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= 019811
(335 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 140 bits (353), Expect = 9e-34, Method: Compositional matrix adjust.
Identities = 68/167 (40%), Positives = 104/167 (62%), Gaps = 4/167 (2%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKS-SYGFIHYFDRRSAAMAILS 113
R +YVGN+ +TE +L++ F GP+ K++ + +K+ +Y F+ Y A +A+ +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 114 LNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV 173
LNG+ + +K+NWA+ S Q+ + FN+FVGDL+ V D TL F +PS V
Sbjct: 61 LNGKQIENNIVKINWAFQS-QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
MWD +TG SRG+GFVSF +Q DAQ+A++ + G+ L R +R NWA K
Sbjct: 120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/196 (21%), Positives = 84/196 (42%), Gaps = 41/196 (20%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG+L +T+ L F V ++ ++M D K ++ + FV + DA A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
GK + + ++ NWA + +QSS +T N
Sbjct: 62 NGKQIENNIVKINWAFQS------QQSS---------------SDDTFN----------- 89
Query: 264 TVYVGNLAPEVTQLDLHRHFHS----LGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
++VG+L V L F L V+ +++ +G+GFV +++ +A A+
Sbjct: 90 -LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM-- 146
Query: 320 GNTTQSSYLFGKQMKV 335
++ Q L G+ +++
Sbjct: 147 -DSMQGQDLNGRPLRI 161
>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 = 114 bits (285), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 51/90 (56%), Positives = 70/90 (77%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SGQ++DTS HF++FVGDLSPE+T + A F+ + SDARV+ D TG+S+G+GFVSF
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
N+ DA++AI + G+WLG RQIR NWAT+
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQIRTNWATR 94
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSA 107
D S V+VG++ ++T ++ F+ G + ++++ YGF+ +F++ A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
AI + G+ L G+ I+ NWA
Sbjct: 71 ENAIQQMGGQWLGGRQIRTNWA 92
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 18/101 (17%)
Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVR 295
++GSS K+T+N + V+VG+L+PE+T D+ F G A V++++
Sbjct: 2 SSGSSGQKKDTSN---------HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA 52
Query: 296 VQRDKGFGFVRYSTHAEAALAI-QMGNTTQSSYLFGKQMKV 335
+ KG+GFV + +A AI QMG +L G+Q++
Sbjct: 53 TGKSKGYGFVSFFNKWDAENAIQQMGG----QWLGGRQIRT 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 113 bits (282), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 50/90 (55%), Positives = 70/90 (77%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SGQ++DTS HF++FVGDLSPE+T + + F+ + SDARV+ D TG+S+G+GFVSF
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
N+ DA++AI + G+WLG RQIR NWAT+
Sbjct: 65 YNKLDAENAIVHMGGQWLGGRQIRTNWATR 94
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSA 107
D S V+VG++ ++T ++ F+ G + ++++ YGF+ ++++ A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
AI+ + G+ L G+ I+ NWA
Sbjct: 71 ENAIVHMGGQWLGGRQIRTNWA 92
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 18/101 (17%)
Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVR 295
++GSS K+T+N + V+VG+L+PE+T D+ F G A V++++
Sbjct: 2 SSGSSGQKKDTSN---------HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMA 52
Query: 296 VQRDKGFGFVRYSTHAEAALAI-QMGNTTQSSYLFGKQMKV 335
+ KG+GFV + +A AI MG +L G+Q++
Sbjct: 53 TGKSKGYGFVSFYNKLDAENAIVHMGG----QWLGGRQIRT 89
>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 = 90.9 bits (224), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 46/80 (57%), Positives = 62/80 (77%)
Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
HF++FVGDLSPE+T A + A F+ + SDARV+ D TG+S+G+GFVSF N+ DA++AI
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 201 NDLTGKWLGSRQIRCNWATK 220
+ G+WLG RQIR NWAT+
Sbjct: 66 QQMGGQWLGGRQIRTNWATR 85
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSL 114
V+VG++ ++T + F+ G + ++++ YGF+ +F++ A AI +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 115 NGRHLFGQPIKVNWA 129
G+ L G+ I+ NWA
Sbjct: 69 GGQWLGGRQIRTNWA 83
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAI-QM 319
V+VG+L+PE+T + F G A V++++ + KG+GFV + +A AI QM
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 320 GNTTQSSYLFGKQMK 334
G +L G+Q++
Sbjct: 69 G----GQWLGGRQIR 79
>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 = 87.8 bits (216), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 51/178 (28%), Positives = 93/178 (52%), Gaps = 13/178 (7%)
Query: 43 PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGF 98
P G++ P S+YVG++H VTE +L E FS GP+ ++ R + Y +
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 99 IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDT---SGHFNIFVGDLSPEVTD 155
+++ A A+ ++N + G+P+++ W+ QR+ + SG NIF+ +L + +
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWS----QRDPSLRKSGVGNIFIKNLDKSIDN 117
Query: 156 ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
L+ FS + + +V+ D+ S+G+GFV F Q+ A+ AI + G L R++
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 45/181 (24%), Positives = 76/181 (41%), Gaps = 35/181 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+++VGDL P+VT+A L+ FS RV D T RS G+ +V+F+ DA+ A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
+ + + +R W+ + S KS V
Sbjct: 77 MNFDVIKGKPVRIMWSQ--------RDPSLRKSGV------------------------- 103
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--KGFGFVRYSTHAEAALAIQMG 320
+++ NL + L+ F + G + +V + KG+GFV + T A AI+
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163
Query: 321 N 321
N
Sbjct: 164 N 164
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 6/95 (6%)
Query: 52 DPSTCRS----VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRR 105
DPS +S +++ N+ + L + FS+ G + CK++ + S YGF+H+ +
Sbjct: 95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 154
Query: 106 SAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
+A AI +NG L + + V + +RE G
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 13/84 (15%)
Query: 260 PQY--TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHA 311
P Y ++YVG+L P+VT+ L+ F AG I +RV RD G+ +V + A
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSP--AGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
+A A+ +T + GK +++
Sbjct: 69 DAERAL---DTMNFDVIKGKPVRI 89
>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 = 87.8 bits (216), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 41/79 (51%), Positives = 53/79 (67%)
Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
FN+FVGDL+ V D TL F +PS VMWD +TG SRG+GFVSF +Q DAQ+A++
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 202 DLTGKWLGSRQIRCNWATK 220
+ G+ L R +R NWA K
Sbjct: 62 SMQGQDLNGRPLRINWAAK 80
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSS-----TGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
+++VG+++ V + L+ F +G V + YGF+ + + A A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM-WDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 113 SLNGRHLFGQPIKVNWA 129
S+ G+ L G+P+++NWA
Sbjct: 62 SMQGQDLNGRPLRINWA 78
>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 = 85.5 bits (210), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 78/144 (54%), Gaps = 9/144 (6%)
Query: 68 VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
+T+ + +F S G +E CKL+R DK + YGF++Y D + A AI +LNG L +
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVR-DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72
Query: 123 PIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRS 182
IKV++A S + N++V L +T L FS Y +R++ DQ TG S
Sbjct: 73 TIKVSYARPSSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS 129
Query: 183 RGFGFVSFRNQQDAQSAINDLTGK 206
RG GF+ F + +A+ AI L G+
Sbjct: 130 RGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 41/180 (22%), Positives = 73/180 (40%), Gaps = 39/180 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L +T + F +++ D+ TG+S G+GFV++ + +DA+ AIN
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
L G L ++ I+ ++A + + D
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRD----------------------------------- 88
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQ 318
+YV L +TQ +L + F G + + V + +G GF+R+ EA AI+
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
>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 = 85.5 bits (210), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/163 (29%), Positives = 88/163 (53%), Gaps = 13/163 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILS 113
S+YVG++H VTE +L E FS GP+ ++ R + Y ++++ A A+ +
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 114 LNGRHLFGQPIKVNWAYASGQREDT---SGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
+N + G+P+++ W+ QR+ + SG NIF+ +L + + L+ FS + +
Sbjct: 72 MNFDVIKGKPVRIMWS----QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
+V+ D+ S+G+GFV F Q+ A+ AI + G L R++
Sbjct: 128 CKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 45/181 (24%), Positives = 76/181 (41%), Gaps = 35/181 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+++VGDL P+VT+A L+ FS RV D T RS G+ +V+F+ DA+ A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
+ + + +R W+ + S KS V
Sbjct: 72 MNFDVIKGKPVRIMWSQ--------RDPSLRKSGV------------------------- 98
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--KGFGFVRYSTHAEAALAIQMG 320
+++ NL + L+ F + G + +V + KG+GFV + T A AI+
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 158
Query: 321 N 321
N
Sbjct: 159 N 159
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 6/95 (6%)
Query: 52 DPSTCRS----VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRR 105
DPS +S +++ N+ + L + FS+ G + CK++ + S YGF+H+ +
Sbjct: 90 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 149
Query: 106 SAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
+A AI +NG L + + V + +RE G
Sbjct: 150 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 184
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 10/70 (14%)
Query: 260 PQY--TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHA 311
P Y ++YVG+L P+VT+ L+ F AG I +RV RD G+ +V + A
Sbjct: 6 PSYPMASLYVGDLHPDVTEAMLYEKFSP--AGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 312 EAALAIQMGN 321
+A A+ N
Sbjct: 64 DAERALDTMN 73
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 81.6 bits (200), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 54/159 (33%), Positives = 84/159 (52%), Gaps = 10/159 (6%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
++ V + +T+ + +F S G +E CKL+R DK + YGF++Y D A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR-DKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
+LNG L + IKV++A S + N++V L ++ + FS Y +R
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG-KWLGS 210
++ DQ TG SRG GF+ F + +A+ AI L G K LG+
Sbjct: 122 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGA 160
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 38/180 (21%), Positives = 71/180 (39%), Gaps = 39/180 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L +T + F +++ D+ TG+S G+GFV++ + DA AIN
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
L G L ++ I+ ++A + + D
Sbjct: 66 LNGLKLQTKTIKVSYARPSSASIRD----------------------------------- 90
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQ 318
+YV L ++Q ++ + F G + + + + +G GF+R+ EA AI+
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
T + V L +TQ + F S+G IE ++ RDK G+GFV YS +A A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGD--IESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 317 IQMGNTTQSSYLFGKQMKV 335
I NT L K +KV
Sbjct: 63 I---NTLNGLKLQTKTIKV 78
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILS 113
++YV + +++ ++++FS G + +++ + GFI + R A AI
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 114 LNGRHLFG--QPIKVNWA 129
LNG+ G +PI V +A
Sbjct: 152 LNGQKPLGAAEPITVKFA 169
>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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 51/153 (33%), Positives = 80/153 (52%), Gaps = 9/153 (5%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
++ V + +T+ L+ +FSS G VE KLIR DK + YGF++Y + A AI
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
+LNG L + IKV++A S + N+++ L +T + FS + ++R
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSR 119
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
V+ DQ TG SRG F+ F + +A+ AI G
Sbjct: 120 VLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 47/182 (25%), Positives = 74/182 (40%), Gaps = 39/182 (21%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 200 INDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENN 259
IN L G L S+ I+ ++A SSE K+
Sbjct: 61 INTLNGLRLQSKTIKVSYARP----------------------SSEVIKD---------- 88
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAAL 315
+Y+ L +TQ D+ F G + V V + +G F+R+ +EA
Sbjct: 89 ---ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 316 AI 317
AI
Sbjct: 146 AI 147
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
T + V L +TQ +L F S+G +E ++ RDK G+GFV Y T +A A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGE--VESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 317 IQMGNTTQSSYLFGKQMKV 335
I NT L K +KV
Sbjct: 61 I---NTLNGLRLQSKTIKV 76
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 51/153 (33%), Positives = 80/153 (52%), Gaps = 9/153 (5%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
++ V + +T+ L+ +FSS G VE KLIR DK + YGF++Y + A AI
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
+LNG L + IKV++A S + N+++ L +T + FS + ++R
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSR 119
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
V+ DQ TG SRG F+ F + +A+ AI G
