL + +F FG +L + VSR+ + RG ++ ++SA NA
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNA 65
Query: 158 IIALDGSDVGGREMRVRFS 176
+ ++ G + MR++++
Sbjct: 66 LRSMQGFPFYDKPMRIQYA 84
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ NL+ +K ++L+ F RFG ++ V K GQ +F +S +++A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 66
Query: 257 R 257
R
Sbjct: 67 R 67
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 98 RPCELYVCNLPRSFDISELLEMFKPFGTV--LSVEVSR-NPETGISRGCGYLTMGSINSA 154
+P ++++ L R+ ++E+F +G + + + V R +P +S+G Y+ + + A
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPH--LSKGYAYVEFENPDEA 60
Query: 155 KNAIIALDGSDVGGREM 171
+ A+ +DG + G+E+
Sbjct: 61 EKALKHMDGGQIDGQEI 77
>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 = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF--SSDAERDAALS 262
L V L + ++LR+ F G V SA+++ D+ + +GF+++ + DAER A +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER-AINT 65
Query: 263 LNGT-VESHTV 272
LNG ++S T+
Sbjct: 66 LNGLRLQSKTI 76
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALSLN 264
++ L+ ++P DL + F G V R++ DR + ++ ++ F A+ L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 87
Query: 265 G 265
G
Sbjct: 88 G 88
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 32.7 bits (73), Expect = 0.23, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSD--AERDAALS 262
LYVG L + DLRNHF +FG + + V+ ++ FI F++ AE A S
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ------CAFIQFATRQAAEVAAEKS 68
Query: 263 LN 264
N
Sbjct: 69 FN 70
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 92 EPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLS--------VEVSRNPETGISRGC 143
+P + +YV L S + +L + FK G V + + + ETG +G
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 144 GYLTMGSINSAKNAIIALDGSDVGGREMRVRFS 176
++ +AK A+ DG D G +++V +
Sbjct: 68 ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 101 ELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
+L++ LP S EL E+ K GTV + + N G +G Y+ + + A A++
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMK 77
Query: 161 LDGSDVGGREMRVRFS 176
+DG + ++V S
Sbjct: 78 MDGMTIKENIIKVAIS 93
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 203 HKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAAL 261
HKL++ L ++ E+L GTV R++ +R G+ + ++ + ++++ A+
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQAV 75
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 35/65 (53%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
LY+ L +L+++ +P+G ++S + + T +G G++ S ++A+ A+ AL
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 162 DGSDV 166
S V
Sbjct: 68 KASGV 72
Score = 28.1 bits (61), Expect = 5.8, Method: Composition-based stats.
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS 262
LY+ L +DL +G +VS + + D+ + +GF+ F S + A++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 193 PKKIFVYESPH-KLYVGNLSWAVKPEDLRNHFGRFGT--VVSARVLHDRKGQTTRVFGFI 249
P ++ Y LY+GNL+W EDL G ++ + +R ++ F +
Sbjct: 58 PNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117
Query: 250 SFSSDAERDAALSL 263
S+A + L
Sbjct: 118 GVGSEASSKKLMDL 131
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 95 SRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSA 154
R + +YV L L E+F G V++ + ++ TG +G G++ S A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 155 KNAIIALDGSDVGGREMRV 173
AI +D + G+ +RV
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 89
>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 = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 120 FKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFS 176
F PFG + +++S +P R C ++T + SA A+ L+G+ V +++V +
Sbjct: 58 FSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
>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 = 32.0 bits (71), Expect = 0.46, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 198 VYESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF--SSDA 255
+Y L V L ++LR+ F G V SA+++ D+ + +GF+++ + DA
Sbjct: 15 LYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 74
Query: 256 ERDAALSLNG-TVESHTV 272
ER A +LNG ++S T+
Sbjct: 75 ER-AINTLNGLRLQSKTI 91
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.0 bits (71), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 88 SSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRN-PETGISRGCGYL 146
SS + P+ + ++ V N+P + E+ E+F FG + +V + + TG RG G++
Sbjct: 5 SSGQVPKKQT-TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 147 TMGSINSAKNAIIAL 161
+ AK A AL
Sbjct: 64 DFITKQDAKKAFNAL 78
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P + V N+P + I E+L+ F + + + E G+ G + S + A A+
Sbjct: 15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 159 IALDGSDVGGREMRV 173
I L+ +G R++++
Sbjct: 75 IDLNDRPIGSRKVKL 89
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 120 FKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFS 176
F PFG + +++S +P R C ++T + SA A+ L+G+ V +++V +
Sbjct: 34 FSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.6 bits (70), Expect = 0.61, Method: Composition-based stats.