Sbjct: 120 VLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 47/182 (25%), Positives = 74/182 (40%), Gaps = 39/182 (21%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 200 INDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENN 259
IN L G L S+ I+ ++A SSE K+
Sbjct: 61 INTLNGLRLQSKTIKVSYARP----------------------SSEVIKD---------- 88
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAAL 315
+Y+ L +TQ D+ F G + V V + +G F+R+ +EA
Sbjct: 89 ---ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 316 AI 317
AI
Sbjct: 146 AI 147
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
T + V L +TQ +L F S+G +E ++ RDK G+GFV Y T +A A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGE--VESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 317 IQMGNTTQSSYLFGKQMKV 335
I NT L K +KV
Sbjct: 61 I---NTLNGLRLQSKTIKV 76
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 44/151 (29%), Positives = 78/151 (51%), Gaps = 9/151 (5%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILS 113
++ V + +T+ L +F + GP+ C+++R K+ Y F+ + + AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 114 LNGRHLFGQPIKVNWAYASGQR-EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
LNG + + +KV++A G+ +DT N++V +L +TD L F Y S
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++ D+ TGR RG FV + +++AQ AI+ L
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 48/183 (26%), Positives = 76/183 (41%), Gaps = 39/183 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L ++TD L+A F + R+M D KTG S G+ FV F ++ D+Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
L G + +++++ ++A G + +D
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 89
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
T +YV NL +T L F G+ ++ + R +G FVRY+ EA AI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 319 MGN 321
N
Sbjct: 150 ALN 152
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFD 103
PG + ++YV N+ +T+ L +F G + ++R DK + F+ Y
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR-DKLTGRPRGVAFVRYNK 140
Query: 104 RRSAAMAILSLNGRHLFG--QPIKVNWA 129
R A AI +LN G QP+ V A
Sbjct: 141 REEAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 71.2 bits (173), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 78/158 (49%), Gaps = 10/158 (6%)
Query: 52 DPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRS 106
DP + + N Q T+ L +F + GP+ C++ R K+ Y F+ +
Sbjct: 9 DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQR-EDTSGHFNIFVGDLSPEVTDATLFACFSVY 165
+ AI LNG + + +KV++A G+ +DT N++V +L +TD L F Y
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKY 124
Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
S ++ D+ TGR RG FV + +++AQ AI+ L
Sbjct: 125 GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 74/183 (40%), Gaps = 39/183 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L + TD L+A F + R+ D KTG S G+ FV F ++ D+Q AI
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
L G + +++++ ++A G + +D
Sbjct: 76 LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 100
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
T +YV NL +T L F G+ ++ + R +G FVRY+ EA AI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 319 MGN 321
N
Sbjct: 161 ALN 163
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFD 103
PG + ++YV N+ +T+ L +F G + ++R DK + F+ Y
Sbjct: 93 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR-DKLTGRPRGVAFVRYNK 151
Query: 104 RRSAAMAILSLNGRHLFG--QPIKVNWAYASGQ 134
R A AI +LN G QP+ V A G+
Sbjct: 152 REEAQEAISALNNVIPEGGSQPLSVRLAEEHGK 184
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 52/75 (69%), Gaps = 2/75 (2%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
R++YVGN+ VTE L+ ++FS GP + CK+I + S+ Y F+ +++ R AA A+ ++
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 115 NGRHLFGQPIKVNWA 129
NGR + G+ +KVNWA
Sbjct: 76 NGRKILGKEVKVNWA 90
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG ED ++VG+LS +VT+ + FS C +++ + + + FV F
Sbjct: 5 SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEF 62
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
+DA +A+ + G+ + ++++ NWAT
Sbjct: 63 YEHRDAAAALAAMNGRKILGKEVKVNWAT 91
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR--DKGFGFVRYSTHAEAA 314
E++ Q T+YVGNL+ +VT++ + + F +G ++ + + + FV + H +AA
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 69
Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
A+ N + + GK++KV
Sbjct: 70 AALAAMNGRK---ILGKEVKV 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 68.2 bits (165), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 35/81 (43%), Positives = 50/81 (61%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FVG LS + + +L FS Y S+ V+ D++T RSRGFGFV+F N DA+ A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 204 TGKWLGSRQIRCNWATKGAGN 224
GK + RQIR + A K + N
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDN 95
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 6/79 (7%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
++VG + E L++VFS G + ++ KD+ + +GF+ + + A A+++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVV-KDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 114 LNGRHLFGQPIKVNWAYAS 132
+NG+ + G+ I+V+ A S
Sbjct: 74 MNGKSVDGRQIRVDQAGKS 92
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
++VG L+ + + L + F G V+++ QR +GFGFV + +A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 321 NTTQSSYLFGKQMKV 335
N + G+Q++V
Sbjct: 75 N---GKSVDGRQIRV 86
>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 = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 46/179 (25%), Positives = 85/179 (47%), Gaps = 19/179 (10%)
Query: 56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAI 111
CR VYVG+I+ ++ E +++ F+ GP++ + + + F+ Y +A +A+
Sbjct: 14 CR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 112 LSLNGRHLFGQPIKVNWAYASGQR--------EDTSGHFNIFVGDLSPEVTD---ATLFA 160
+N L G+ IKV GQ E+ I+V + +++D ++F
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
F SC+ AR D TG+ +G+GF+ + Q +Q A++ + LG + +R A
Sbjct: 133 AFGKIKSCTLAR---DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/170 (21%), Positives = 71/170 (41%), Gaps = 32/170 (18%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG + E+ + T+ F+ + + WD T + +GF FV + + AQ A+ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
LG R I+ G +N A+ +++ + E +
Sbjct: 76 NSVMLGGRNIKV-----GRPSN----IGQAQPIID---------------QLAEEARAFN 111
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRY 307
+YV ++ +++ D+ F + G I+ + RD KG+GF+ Y
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGK--IKSCTLARDPTTGKHKGYGFIEY 159
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
VYVG++ E+ + + + F G I+ + + D KGF FV Y A LA++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGP--IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 319 MGNTTQSSYLFGKQMKV 335
N S L G+ +KV
Sbjct: 74 QMN---SVMLGGRNIKV 87
>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 = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 83/173 (47%), Gaps = 12/173 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAILSL 114
VYVG+I+ ++ E +++ F+ GP++ + + + F+ Y +A +A+ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 115 NGRHLFGQPIKVNWAYASGQRE-------DTSGHFN-IFVGDLSPEVTDATLFACFSVYP 166
N L G+ IKV GQ + + + FN I+V + +++D + + F +
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 167 SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
A + D TG+ +G+GF+ + Q +Q A++ + LG + +R A
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 34/170 (20%), Positives = 69/170 (40%), Gaps = 32/170 (18%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG + E+ + T+ F+ + + WD T + +GF FV + + AQ A+ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
LG R I+ + A+ +++ + E +
Sbjct: 91 NSVMLGGRNIKVGRPSN---------IGQAQPIID---------------QLAEEARAFN 126
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRY 307
+YV ++ +++ D+ F + G I+ + RD KG+GF+ Y
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGK--IKSATLARDPTTGKHKGYGFIEY 174
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
+ VYVG++ E+ + + + F G I+ + + D KGF FV Y A LA
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGP--IKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 317 IQMGNTTQSSYLFGKQMKV 335
++ N S L G+ +KV
Sbjct: 87 LEQMN---SVMLGGRNIKV 102
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 53/84 (63%), Gaps = 3/84 (3%)
Query: 141 HFNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
+++FVGDL+P+V D L+ F VYPSC +V+ DQ TG S+G+GFV F ++ + + A
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA 67
Query: 200 INDLTGK-WLGSRQIRCNWATKGA 222
+ + G LGS+ +R + A A
Sbjct: 68 LTECQGAVGLGSKPVRLSVAIPKA 91
Score = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSL------GAGVIEEVRVQRDKGFGFVRYSTHA 311
+ P+Y+ ++VG+L P+V L+ F + G V+++ V KG+GFV+++
Sbjct: 6 SGPEYS-LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS--KGYGFVKFTDEL 62
Query: 312 EAALAI 317
E A+
Sbjct: 63 EQKRAL 68
>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 = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 46/173 (26%), Positives = 82/173 (47%), Gaps = 24/173 (13%)
Query: 56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAI 111
CR VYVG+I+ ++ E +++ F+ GP++ + + F+ Y +A +A+
Sbjct: 13 CR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 112 LSLNGRHLFGQPIKVNWAYASGQR--------EDTSGHFNIFVGDLSPEVTD---ATLFA 160
N L G+ IKV GQ E+ I+V + +++D ++F
Sbjct: 72 EQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-----DLTGKWL 208
F SC+ AR D TG+ +G+GF+ + Q +Q A++ DL G++L
Sbjct: 132 AFGKIKSCTLAR---DPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/184 (19%), Positives = 72/184 (39%), Gaps = 32/184 (17%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG + E+ + T+ F+ + WD T + +GF FV + + AQ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
LG R I+ + S+ + + +E+ + +
Sbjct: 75 NSVXLGGRNIKVG------------RPSNIGQAQPIIDQLAEEARA------------FN 110
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
+YV ++ +++ D+ F + G I+ + RD KG+GF+ Y + A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGK--IKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 318 QMGN 321
N
Sbjct: 169 SSXN 172
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+YV ++H +++ ++ VF + G ++ C L R + YGFI Y +S+ A+ S
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 115 NGRHLFGQPIKVNWA 129
N L GQ ++V A
Sbjct: 172 NLFDLGGQYLRVGKA 186
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
VYVG++ E+ + + + F G I+ + D KGF FV Y A LA++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGP--IKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 319 MGNTTQSSYLFGKQMKV 335
N S L G+ +KV
Sbjct: 73 QXN---SVXLGGRNIKV 86
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 54/93 (58%), Gaps = 5/93 (5%)
Query: 49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDR 104
P D S RSV+VGNI + TE L+++FS GPV +L+ ++ YGF Y D+
Sbjct: 2 PAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQRED 137
+A A+ +LNGR G+ ++V+ A + +E+
Sbjct: 61 ETALSAMRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 48/86 (55%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
++FVG++ E T+ L FS R+++D++TG+ +G+GF +++Q+ A SA+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDK 228
L G+ R +R + A E K
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELK 95
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQM 319
+V+VGN+ E T+ L F +G V + R+ KG+GF Y A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 320 GNTTQSSYLFGKQMKV 335
N + S G+ ++V
Sbjct: 70 LNGREFS---GRALRV 82
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 75/142 (52%), Gaps = 12/142 (8%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAM 109
+C+ +++G ++ TE L+E F G V K+++ + +GF+ F++ S+
Sbjct: 2 ESCK-MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS-FEKPSSVD 59
Query: 110 AILSLNGRHLF-GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
++ +H+ G+ I A +++ T IFVG + P+V FS + +
Sbjct: 60 EVVKT--QHILDGKVIDPKRAIPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 169 SDARVMWDQKTGRSRGFGFVSF 190
DA++M D+ TG+SRGFGFV++
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTY 136
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/173 (24%), Positives = 70/173 (40%), Gaps = 45/173 (26%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G L+ + T+ L F Y + +D ++M D TGRSRGFGF+SF
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF------------ 52
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
++ S VV+ + DGK A + Q
Sbjct: 53 -------------------------EKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQD 85
Query: 263 TT--VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYST 309
T ++VG + P+V + F G + ++ + +D +GFGFV Y +
Sbjct: 86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 50/157 (31%), Positives = 77/157 (49%), Gaps = 15/157 (9%)
Query: 47 LPPGFDPSTCR-SVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDR 104
L PG T R ++VGN+ T +TE + +F G P E I +D+ +GFI R
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEV--FINRDRG-FGFIRLESR 68
Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSV 164
A +A L+G L +P+++ +A T G + V +LSP V++ L FS
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFA--------THGA-ALTVKNLSPVVSNELLEQAFSQ 119
Query: 165 YPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
+ A V+ D + GR+ G GFV F + A+ A+
Sbjct: 120 FGPVEKAVVVVDDR-GRATGKGFVEFAAKPPARKALE 155
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+FVG+L ++T+ F Y S+ + R RGFGF+ ++ A+ A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 203 LTGKWLGSRQIRCNWATKGAG 223
L G L SR +R +AT GA
Sbjct: 78 LDGTILKSRPLRIRFATHGAA 98
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
Q ++VGNL ++T+ D R F G EV + RD+GFGF+R + A +A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEP--SEVFINRDRGFGFIRLESRTLAEIA 74
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+F+G L+ E + L A F + S+ ++ D +T +SRGF F++F N DA++A D+
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 204 TGKWLGSRQIRCNWATK 220
GK L + I+ A K
Sbjct: 69 NGKSLHGKAIKVEQAKK 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 9/85 (10%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+++G ++ + E +L+ VF GP+ LI KD++S + FI + + A A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLI-KDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 115 NGRHLFGQPIKVNWA----YASGQR 135
NG+ L G+ IKV A + SG R
Sbjct: 69 NGKSLHGKAIKVEQAKKPSFQSGGR 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/154 (30%), Positives = 75/154 (48%), Gaps = 13/154 (8%)
Query: 49 PGFDPSTCRS-VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA 107
PG T RS ++VGN+ +TE ++++F G G I KDK +GFI R A
Sbjct: 14 PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKDK-GFGFIRLETRTLA 71
Query: 108 AMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS 167
+A + L+ L G+ ++V +A S ++ V +L V++ L FSV+
Sbjct: 72 EIAKVELDNMPLRGKQLRVRFACHSA---------SLTVRNLPQYVSNELLEEAFSVFGQ 122
Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
A V+ D + GR G G V F + A+ A++
Sbjct: 123 VERAVVIVDDR-GRPSGKGIVEFSGKPAARKALD 155
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 9/77 (11%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRVQRDKGFGFVRYSTHAEAALA-IQ 318
Q + ++VGNL P++T+ ++ + F G AG EV + +DKGFGF+R T A +A ++
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAG---EVFIHKDKGFGFIRLETRTLAEIAKVE 77
Query: 319 MGNTTQSSYLFGKQMKV 335
+ N L GKQ++V
Sbjct: 78 LDNMP----LRGKQLRV 90
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+FVG+L P++T+ + F Y + + D +GFGF+ + A+ A +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 203 LTGKWLGSRQIRCNWATKGA 222
L L +Q+R +A A
Sbjct: 78 LDNMPLRGKQLRVRFACHSA 97
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L+ EV D L A F + +D ++ D +T + RGF FV F +DA +AI+++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 204 TGKWLGSRQIRCNWA 218
L R IR N A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 11/78 (14%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAI 317
+YVG LA EV LH F G I ++++ ++ +GF FV + +AA AI
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGD--ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 318 QMGNTTQSSYLFGKQMKV 335
N ++ LFG+ ++V
Sbjct: 123 DNMNESE---LFGRTIRV 137
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAM 109
+T R +YVG + +V + +L F G + ++ ++ + F+ + AA
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120
Query: 110 AILSLNGRHLFGQPIKVNWA 129
AI ++N LFG+ I+VN A
Sbjct: 121 AIDNMNESELFGRTIRVNLA 140
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 76 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 105
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 157
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 64/148 (43%), Gaps = 12/148 (8%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y +
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA---TV 66
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
++N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 67 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 126
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSF 190
Y +M D+ +G+ RGF FV+F
Sbjct: 127 EQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 251 TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVR 306
+ +E+P+ Q +++G L+ E T L HF G V+ + +R +GFGFV
Sbjct: 3 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 307 YSTHAEAALAI 317
Y+T E A+
Sbjct: 63 YATVEEVDAAM 73
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 75 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 104
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 35/148 (23%), Positives = 63/148 (42%), Gaps = 12/148 (8%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
A +N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 69 DAA---MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSF 190
Y +M D+ +G+ RGF FV+F
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 251 TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVR 306
+ +E+P+ Q +++G L+ E T L HF G V+ + +R +GFGFV
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 307 YSTHAEAALAI 317
Y+T E A+
Sbjct: 62 YATVEEVDAAM 72
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 74 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 103
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 155
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/148 (22%), Positives = 64/148 (43%), Gaps = 12/148 (8%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y +
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA---TV 64
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
++N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 65 EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 124
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSF 190
Y +M D+ +G+ RGF FV+F
Sbjct: 125 EQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 251 TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVR 306
+ +E+P+ Q +++G L+ E T L HF G V+ + +R +GFGFV
Sbjct: 1 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 60
Query: 307 YSTHAEAALAI 317
Y+T E A+
Sbjct: 61 YATVEEVDAAM 71
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 73 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 102
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 154
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 35/158 (22%), Positives = 65/158 (41%), Gaps = 12/158 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y
Sbjct: 7 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
A +N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 67 DAA---MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 123
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
Y +M D+ +G+ RGF FV+F + +
Sbjct: 124 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRY 307
+E+P+ Q +++G L+ E T L HF G V+ + +R +GFGFV Y
Sbjct: 1 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 60
Query: 308 STHAEAALAI 317
+T E A+
Sbjct: 61 ATVEEVDAAM 70
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 75 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 104
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 35/158 (22%), Positives = 65/158 (41%), Gaps = 12/158 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
A +N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 69 DAA---MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 125
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
Y +M D+ +G+ RGF FV+F + +
Sbjct: 126 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 251 TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVR 306
+ +E+P+ Q +++G L+ E T L HF G V+ + +R +GFGFV
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 307 YSTHAEAALAI 317
Y+T E A+
Sbjct: 62 YATVEEVDAAM 72
>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 = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L+ EV D L A F + +D ++ D +T + RGF FV F +DA +AI+++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 204 TGKWLGSRQIRCNWA 218
L R IR N A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
+YVG LA EV LH F G I ++++ ++ +GF FV + +AA AI
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGD--ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 319 MGNTTQSSYLFGKQMKV 335
N ++ LFG+ ++V
Sbjct: 63 NMNESE---LFGRTIRV 76
Score = 34.7 bits (78), Expect = 0.080, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAMAIL 112
R +YVG + +V + +L F G + ++ + + F+ + AA AI
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 113 SLNGRHLFGQPIKVNWA 129
++N LFG+ I+VN A
Sbjct: 63 NMNESELFGRTIRVNLA 79
>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 = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L+ EV D L A F + +D ++ D +T + RGF FV F +DA +AI+++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 204 TGKWLGSRQIRCNWA 218
L R IR N A
Sbjct: 70 NESELFGRTIRVNLA 84
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
+YVG LA EV LH F G I ++++ ++ +GF FV + +AA AI
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGD--ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 319 MGNTTQSSYLFGKQMKV 335
N ++ LFG+ ++V
Sbjct: 68 NMNESE---LFGRTIRV 81
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAM 109
+T R +YVG + +V + +L F G + ++ + + F+ + AA
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 110 AILSLNGRHLFGQPIKVNWA 129
AI ++N LFG+ I+VN A
Sbjct: 65 AIDNMNESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L+ EV D L A F + +D ++ D +T + RGF FV F +DA +AI+++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 204 TGKWLGSRQIRCNWA 218
L R IR N A
Sbjct: 68 NESELFGRTIRVNLA 82
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
+YVG LA EV LH F G I ++++ ++ +GF FV + +AA AI
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGD--ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 319 MGNTTQSSYLFGKQMKV 335
N ++ LFG+ ++V
Sbjct: 66 NMNESE---LFGRTIRV 79
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAM 109
+T R +YVG + +V + +L F G + ++ + + F+ + AA
Sbjct: 3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62
Query: 110 AILSLNGRHLFGQPIKVNWA 129
AI ++N LFG+ I+VN A
Sbjct: 63 AIDNMNESELFGRTIRVNLA 82
>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 = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+F+G LS E TD +L + F + + +D VM D T RSRGFGFV++ ++ +A+N
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
K G VVE S + +++ P +
Sbjct: 68 RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 97
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
++VG + + + L +F G + E+ R +GF FV + H
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 35/158 (22%), Positives = 65/158 (41%), Gaps = 12/158 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSA 107
+P R +++G + + T+ L+ F G + C ++R K +GF+ Y
Sbjct: 2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 108 AMAILSLNGR--HLFGQPIKVNWAYASGQREDTSGHF---NIFVGDLSPEVTDATLFACF 162
A +N R + G+ ++ A + + H IFVG + + + L F
Sbjct: 62 DAA---MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 118
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
Y +M D+ +G+ RGF FV+F + +
Sbjct: 119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 34.7 bits (78), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALA 316
Q +++G L+ E T L HF G V+ + +R +GFGFV Y+T E A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 317 I 317
+
Sbjct: 65 M 65
>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 = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 144 IFVGDLSPEVTDATLF-ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+++G + + T+ + C +V P + ++M+D +TGRS+G+ F+ FR+ + + SA+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 203 LTGKWLGSRQIRCNWAT 219
L G LGSR ++C +++
Sbjct: 66 LNGYQLGSRFLKCGYSS 82
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
R VY+G+I TE + ++ S+ GPV K++ ++ Y FI + D S+A A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 113 SLNGRHLFGQPIKVNWA 129
+LNG L + +K ++
Sbjct: 65 NLNGYQLGSRFLKCGYS 81
>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 = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 144 IFVGDLSPEVTDATLF-ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+++G + + T+ + C +V P + ++M+D +TGRS+G+ F+ FR+ + + SA+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 203 LTGKWLGSRQIRCNWAT 219
L G LGSR ++C +++
Sbjct: 65 LNGYQLGSRFLKCGYSS 81
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
R VY+G+I TE + ++ S+ GPV K++ ++ Y FI + D S+A A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 113 SLNGRHLFGQPIKVNWA 129
+LNG L + +K ++
Sbjct: 64 NLNGYQLGSRFLKCGYS 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
+VYVG + +V+EPLL E+F GPV + KD+ + YGF+ + A AI
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHM-PKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 113 SLNGRHLFGQPIKVNWAYA 131
++ L+G+PI+VN A A
Sbjct: 76 IMDMIKLYGKPIRVNKASA 94
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L +V++ L+ F + + D+ TG+ +G+GFV F +++DA AI +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 204 TGKWLGSRQIRCNWAT 219
L + IR N A+
Sbjct: 78 DMIKLYGKPIRVNKAS 93
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 53.5 bits (127), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 45/80 (56%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L ++TD L+A F + R+M D KTG S G+ FV F ++ D+Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 203 LTGKWLGSRQIRCNWATKGA 222
L G + +++++ ++A G
Sbjct: 65 LNGITVRNKRLKVSYARPGG 84
Score = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 68 VTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSLNGRHLFGQP 123
+T+ L +F + GP+ C+++R K+ Y F+ + + AI LNG + +
Sbjct: 15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 124 IKVNWAYASGQ 134
+KV++A G+
Sbjct: 75 LKVSYARPGGE 85
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 47/88 (53%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG R + + + V LS T+ L FS Y +D +++DQ++ RSRGF FV F
Sbjct: 5 SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
N DA+ A G L R+IR +++
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRVDFS 92
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSA 107
DP+ C V+ +++T TE L+EVFS GP+ ++ +S + F+++ + A
Sbjct: 13 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
A NG L G+ I+V+++
Sbjct: 71 KEAKERANGMELDGRRIRVDFS 92
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 53.5 bits (127), Expect = 2e-07, Method: Composition-based stats.