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 203 HKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVL 235
+KLY+GNLS AV +DLR FG ++ +VL
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL 41
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 31.2 bits (69), Expect = 0.65, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGT--VVSARVLHDRKGQTTRVFGFISFSSDAERDAALS 262
LY+GNL+W EDL G ++ + +R ++ F + S+A +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 263 LNGTVESH 270
L E H
Sbjct: 64 LLPKRELH 71
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
LYVGNLS+ E + F + G + + D+ +T F F+ + S A+ + A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 264 NGT 266
NGT
Sbjct: 102 NGT 104
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 31.2 bits (69), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P + V N+P + I E+L+ F + + + E G+ G + S + A A+
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 159 IALDGSDVGGREMRV 173
I L+ +G R++++
Sbjct: 75 IDLNDRPIGSRKVKL 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 30.8 bits (68), Expect = 0.86, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 200 ESPHKLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDA 259
+S L V L + ++ ++ FG G + S +++ D+ + +GF+++S + D
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 260 AL-SLNG 265
A+ +LNG
Sbjct: 62 AINTLNG 68
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 102 LYVCNLPRSFDISELLEMFKPFG-TVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIA 160
L++ +L D + + F G TV+SV++ RN TGI G ++ + +A+ +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 161 LDGSDVGGREMRVRFSID 178
++G + G RF ++
Sbjct: 72 INGKPLPGATPAKRFKLN 89
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 45/103 (43%), Gaps = 14/103 (13%)
Query: 79 VGGNEVDDDSSVEEPRSRARPCE-----LYVCNLPRSFDISELLEMFKPFGTVLSVEVSR 133
V GNE+ +E+P+ + E L NLP EL E+F+ + E+
Sbjct: 72 VFGNEI----KLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFED-----AAEIRL 122
Query: 134 NPETGISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRFS 176
+ G S+G Y+ + A+ G+++ GR + + ++
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYT 165
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNP--------ETGISRGCGYLTMGSINS 153
++V L + I + + FK G + + + + P ETG +G ++ S
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 154 AKNAIIALDGSDVGGREMRVRFS 176
AK AI DG + G ++V F+
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L+V P SEL E+F PFG + E I G ++ SA AI +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPM--------KEVKILNGFAFVEFEEAESAAKAIEEV 58
Query: 162 DGSDVGGREMRVRFS 176
G + + V +S
Sbjct: 59 HGKSFANQPLEVVYS 73
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/94 (18%), Positives = 42/94 (44%)
Query: 82 NEVDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISR 141
+ V+ D P+ L+V + ++ + F +G + ++ ++ + TG +
Sbjct: 6 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 142 GCGYLTMGSINSAKNAIIALDGSDVGGREMRVRF 175
G + + A+ A+ L+G D+ G+ + V +
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHD 237
KL+VGN+S ++LR F +G V+ ++ D
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L+V P SEL E+F PFG + V+ I G ++ SA AI +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFVEFEEAESAAKAIEEV 85
Query: 162 DGSDVGGREMRVRFS 176
G + + V +S
Sbjct: 86 HGKSFANQPLEVVYS 100
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 34/75 (45%)
Query: 99 PCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAI 158
P + V N P + I E+L+ F + + + E G G + S + A A+
Sbjct: 15 PTVIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAV 74
Query: 159 IALDGSDVGGREMRV 173
I L+ +G R++++
Sbjct: 75 IDLNDRPIGSRKVKL 89
>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 = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 205 LYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISFSSDAERDAALS-L 263
LYVGNLS+ E + F + G + ++ K +T F F+ + S A+ + A+ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKI-IMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 264 NGT 266
NGT
Sbjct: 80 NGT 82
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVS---ARVLHDRKGQTTRVFGFISFSSDA 255
H +Y+ NL+ +K ++L+ F RFG ++ +R L R GQ +F +S +++A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR-GQAFVIFKEVSSATNA 67