Identities = 29/91 (31%), Positives = 53/91 (58%), Gaps = 5/91 (5%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSC-SDARVMWDQKTGRSRGFGFVSFRNQQDA 196
+SG IF+G+L PE+ + L+ FS + ++M D TG S+G+ F++F + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 197 QSAINDLTGKWLGSRQIRCNWA----TKGAG 223
+AI + G++L +R I ++A +KG+G
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGSG 92
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 51/92 (55%), Gaps = 9/92 (9%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAA 108
S +++GN+ ++ E LL + FS+ G + I +D + Y FI++ ++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 109 MAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
AI ++NG++L +PI V++A+ ++D+ G
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAF----KKDSKG 90
Score = 31.6 bits (70), Expect = 0.69, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
+++GNL PE+ + L+ F + G +++ ++ RD KG+ F+ +++ + AI+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGV-ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 319 MGN 321
N
Sbjct: 67 AMN 69
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG L+ EV D L A F + +D ++ D +T + RGF FV F +DA +AI+++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 204 TGKWLGSRQIRCNWA 218
L R IR N A
Sbjct: 75 NESELFGRTIRVNLA 89
Score = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
+YVG LA EV LH F G I ++++ ++ +GF FV + +AA AI
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGD--ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 319 MGNTTQSSYLFGKQMKV 335
N ++ LFG+ ++V
Sbjct: 73 NMNESE---LFGRTIRV 86
Score = 34.7 bits (78), Expect = 0.073, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAM 109
+T R +YVG + +V + +L F G + ++ + + F+ + AA
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69
Query: 110 AILSLNGRHLFGQPIKVNWA 129
AI ++N LFG+ I+VN A
Sbjct: 70 AIDNMNESELFGRTIRVNLA 89
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 43/79 (54%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 200 INDLTGKWLGSRQIRCNWA 218
IN L G L S+ I+ ++A
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/70 (42%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 68 VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
+T+ L+ +FSS G VE KLIR DK + YGF++Y + A AI +LNG L +
Sbjct: 16 MTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 74
Query: 123 PIKVNWAYAS 132
IKV++A S
Sbjct: 75 TIKVSYARPS 84
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 39/82 (47%), Gaps = 11/82 (13%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEA 313
P T + V L +TQ +L F S+G +E ++ RDK G+GFV Y T +A
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGE--VESAKLIRDKVAGHSLGYGFVNYVTAKDA 59
Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
AI NT L K +KV
Sbjct: 60 ERAI---NTLNGLRLQSKTIKV 78
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 47/91 (51%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG R + + + V LS T+ L FS Y +D +++DQ++ RSRGF FV F
Sbjct: 5 SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
N DA+ A G L R+IR + + G
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRVSGPSSG 95
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSA 107
DP+ C V+ +++T TE L+EVFS GP+ ++ +S + F+++ + A
Sbjct: 13 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 108 AMAILSLNGRHLFGQPIKVN 127
A NG L G+ I+V+
Sbjct: 71 KEAKERANGMELDGRRIRVS 90
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 34/103 (33%), Positives = 54/103 (52%), Gaps = 6/103 (5%)
Query: 42 IPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS--YG 97
IP + P +P R++ V I T V E L+++F GP+E K++ R+ + S YG
Sbjct: 30 IPPTQMNP--EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
Query: 98 FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
F+ + SA AI LNG ++ + +KV A + QR +G
Sbjct: 88 FVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V + V + L F Y +++ D++T +SRG+GFV F++ AQ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 203 LTGKWLGSRQIRCNWATKG 221
L G + +++++ A G
Sbjct: 104 LNGFNILNKRLKVALAASG 122
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 47/76 (61%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+++G + + T+ + S + ++M+D +TGRS+G+ F+ FR+ + + SA+ +L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 204 TGKWLGSRQIRCNWAT 219
G LGSR ++C +++
Sbjct: 65 NGYQLGSRFLKCGYSS 80
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 8/88 (9%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
R VY+G+I TE + ++ S+ GPV K++ ++ Y FI + D S+A A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSG 140
+LNG L + +K ++ S D SG
Sbjct: 63 NLNGYQLGSRFLKCGYSSNS----DISG 86
>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 = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 43/85 (50%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
D G ++ V +L+ + TL F Y D + D+ T SRGF FV F +++DA
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
+ A++ + G L R++R A G
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYG 127
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
LS T+ L FS Y +D +++DQ++ RSRGF FV F N DA+ A G L
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 209 GSRQIRCNWA 218
R+IR +++
Sbjct: 114 DGRRIRVDFS 123
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSA 107
DP+ C V+ +++T TE L+EVFS GP+ ++ +S + F+++ + A
Sbjct: 44 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 101
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
A NG L G+ I+V+++
Sbjct: 102 KEAKERANGMELDGRRIRVDFS 123
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGP---VEGCKLIRKDKSSYGFIHYFDRRSAAMAILS 113
R+V+VGN+ +V E +L E+F GP V CK S+GF+ + S + AI
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 114 LNGRHLFGQPIKVN 127
LNG L+G+PI V+
Sbjct: 77 LNGIRLYGRPINVS 90
Score = 31.2 bits (69), Expect = 0.96, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTH 310
P TV+VGNL V + L+ F L AG + +V + +D K FGFV +
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELF--LQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ AI + N + L+G+ + V
Sbjct: 68 ESVSYAIALLNGIR---LYGRPINV 89
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
LS T+ L FS Y +D +++DQ++ RSRGF FV F N DA+ A G L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 209 GSRQIRCNWA 218
R+IR +++
Sbjct: 80 DGRRIRVDFS 89
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSA 107
DP+ C V+ +++T TE L+EVFS GP+ ++ +S + F+++ + A
Sbjct: 10 DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 67
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
A NG L G+ I+V+++
Sbjct: 68 KEAKERANGMELDGRRIRVDFS 89
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+F+ L E TD L + F + + A+V D++T S+ FGFVSF N AQ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 203 LTGKWLGSRQIR 214
+ G +G+++++
Sbjct: 102 MNGFQVGTKRLK 113
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 43/85 (50%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
D G ++ V +L+ + TL F Y D + D+ T SRGF FV F +++DA
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
+ A++ + G L R++R A G
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 52 DPSTCRS-VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAM 109
DP + S V++GN++T V + ++ +FS G V GC + + Y F+ Y + R A
Sbjct: 22 DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK----GYAFVQYSNERHARA 77
Query: 110 AILSLNGRHLFGQPIKVNWA 129
A+L NGR L GQ + +N A
Sbjct: 78 AVLGENGRVLAGQTLDINMA 97
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 47/86 (54%)
Query: 135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
++ ++G ++VG L +T+ L F + ++M D +TGRS+G+GF++F + +
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 195 DAQSAINDLTGKWLGSRQIRCNWATK 220
A+ A+ L G L R ++ T+
Sbjct: 80 CAKKALEQLNGFELAGRPMKVGHVTE 105
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+YVG++H +TE +L+ +F G +E +L+ ++ YGFI + D A A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 115 NGRHLFGQPIKV 126
NG L G+P+KV
Sbjct: 89 NGFELAGRPMKV 100
Score = 28.1 bits (61), Expect = 6.5, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ------RDKGFGFVRYSTHAEAALAIQ 318
+YVG+L +T+ L F G IE +++ R KG+GF+ +S A A++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGR--IESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 319 MGNTTQSSYLFGKQMKV 335
N + L G+ MKV
Sbjct: 87 QLNGFE---LAGRPMKV 100
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 54/100 (54%), Gaps = 6/100 (6%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG R N++V +L + D L FS + + + A+VM + GRS+GFGFV F
Sbjct: 5 SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCF 62
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
+ ++A A+ ++ G+ + ++ + A + E++QS
Sbjct: 63 SSPEEATKAVTEMNGRIVATKPLYVALAQR----KEERQS 98
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSLNG 116
+YV N+ + + L++ FS G + K++ + S +GF+ + A A+ +NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 117 RHLFGQPIKVNWAYASGQRE 136
R + +P+ V A +R+
Sbjct: 78 RIVATKPLYVALAQRKEERQ 97
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ--RDKGFGFVRYSTHAEAALAI 317
Q +YV NL + L + F G +V ++ R KGFGFV +S+ EA A+
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV 72
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
A Q+E G N+F+ L E D L F + + A+V D++T S+ FGFVS+
Sbjct: 16 AGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNW 217
N AQ+AI + G +G ++++
Sbjct: 75 DNPVSAQAAIQSMNGFQIGMKRLKVQL 101
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAAL 315
P+ +++ +L E DL + F G V +V + + K FGFV Y A
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82
Query: 316 AIQMGNTTQ 324
AIQ N Q
Sbjct: 83 AIQSMNGFQ 91
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV LS + T+ TL F AR++ D++TG S+GFGFV F +++DA++A +
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 204 TGKWLGSRQIRCNWA 218
+ ++ +WA
Sbjct: 75 EDGEIDGNKVTLDWA 89
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 264 TVYVGNLAPEVTQLDLHRHFH-SLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
T++V L+ + T+ L F S+ A ++ + KGFGFV +++ +A A +
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 5/89 (5%)
Query: 44 SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---YGFIH 100
SG+ P ++++V + TE L+E F G V + ++ S +GF+
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVD 60
Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
+ A A ++ + G + ++WA
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 44/83 (53%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
+SG ++VG L +T+ L F + + +M D TGRS+G+GF++F + + A+
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 198 SAINDLTGKWLGSRQIRCNWATK 220
A+ L G L R +R T+
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTE 84
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAM 109
S +YVG++H +TE +L+ +F G ++ L++ + YGFI + D A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 110 AILSLNGRHLFGQPIKV 126
A+ LNG L G+P++V
Sbjct: 63 ALEQLNGFELAGRPMRV 79
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
IFVG L TDA+L F + +A V+ D++TG+SRG+GFV+ ++ A+ A D
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 203 LTGKWLGSRQIRCNWATKGA 222
+ R+ N A GA
Sbjct: 79 -PNPIIDGRKANVNLAYLGA 97
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAE 312
+ + +T ++VG L T L ++F G A VI + + + +G+GFV + A
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 313 AALAIQ 318
A A +
Sbjct: 72 AERACK 77
>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 = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 7/76 (9%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA-IQM 319
Q + ++VGNL P++T+ ++ + F G EV + +DKGFGF+R T A +A +++
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKDKGFGFIRLETRTLAEIAKVEL 71
Query: 320 GNTTQSSYLFGKQMKV 335
N L GKQ++V
Sbjct: 72 DNMP----LRGKQLRV 83
Score = 35.0 bits (79), Expect = 0.059, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
++VGN+ +TE ++++F G G I KDK +GFI R A +A + L+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMP 75
Query: 119 LFGQPIKVNWAYASG 133
L G+ ++V +A S
Sbjct: 76 LRGKQLRVRFACHSA 90
Score = 35.0 bits (79), Expect = 0.064, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FVG+L P++T+ + F Y + + D +GFGF+ + A+ A +L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 204 TGKWLGSRQIRCNWATKGA 222
L +Q+R +A A
Sbjct: 72 DNMPLRGKQLRVRFACHSA 90
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
G NIF+ +L + + L+ FS + + +V+ D+ S+G+GFV F Q+ A+ A
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
Query: 200 INDLTGKWLGSRQI 213
I + G L R++
Sbjct: 62 IEKMNGMLLNDRKV 75
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 55/124 (44%), Gaps = 19/124 (15%)
Query: 41 PIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGF 98
P+ SGN +++ N+ + L + FS+ G + CK++ + S YGF
Sbjct: 2 PLGSGN------------IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 49
Query: 99 IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG-----HFNIFVGDLSPEV 153
+H+ + +A AI +NG L + + V + +RE G N+++ + P
Sbjct: 50 VHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGS 109
Query: 154 TDAT 157
T A
Sbjct: 110 TRAA 113
>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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 42/181 (23%), Positives = 78/181 (43%), Gaps = 8/181 (4%)
Query: 139 SGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
+G+ + V +L+PE VT +LF F VY ++++++K V + AQ
Sbjct: 32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQ 86
Query: 198 SAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPE 257
A++ L G L + IR + + D + N K+ +
Sbjct: 87 LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146
Query: 258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-VQRDKGFGFVRYSTHAEAALA 316
P T+++ N+ P V++ DL F S G GV++ + Q+D+ ++ + EA A
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFKFFQKDRKMALIQMGSVEEAVQA 205
Query: 317 I 317
+
Sbjct: 206 L 206
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 49 PGFDPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA 107
PG + + V N++ + VT L +F G V+ K++ +K + D A
Sbjct: 27 PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-NKKENALVQMADGNQA 85
Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
+A+ LNG L G+PI++ +
Sbjct: 86 QLAMSHLNGHKLHGKPIRITLS 107
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
+++P+ TVY G +A +T + + F G I E+RV +KG+ FVR+STH AA A
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ--IMEIRVFPEKGYSFVRFSTHESAAHA 77
Query: 317 IQMGNTT 323
I N T
Sbjct: 78 IVSVNGT 84
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
P C +VY G I + +T+ L+++ FS G + ++ + Y F+ + SAA AI+
Sbjct: 23 PKNC-TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF--PEKGYSFVRFSTHESAAHAIV 79
Query: 113 SLNGRHLFGQPIKVNWAYAS 132
S+NG + G +K W S
Sbjct: 80 SVNGTTIEGHVVKCYWGKES 99
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++ G ++ +TD + FS + + RV + +G+ FV F + A AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 204 TGKWLGSRQIRCNWA 218
G + ++C W
Sbjct: 82 NGTTIEGHVVKCYWG 96
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
SG NIF+ +L + + L+ FS + + +V+ D+ S+G+GFV F Q+ A+
Sbjct: 9 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 66
Query: 199 AINDLTGKWLGSRQI 213
AI + G L R++
Sbjct: 67 AIEKMNGMLLNDRKV 81
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/93 (27%), Positives = 47/93 (50%), Gaps = 6/93 (6%)
Query: 50 GFDPSTCRS----VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFD 103
G DPS +S +++ N+ + L + FS+ G + CK++ + S YGF+H+
Sbjct: 1 GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET 60
Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
+ +A AI +NG L + + V + +RE
Sbjct: 61 QEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 93
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N++V +L +TD L F Y S ++ D+ TGR RG FV + +++AQ AI+
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 203 L 203
L
Sbjct: 75 L 75
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFD 103
PG + ++YV N+ +T+ L +F G + ++R DK + F+ Y
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR-DKLTGRPRGVAFVRYNK 64
Query: 104 RRSAAMAILSLNGRHLFG--QPIKVNWAYASGQ 134
R A AI +LN G QP+ V A G+
Sbjct: 65 REEAQEAISALNNVIPEGGSQPLSVRLAEEHGK 97
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/176 (23%), Positives = 75/176 (42%), Gaps = 8/176 (4%)
Query: 144 IFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+ V +L+PE VT +LF F VY ++++++K V + AQ A++
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 60
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
L G L + IR + + D + N K+ + P
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-VQRDKGFGFVRYSTHAEAALAI 317
T+++ N+ P V++ DL F S G GV++ + Q+D+ ++ + EA A+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 59 VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
+ V N++ + VT L +F G V+ K++ K + + D A +A+ LNG
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-ALVQMADGNQAQLAMSHLNGH 64
Query: 118 HLFGQPIKVNWA 129
L G+PI++ +
Sbjct: 65 KLHGKPIRITLS 76
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/201 (22%), Positives = 83/201 (41%), Gaps = 35/201 (17%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY- 101
+ R +YVGNI +TE + + F++ PV + I +DK+ + F+ +
Sbjct: 2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFR 59
Query: 102 -FDRRSAAMAILSLNGRHLFGQPIKV----NWAYASGQREDTSGHF-------------N 143
D + AMA +G GQ +K+ ++ G E+ S +
Sbjct: 60 SVDETTQAMA---FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+F+G L + D + + + ++ D TG S+G+ F + + AI L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 204 TGKWLGSRQIRCNWATKGAGN 224
G LG +++ A+ GA N
Sbjct: 177 NGMQLGDKKLLVQRASVGAKN 197
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAA 108
P + +++G + + + ++E+ +S GP++ L++ + Y F Y D
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 109 MAILSLNGRHLFGQPIKVNWA 129
AI LNG L + + V A
Sbjct: 171 QAIAGLNGMQLGDKKLLVQRA 191
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 21/178 (11%)
Query: 55 TCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY-- 101
+ R +YVGNI +TE + + F++ PV + I +DK+ + F+ +
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFRS 62
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFAC 161
D + AMA +G GQ +K+ + + G +F+G L + D +
Sbjct: 63 VDETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKEL 116
Query: 162 FSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
+ + ++ D TG S+G+ F + + AI L G LG +++ A+
Sbjct: 117 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+ V +L P +T + S +++ ++TG+S+G+GF + + A A +DL
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 204 TGKWLGSRQIRCNWATKG 221
GK LG R + +W G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 71/169 (42%), Gaps = 8/169 (4%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+ V N+ +T+ +E+ G +E C L+ +++ YGF Y + SAA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD-LSPEVTDA-TLFACFSVYPSCSDAR 172
G+ L + + V+W A GQ H D L P D L S S + +
Sbjct: 158 LGKPLGPRTLYVHWTDA-GQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
+ Q G+ +GF + + + A+ A G LG +R ++ G
Sbjct: 217 LACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+ V +L P +T + S +++ ++TG+S+G+GF + + A A +DL
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 204 TGKWLGSRQIRCNWATKG 221
GK LG R + +W G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 71/169 (42%), Gaps = 8/169 (4%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+ V N+ +T+ +E+ G +E C L+ +++ YGF Y + SAA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD-LSPEVTDA-TLFACFSVYPSCSDAR 172
G+ L + + V+W A GQ H D L P D L S S + +
Sbjct: 158 LGKPLGPRTLYVHWTDA-GQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
+ Q G+ +GF + + + A+ A G LG +R ++ G
Sbjct: 217 LACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+ V +L P +T + S +++ ++TG+S+G+GF + + A A +DL
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 204 TGKWLGSRQIRCNWATKG 221
GK LG R + +W G
Sbjct: 156 LGKPLGPRTLYVHWTDAG 173
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 71/169 (42%), Gaps = 8/169 (4%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
+ V N+ +T+ +E+ G +E C L+ +++ YGF Y + SAA A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD-LSPEVTDA-TLFACFSVYPSCSDAR 172
G+ L + + V+W A GQ H D L P D L S S + +
Sbjct: 156 LGKPLGPRTLYVHWTDA-GQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 214
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
+ Q G+ +GF + + + A+ A G LG +R ++ G
Sbjct: 215 LACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 262
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 21/178 (11%)
Query: 55 TCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY-- 101
+ R +YVGNI +TE + + F++ PV + I +DK+ + F+ +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFRS 60
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFAC 161
D + AMA +G GQ +K+ + + G +F+G L + D +
Sbjct: 61 VDETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKEL 114
Query: 162 FSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
+ + ++ D TG S+G+ F + + AI L G LG +++ A+
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L T L + FS A+++ D+ G S G+GFV++ +DA+ AIN
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 203 LTGKWLGSRQIRCNWA 218
L G L S+ I+ ++A
Sbjct: 81 LNGLRLQSKTIKVSYA 96
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 6/69 (8%)
Query: 69 TEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQP 123
T+ L+ +FSS G VE KLIR DK + YGF++Y + A AI +LNG L +
Sbjct: 32 TQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 90
Query: 124 IKVNWAYAS 132
IKV++A S
Sbjct: 91 IKVSYARPS 99
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAA 314
Q T + V L TQ +L F S+G +E ++ RDK G+GFV Y T +A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGE--VESAKLIRDKVAGHSLGYGFVNYVTAKDAE 75
Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
AI NT L K +KV
Sbjct: 76 RAI---NTLNGLRLQSKTIKV 93
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 74/153 (48%), Gaps = 10/153 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAI 111
++VG + +E L+E+F G V ++R D+S S G F+ ++ R++A A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 112 LSL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