Query: 256 ER 257
R
Sbjct: 68 LR 69
>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 = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVS---ARVLHDRKGQTTRVFGFISFSSDA 255
H +Y+ NL+ +K ++L+ F RFG ++ +R L R GQ +F +S +++A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR-GQAFVIFKEVSSATNA 68
Query: 256 ER 257
R
Sbjct: 69 LR 70
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVS---ARVLHDRKGQTTRVFGFISFSSDA 255
H +Y+ NL+ +K ++L+ F RFG ++ +R L R GQ +F +S +++A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR-GQAFVIFKEVSSATNA 65
Query: 256 ER 257
R
Sbjct: 66 LR 67
>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 = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/92 (18%), Positives = 41/92 (44%)
Query: 84 VDDDSSVEEPRSRARPCELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGC 143
V+ D P+ L+V + ++ + F +G + ++ ++ + TG +G
Sbjct: 7 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 144 GYLTMGSINSAKNAIIALDGSDVGGREMRVRF 175
+ + A+ A+ L+G D+ G+ + V +
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 203 HKLYVGNLSWAVKPEDLRNH----FGRFGTVVSARVLHDRK--GQTTRVFGFISFSSDAE 256
H +Y+ N++ +K E+L+ F +FG VV L K GQ +F + S++A
Sbjct: 7 HTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNAL 66
Query: 257 R 257
R
Sbjct: 67 R 67
Score = 28.1 bits (61), Expect = 7.0, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 116 LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIALDGSDVGGREMRVRF 175
L +F FG V+ + + T RG ++ + S+ NA+ L G G+ MR+++
Sbjct: 27 LYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTNALRQLQGFPFYGKPMRIQY 83
Query: 176 S 176
+
Sbjct: 84 A 84
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIAL 161
L++ N+P S +L +F G V V R + MGS+ A A+I L
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 178
Query: 162 DGSDVG-GREMRVRFS 176
D+G +RV FS
Sbjct: 179 HNHDLGENHHLRVSFS 194
>pdb|3UT2|A Chain A, Crystal Structure Of Fungal Magkatg2
pdb|3UT2|B Chain B, Crystal Structure Of Fungal Magkatg2
Length = 764
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 168 GREMRVRFSIDMNSRTRNAEALISPPKKIFVYESPHKLYVGNLSWAVKPEDLRNHFGRFG 227
G ++R S+D+N+R E ++ +Y +P G A +D+R FGR G
Sbjct: 220 GNDVRYNNSVDINARADKLEKPLAATHMGLIYVNPEGPN-GTPDPAASAKDIREAFGRMG 278
>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 = 28.5 bits (62), Expect = 4.4, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 102 LYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNP--------ETGISRGCGYLTMGSINS 153
++V L + I + + FK G + + + + P ETG +G ++ S
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 154 AKNAIIALDGSDVGGREMRVRFS 176
AK AI DG + G ++V F+
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 100 CELYVCNLPRSFDISELLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAII 159
L++ N+P S +L +F G V+ + R + MGS+ A A+I
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 207
Query: 160 ALDGSDVG-GREMRVRFS 176
L D+G +RV FS
Sbjct: 208 DLHNHDLGENHHLRVSFS 225
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 204 KLYVGNLSWAVKPEDLRNHFGRFGTVVSARVLHDRKGQTTRVFGFISF 251
+L+V NLS+ EDL F +G + D + + F F++F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2KKN|A Chain A, Solution Nmr Structure Of Themotoga Maritima Protein
Tm1076: Northeast Structural Genomics Consortium Target
Vt57
Length = 178
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 116 LLEMFKPFGTVLSVEVSRNPETGISRGCGYLTMGSINSAKNAIIALDGSDV 166
LL++F V+ + PE + G +L GS+ A++ LDG +V
Sbjct: 121 LLKVFNEKPQVILFGHTHEPEDTVKAGVRFLNPGSLAEGSYAVLELDGGEV 171
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
0.320 0.136 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,204,538
Number of Sequences: 62578
Number of extensions: 306280
Number of successful extensions: 915
Number of sequences better than 100.0: 171
Number of HSP's better than 100.0 without gapping: 124
Number of HSP's successfully gapped in prelim test: 47
Number of HSP's that attempted gapping in prelim test: 619
Number of HSP's gapped (non-prelim): 305
length of query: 302
length of database: 14,973,337
effective HSP length: 98
effective length of query: 204
effective length of database: 8,840,693
effective search space: 1803501372
effective search space used: 1803501372
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)