+L N + L G + A ++ + +F+G +S + T+ + FS + +
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 136
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
R++ G SRG FV+F + AQ+AI +
Sbjct: 137 CRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 168
Score = 34.3 bits (77), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSSYG--FIHYFDRRSAAMAILS 113
R +++G I + TE ++ +FSS G +E C+++R D S G F+ + R A AI +
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 114 LN 115
++
Sbjct: 168 MH 169
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/150 (26%), Positives = 72/150 (48%), Gaps = 10/150 (6%)
Query: 60 YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAIL 112
+VG + +E L+E+F G V ++R D+S S G F+ ++ R++A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 113 SL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDA 171
+L N + L G + A ++ + +F+G +S + T+ + FS + +
Sbjct: 66 ALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEEC 125
Query: 172 RVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
R++ G SRG FV+F + AQ+AI
Sbjct: 126 RILRG-PDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSSYG--FIHYFDRRSAAMAI 111
R +++G I + TE ++ FSS G +E C+++R D S G F+ + R A AI
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 74/153 (48%), Gaps = 10/153 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAI 111
++VG + +E L+E+F G V ++R D+S S G F+ ++ R++A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 112 LSL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
+L N + L G + A ++ + +F+G +S + T+ + FS + +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
R++ G SRG FV+F + AQ+AI +
Sbjct: 125 CRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156
Score = 34.3 bits (77), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSSYG--FIHYFDRRSAAMAILS 113
R +++G I + TE ++ +FSS G +E C+++R D S G F+ + R A AI +
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 114 LN 115
++
Sbjct: 156 MH 157
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
S+ + +YV N+ +E ++++ F++ P VE K IR Y F+H+ +R A A+
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAM 68
Query: 112 LSLNGRHLFGQPIKVNWA 129
+LNG+ L G PI+V A
Sbjct: 69 KALNGKVLDGSPIEVTLA 86
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 21/42 (50%)
Query: 177 QKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
++ + R + FV F N++DA A+ L GK L I A
Sbjct: 45 ERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
+ ++V N+ VTE +L++ FS G +E K ++ Y FIH+ +R A A+ +NG
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK----DYAFIHFDERDGAVKAMEEMNG 67
Query: 117 RHLFGQPIKVNWAYASGQR 135
+ L G+ I++ +A Q+
Sbjct: 68 KDLEGENIEIVFAKPPDQK 86
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE----GCKLIRKDKSSYGFIHYFDRRSAA 108
+C ++YVGN+ TE + E+FS +G ++ G ++K + F+ Y+ R A
Sbjct: 37 KKSC-TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 109 MAILSLNGRHLFGQPIKVNW 128
A+ +NG L + I+ +W
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 3/92 (3%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG+LS T+ ++ FS + D+ + GF FV + ++ DA++A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
G L R IR +W AG E +Q +S
Sbjct: 102 NGTRLDDRIIRTDWD---AGFKEGRQYGRGRS 130
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFV 305
N E + + T+YVGNL+ T+ ++ F +G I+++ + DK GF FV
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK--SGDIKKIIMGLDKMKKTACGFCFV 86
Query: 306 RYSTHAEAALAIQMGNTTQ 324
Y + A+A A++ N T+
Sbjct: 87 EYYSRADAENAMRYINGTR 105
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 50 GFDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIH 100
G +P RSV +V +H + TE + + F+ G ++ L ++ Y +
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWAYA 131
Y + A A+ LNG+ L GQPI V+W +
Sbjct: 71 YETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYS 308
P+ + + ++V + E T+ D+H F G I+ + + D KG+ V Y
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 309 THAEAALAIQ 318
T+ EA A++
Sbjct: 73 TYKEAQAAME 82
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 51 FDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHY 101
+P RSV +V +IH + E +QE F G ++ L ++ Y + Y
Sbjct: 62 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
+ A A +LNG + GQ I+V+W + G
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 153
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E + + F Y + + D++TG S+G+ V + + A +A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 204 TGKWLGSRQIRCNW 217
G + + I+ +W
Sbjct: 135 NGAEIMGQTIQVDW 148
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 29/125 (23%), Positives = 49/125 (39%), Gaps = 19/125 (15%)
Query: 220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDL 279
KG G D + +A E +D E P+ + + ++V ++ E + ++
Sbjct: 34 KGRGFGSDSNTREAIHSYERVRNEDDDELEP----GPQRSVEGWILFVTSIHEEAQEDEI 89
Query: 280 HRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ-------MGNTTQSS 326
F G I+ + + D KG+ V Y TH +A A + MG T Q
Sbjct: 90 QEKFCDYGE--IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147
Query: 327 YLFGK 331
+ F K
Sbjct: 148 WCFVK 152
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
FN+F+G+L+P + A L S + +D V+ D +TG +R FG+V F + +D + A+
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKAL- 71
Query: 202 DLTGKWLGSRQIRC 215
+LTG + +I+
Sbjct: 72 ELTGLKVFGNEIKL 85
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/122 (18%), Positives = 54/122 (44%), Gaps = 7/122 (5%)
Query: 96 YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTD 155
+G++ + A L L G +FG IK+ ++ + + +LS +T+
Sbjct: 56 FGYVDFESAEDLEKA-LELTGLKVFGNEIKLEKPKGRDSKKVRAAR-TLLAKNLSFNITE 113
Query: 156 ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
L V+ + R++ + G+S+G ++ F+++ DA+ + + G + R +
Sbjct: 114 DELK---EVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
Query: 216 NW 217
+
Sbjct: 169 YY 170
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
++ V + +T+ + +F S G +E CKL+R DK + YGF++Y D A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR-DKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 113 SLNGRHLFGQPIKVNWAYAS 132
+LNG L + IKV++A S
Sbjct: 65 TLNGLKLQTKTIKVSYARPS 84
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 40/76 (52%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N+ V L +T + F +++ D+ TG+S G+GFV++ + DA AIN
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 203 LTGKWLGSRQIRCNWA 218
L G L ++ I+ ++A
Sbjct: 66 LNGLKLQTKTIKVSYA 81
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
T + V L +TQ + F S+G IE ++ RDK G+GFV YS +A A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGD--IESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 317 IQMGNTTQSSYLFGKQMKV 335
I NT L K +KV
Sbjct: 63 I---NTLNGLKLQTKTIKV 78
>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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 9/93 (9%)
Query: 50 GFDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIH 100
G +P RSV +V +H + TE + + F+ G ++ L ++ Y +
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
Y + A A+ LNG+ L GQPI V+W + G
Sbjct: 72 YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 86 NGQDLMGQPISVDW 99
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 245 EDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----- 299
+DG E P+ + + ++V + E T+ D+H F G I+ + + D
Sbjct: 10 QDGDEP----GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGY 63
Query: 300 -KGFGFVRYSTHAEAALAIQ 318
KG+ V Y T+ EA A++
Sbjct: 64 LKGYTLVEYETYKEAQAAME 83
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
N++V L ++ + FS Y +R++ DQ TG SRG GF+ F + +A+ AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 203 LTGK 206
L G+
Sbjct: 63 LNGQ 66
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILS 113
++YV + +++ ++++FS G + +++ + GFI + R A AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 114 LNGRHLFG--QPIKVNWAYASGQ 134
LNG+ G +PI V +A Q
Sbjct: 63 LNGQKPLGAAEPITVKFANNPSQ 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
++V +H + TE + + F+ G ++ L ++ Y + Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAYASG 133
NG+ L GQPI V+W + G
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
P+ + + ++V + E T+ D+H F G I+ + + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 310 HAEAALAIQ 318
+ EA A++
Sbjct: 59 YKEAQAAME 67
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 39/70 (55%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV ++ + T++ L F VY +++ +++G+ RG+ F+ + +++D SA
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 204 TGKWLGSRQI 213
GK + R++
Sbjct: 165 DGKKIDGRRV 174
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/175 (21%), Positives = 78/175 (44%), Gaps = 18/175 (10%)
Query: 50 GFDPSTCRSVYVGNIHTQVTEPLLQ----EVFSSTG-PVEGCK--LIRKDKSSYGFIHYF 102
G +P+T +++VGN++ + P L+ +VF+ V + + RK +G++ +
Sbjct: 1 GTEPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRK----FGYVDFE 56
Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACF 162
A L L G +FG IK+ +++ + +L +VT L
Sbjct: 57 SAEDLEKA-LELTGLKVFGNEIKLEKPKGKDSKKERDAR-TLLAKNLPYKVTQDELK--- 111
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
V+ ++ R++ K G+S+G ++ F+ + DA+ + G + R I +
Sbjct: 112 EVFEDAAEIRLV--SKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYY 164
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 53 PSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFD 103
P RSV +V +H + TE + + F+ G ++ L ++ Y + Y
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
+ A A+ LNG+ L GQPI V+W + G
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISVDWCFVRG 90
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYS 308
P+ + + ++V + E T+ D+H F G I+ + + D KG+ V Y
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGYLKGYTLVEYE 59
Query: 309 THAEAALAIQ 318
T+ EA A++
Sbjct: 60 TYKEAQAAME 69
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
++V +H + TE + + F+ G ++ L ++ Y + Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAYASG 133
NG+ L GQPI V+W + G
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
P+ + + ++V + E T+ D+H F G I+ + + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 310 HAEAALAIQ 318
+ EA A++
Sbjct: 59 YKEAQAAME 67
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 34/58 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
+F+G LS E T+ +L + + +D VM D + RSRGFGFV+F + + +A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
Q+ +++G L+ E T+ L ++ G V+ + +R +GFGFV +S+ AE A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 317 I 317
+
Sbjct: 86 M 86
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 39/70 (55%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV ++ + T++ L F VY +++ +++G+ RG+ F+ + +++D SA
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 204 TGKWLGSRQI 213
GK + R++
Sbjct: 165 DGKKIDGRRV 174
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 38/85 (44%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
D G + V +L+ + +L F Y D + + T RGF FV F +++DA
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
Q A + G L R++R A G
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYG 93
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 11/90 (12%)
Query: 116 GRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMW 175
G H+ P+ + +++ FN+F+G+L+P + A L S + +D V+
Sbjct: 1 GSHMLEDPV---------EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV- 50
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
D +TG +R FG+V F + +D + A+ +LTG
Sbjct: 51 DVRTGTNRKFGYVDFESAEDLEKAL-ELTG 79
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
IFVG LS T + F + DA +M+D+ T R RGFGFV+F + +D + ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 204 TGKWLGSRQIRCNWA 218
+ ++ + C A
Sbjct: 61 HFHEINNKMVECKKA 75
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 51 FDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHY 101
+P RSV +V +IH + E +QE F G ++ L ++ Y + Y
Sbjct: 16 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
+ A A +LNG + GQ I+V+W + G +
Sbjct: 76 ETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E + + F Y + + D++TG S+G+ V + + A +A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 204 TGKWLGSRQIRCNW 217
G + + I+ +W
Sbjct: 89 NGAEIMGQTIQVDW 102
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 29/50 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
+FVG L T TL + FS Y D +M D+ T +SRGFGFV F++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
++V +H + TE + + F+ G ++ L ++ Y + Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAY 130
NG+ L GQPI V+W +
Sbjct: 70 NGQDLMGQPISVDWCF 85
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+FV + E T+ + F+ Y + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 204 TGKWLGSRQIRCNW 217
G+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
P+ + + ++V + E T+ D+H F G I+ + + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 310 HAEAALAIQ 318
+ EA A++
Sbjct: 59 YKEAQAAME 67
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
P C+ VYVGN+ + L+ F GP+ + R + + F+ + D R AA A+
Sbjct: 71 PLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVR 128
Query: 113 SLNGRHLFGQPIKV 126
L+GR L G ++V
Sbjct: 129 DLDGRTLCGCRVRV 142
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG+L L F Y R +W + GF FV F + +DA A+ DL
Sbjct: 76 VYVGNLGNNGNKTELERAFGYY---GPLRSVWVARN--PPGFAFVEFEDPRDAADAVRDL 130
Query: 204 TGKWLGSRQIR 214
G+ L ++R
Sbjct: 131 DGRTLCGCRVR 141
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQ 318
P VYVGNL + +L R F G + V V R+ GF FV + +AA A++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGP--LRSVWVARNPPGFAFVEFEDPRDAADAVR 128
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
P C+ VYVGN+ + L+ F GP+ + R + + F+ + D R AA A+
Sbjct: 71 PLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVR 128
Query: 113 SLNGRHLFGQPIKV 126
L+GR L G ++V
Sbjct: 129 ELDGRTLCGCRVRV 142
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQ 318
P VYVGNL + +L R F G + V V R+ GF FV + +AA A++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGP--LRSVWVARNPPGFAFVEFEDPRDAADAVR 128
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG+L L F Y R +W + GF FV F + +DA A+ +L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYY---GPLRSVWVARN--PPGFAFVEFEDPRDAADAVREL 130
Query: 204 TGKWLGSRQIR 214
G+ L ++R
Sbjct: 131 DGRTLCGCRVR 141
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR-----DKGFGFVRYSTHAEAA 314
P + ++VG L + ++ D+ R F + G IEE + R KG FV+YS+HAEA
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGN--IEECTILRGPDGNSKGCAFVKYSSHAEAQ 70
Query: 315 LAIQMGNTTQS 325
AI + +Q+
Sbjct: 71 AAINALHGSQT 81
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSSYG--FIHYFDRRSAAM 109
P + R ++VG ++ Q +E ++ +F + G +E C ++R D +S G F+ Y A
Sbjct: 12 PPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQA 71
Query: 110 AILSLNG 116
AI +L+G
Sbjct: 72 AINALHG 78
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
H +FVG L+ + ++ + F + + + ++ G S+G FV + + +AQ+AI
Sbjct: 15 HRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAI 73
Query: 201 NDLTG 205
N L G
Sbjct: 74 NALHG 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 42/88 (47%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG + I V +LS + + L F + S S + D+ TG+S+GF F+SF
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
++DA AI ++G + WA
Sbjct: 65 HRREDAARAIAGVSGFGYDHLILNVEWA 92
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------ 300
G N A +N T+ V NL+ + + DL F G+ I + + +DK
Sbjct: 4 GSSGPNRRADDN----ATIRVTNLSEDTRETDLQELFRPFGS--ISRIYLAKDKTTGQSK 57
Query: 301 GFGFVRYSTHAEAALAI 317
GF F+ + +AA AI
Sbjct: 58 GFAFISFHRREDAARAI 74
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 47/92 (51%), Gaps = 5/92 (5%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+++ +LSP VT+ L + F+ + + + TGR RG F++F N++ A A++ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
G L + + + G N+ ++SS S
Sbjct: 88 NGYKLYGKILVIEF-----GKNKKQRSSGPSS 114
>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 = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 30/58 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
+F+G LS + T L FS + D + D TGRSRGFGFV F+ + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
+ ++V N+ T VTE +L++ FS G +E K ++ Y F+H+ DR +A A+ +NG
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK----DYAFVHFEDRGAAVKAMDEMNG 71
Query: 117 R 117
+
Sbjct: 72 K 72
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYG--FIHYFDRRSAAMAILSL 114
++YVGN+ TE + E+FS +G ++ + + K K++ G F+ Y+ R A A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 115 NGRHLFGQPIKVNW 128
NG L + I+ +W
Sbjct: 80 NGTRLDDRIIRTDW 93
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDAR--VMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
++VG+LS T+ ++ FS D + +M K + GF FV + ++ DA++A+
Sbjct: 21 LYVGNLSFYTTEEQIYELFS---KSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 202 DLTGKWLGSRQIRCNW 217
+ G L R IR +W
Sbjct: 78 YINGTRLDDRIIRTDW 93
Score = 32.0 bits (71), Expect = 0.56, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 7/66 (10%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----GFGFVRYSTHAEAALAIQ 318
T+YVGNL+ T+ ++ F +G I+++ + DK GF FV Y + A+A A++
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSK--SGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 319 MGNTTQ 324
N T+
Sbjct: 78 YINGTR 83
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+ V ++ D L F + D ++++++ S+GFGFV+F N DA A L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 204 TGKWLGSRQIRCNWAT 219
G + R+I N AT
Sbjct: 76 HGTVVEGRKIEVNNAT 91
Score = 35.0 bits (79), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAIL 112
T + ++V NI + +P L+++F G + ++I ++ S +GF+ + + A A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73
Query: 113 SLNGRHLFGQPIKVNWAYA 131
L+G + G+ I+VN A A
Sbjct: 74 KLHGTVVEGRKIEVNNATA 92
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 28/50 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
+F+G LS + T L F + + VM D T RSRGFGFV+F +Q
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
Score = 28.9 bits (63), Expect = 3.9, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHA 311
+++G L+ + TQ L +F G ++E V RD +GFGFV + A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGE--VKECLVMRDPLTKRSRGFGFVTFMDQA 53
>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 = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
+FVG + + + + + F+ Y S + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 12/66 (18%)
Query: 42 IPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYG 97
+P G + P +V+VG I ++ E ++ F+ G V+ K+I D++ YG
Sbjct: 2 LPEGKIMPN-------TVFVGGIDVRMDETEIRSFFARYGSVKEVKII-TDRTGVSKGYG 53
Query: 98 FIHYFD 103
F+ +++
Sbjct: 54 FVSFYN 59
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
+F+G LS + T L F + + VM D T RSRGFGFV+F +Q
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHA 311
+++G L+ + TQ L +F G ++E V RD +GFGFV + A
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGE--VKECLVMRDPLTKRSRGFGFVTFMDQA 78
>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: Composition-based stats.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
+FVG + + + + + F+ Y S + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 12/66 (18%)
Query: 42 IPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYG 97
+P G + P +V+VG I ++ E ++ F+ G V+ K+I D++ YG
Sbjct: 2 LPEGKIMPN-------TVFVGGIDVRMDETEIRSFFARYGSVKEVKII-TDRTGVSKGYG 53
Query: 98 FIHYFD 103
F+ +++
Sbjct: 54 FVSFYN 59
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
AS ED FVG LS + + L F+ + D + D TGRSRGFGF+ F
Sbjct: 4 ASKNEEDAG---KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Query: 191 RNQQDAQSAIN 201
++ + ++
Sbjct: 61 KDAASVEKVLD 71
>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 = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
+FVG + + + + + F+ Y S + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 68
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 12/67 (17%)
Query: 41 PIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SY 96
P+ SG + P +V+VG I ++ E ++ F+ G V+ K+I D++ Y
Sbjct: 2 PLGSGKIMPN-------TVFVGGIDVRMDETEIRSFFARYGSVKEVKII-TDRTGVSKGY 53
Query: 97 GFIHYFD 103
GF+ +++
Sbjct: 54 GFVSFYN 60
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-- 201
IFVG + + L F + ++ +++D + R RGFGF++F ++Q A+N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 202 --DLTGK 206
D+ GK
Sbjct: 73 FHDIMGK 79
Score = 27.7 bits (60), Expect = 8.9, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAG----VIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
++VG + + +L +F G +I + QR +GFGF+ + A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
+SG +++ L P TD L Y + + D+ T + +G+GFV F + AQ
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 198 SAINDL 203
A+ L
Sbjct: 62 KAVTAL 67
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI 317
P+ TT Y+GN+ T+ DL F + G I + + +KG F++Y TH +AA+ I
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNF--GFILDFKHYPEKGCCFIKYDTHEQAAVCI 80
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
+++GN+ + TE ++ +F G V C +I+ +YGF+H D+ +A AI +L+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK----NYGFVHIEDKTAAEDAIRNLHHYK 66
Query: 119 LFGQPIKVNWAYASGQREDTSG 140
L G + +N + + + +SG
Sbjct: 67 LHG--VNINVEASKNKSKASSG 86
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
+SG +F+G+L E T+ + + F Y + ++ + +GFV ++ A+
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAE 56
Query: 198 SAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
AI +L L I A N+ K SS S
Sbjct: 57 DAIRNLHHYKLHGVNINVE-----ASKNKSKASSGPSS 89
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
E+ S + V ++ D L F + D ++++++ S+GFGFV+F N D
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSAD 81
Query: 196 AQSAINDLTGKWLGSRQIRCNWAT 219
A A L G + R+I N AT
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNAT 105
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 48/92 (52%), Gaps = 2/92 (2%)
Query: 42 IPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFI 99
+P G+ + S + ++V NI + +P L+++F G + ++I ++ S +GF+
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 74
Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA 131
+ + A A L+G + G+ I+VN A A
Sbjct: 75 TFENSADADRAREKLHGTVVEGRKIEVNNATA 106
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
NI+VG+L T + FS + + ++++D++T + +GFGFV + ++ AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 203 LTGKWLGSRQIRCNWA 218
L R IR A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAMAIL 112
R++YVGN+ T ++E+FS G V KLI K +GF+ S + AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 113 SLNGRHLFGQPIKVNWA 129
L+ G+ I+V A
Sbjct: 61 KLDNTDFMGRTIRVTEA 77
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
+YVGNL T + F G +I + ++ KGFGFV + + ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 321 NT 322
NT
Sbjct: 64 NT 65
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
++VGN+ T L+ +F G V C +++ Y F+H A AI LNG+
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVK----DYAFVHMEKEADAKAAIAQLNGKE 67
Query: 119 LFGQPIKVNWAYASGQRE 136
+ G+ I V + GQ++
Sbjct: 68 VKGKRINVELS-TKGQKK 84
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
G + + IFVG++S T L + F + V+ D + FV
Sbjct: 1 GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEK 52
Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWATKG 221
+ DA++AI L GK + ++I +TKG
Sbjct: 53 EADAKAAIAQLNGKEVKGKRINVELSTKG 81
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFS---VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
+SG +F+ +L+ T+ TL FS SC+ ++ S GFGFV ++ +
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 195 DAQSAINDLTG 205
AQ A+ L G
Sbjct: 62 QAQKALKQLQG 72
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR-----DKGFGFVRYSTHAEAALAIQM 319
++VG L + T D+ + F G I+E V R KG FV++ THAEA AI
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFG--TIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI-- 70
Query: 320 GNTTQSS 326
NT SS
Sbjct: 71 -NTLHSS 76
Score = 34.3 bits (77), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+FVG L + TD + F + + + V+ G S+G FV F+ +AQ+AIN
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 203 L 203
L
Sbjct: 73 L 73
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
VYVGN+ T + L+ FS GP+ I ++ + F+ + D R A A+ L+G+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTV-WIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 119 LFGQPIKVNWAYASGQR 135
+ G ++V + +R
Sbjct: 62 ICGSRVRVELSTGMPRR 78
Score = 35.4 bits (80), Expect = 0.050, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
++VG+L L FS Y R +W + GF FV F + +DA+ A+ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYY---GPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGL 57
Query: 204 TGKWLGSRQIRCNWAT 219
GK + ++R +T
Sbjct: 58 DGKVICGSRVRVELST 73
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
+VYV N+ +T L +FS G V I KDK + FI + D+ SA
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVT-IMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 113 SLNGRHLFGQPIKVNWA 129
++N + LFG+ IK + A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAAL 315
P +TVYV NL +T DL+R F G ++++ ++ KG F+ + A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 316 AIQMGNTTQSSYLFGKQMK 334
+ N Q LFG+ +K
Sbjct: 74 CTRAINNKQ---LFGRVIK 89
>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 = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
IFVG LSP+ + + F + + D KT + RGF F++F+ ++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
IFVG LSP+ + + F + + D KT + RGF F++F+ ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
TT+YVG L +T+ DL HF+ G I + V + + F++++T A +A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGE--IRTITVVQRQQCAFIQFATRQAAEVA 64
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
+ T ++YVG + +TE L+ F G + ++++ + + FI + R++A +A
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCA--FIQFATRQAAEVAA 65
Query: 112 -LSLNGRHLFGQPIKVNW 128
S N + G+ + V W
Sbjct: 66 EKSFNKLIVNGRRLNVKW 83
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.2 bits (82), Expect = 0.024, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 68 VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN 127
V E L E+F GP++ K++ + + F+ + + SAA AI ++G+ QP++V
Sbjct: 43 VQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
Query: 128 WAYASGQR 135
++ +R
Sbjct: 99 YSKLPAKR 106
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR-----DKGFGFVRYSTHAEAALAIQM 319
++VG L + ++ D+ R F G VI+E V R KG FV++S+H EA AI
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFG--VIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 320 GNTTQS 325
+ +Q+
Sbjct: 76 LHGSQT 81
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 143 NIFVGDLSPEVTDAT---LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
+FVG L+ + ++ LF F V C+ R G S+G FV F + +AQ+A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR----GPDGSSKGCAFVKFSSHTEAQAA 72
Query: 200 INDLTG 205
I+ L G
Sbjct: 73 IHALHG 78
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 38/90 (42%), Gaps = 2/90 (2%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK-TGRSRGFGFVS 189
+SGQ I V ++ + + FS + R+ TG RGFGFV
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 190 FRNQQDAQSAINDLT-GKWLGSRQIRCNWA 218
F +QDA+ A N L L R++ WA
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEWA 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+FV +LS ++ L FS Y S+ D T + +GF FV+F + A A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 203 LTGKWLGSRQIRCNWAT 219
+ G+ R + +T
Sbjct: 70 VDGQVFQGRMLHVLPST 86
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 54 STCRSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
S +Y+GN+ VT L+++F P+ G L+ KS Y F+ Y D+ A AI
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIE 62
Query: 113 SLNGR-HLFGQPIKVNWAYASGQR 135
+L+G+ L G+ ++V+++ + R
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLR 86
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
+SG +++G+LSP VT L F D ++ + G+ FV + +Q A
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAI 58
Query: 198 SAINDLTGK 206
AI L+GK
Sbjct: 59 RAIETLSGK 67
Score = 29.3 bits (64), Expect = 3.6, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQ 324
+Y+GNL+P VT DL + F + +V ++ G+ FV Y A AI+ +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK--SGYAFVDYPDQNWAIRAIE--TLSG 66
Query: 325 SSYLFGKQMKV 335
L GK M+V
Sbjct: 67 KVELHGKIMEV 77
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.4 bits (80), Expect = 0.043, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 68 VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN 127
V E L E+F GP++ K++ + + F+ + + SAA AI ++G+ QP++V
Sbjct: 16 VQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 71
Query: 128 WA 129
++
Sbjct: 72 YS 73
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+ + +LS T+ TL V+ + +V +Q G+S+G+ F+ F + +DA+ A+N
Sbjct: 18 LVLSNLSYSATEETLQ---EVFEKATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEALNSC 73
Query: 204 TGKWLGSRQIR 214
+ + R IR
Sbjct: 74 NKREIEGRAIR 84
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 16/78 (20%)
Query: 146 VGDLSPEVTDATLFAC---------------FSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
V +LSPE DA C FS D R++ D+ + RS+G +V F
Sbjct: 15 VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
Query: 191 RNQQDAQSAINDLTGKWL 208
Q AI LTG+ L
Sbjct: 75 CEIQSVPLAIG-LTGQRL 91
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 34.3 bits (77), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 144 IFVGDLSPEVTDATLFACFSVYP--SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
I + +L+P T ++ + Y S S+ RV+ D++T +RGF F+ + AQ
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQ 81
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 34.3 bits (77), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
++VGNI T L+ F GPV C +++ Y F+H A AI L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK----DYAFVHMERAEDAVEAIRGLDNTE 68
Query: 119 LFGQPIKVNWA 129
G+ + V +
Sbjct: 69 FQGKRMHVQLS 79
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSSYGF--IHYFDRRSAAMAILSL 114
+V+V N+ +V L+EVFS G V ++ KD S G + + A AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 115 NGRHLFGQPIKVN 127
NG+ LF +P+ V
Sbjct: 77 NGQLLFDRPMHVK 89
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+FV +L +V L FS+ A ++ D K G+SRG G V+F +A AI+
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 203 LTGKWLGSRQIRCN 216
G+ L R +
Sbjct: 76 FNGQLLFDRPMHVK 89
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 36/81 (44%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
+F+G L + D + + + ++ D TG S+G+ F + + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 204 TGKWLGSRQIRCNWATKGAGN 224
G LG +++ A+ GA N
Sbjct: 64 NGMQLGDKKLLVQRASVGAKN 84
Score = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
+++G + + + ++E+ +S GP++ L++ + Y F Y D AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 115 NGRHL 119
NG L
Sbjct: 64 NGMQL 68
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
+SG + ++ V L + T+ L FS + +V D KTG S+GFGFV F
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 191 ---RNQQDAQSAINDLTGKW 207
Q S + + G+W
Sbjct: 65 TEYETQVKVMSQRHMIDGRW 84
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 8/52 (15%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTH 310
+ V L + T+ DL +F + G ++ V+V++D KGFGFVR++ +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLM--VQVKKDLKTGHSKGFGFVRFTEY 67
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 184 GFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
G VSFR+ ++A I L G+W G RQI
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
+ V N+ VT +L ++FS G V K+ + Y D SA A LSL+G++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108
Query: 119 LF 120
++
Sbjct: 109 IY 110
>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 = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 12/78 (15%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
++YVGN+ T +L HFH G G + V + D KGF ++ +S ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFH--GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 318 QMGNTTQSSYLFGKQMKV 335
+ S G+Q+KV
Sbjct: 65 AL----DESLFRGRQIKV 78
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+I+VG++ T L A F S + ++ D+ +G +GF ++ F +++ ++++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 65
Query: 203 LTGKWLGSRQIR 214
L RQI+
Sbjct: 66 LDESLFRGRQIK 77
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
RS+YVGN+ T L+ F G V ++ DK S + +I + D+ S +
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTIL-CDKFSGHPKGFAYIEFSDKESVRTS- 63
Query: 112 LSLNGRHLFGQPIKV 126
L+L+ G+ IKV
Sbjct: 64 LALDESLFRGRQIKV 78
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
+ V N+ VT +L ++FS G V K+ + Y D SA A LSL+G++
Sbjct: 36 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 95
Query: 119 LF 120
++
Sbjct: 96 IY 97
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
+ V N+ VT +L ++FS G V K+ + Y D SA A LSL+G++
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90
Query: 119 LFG 121
++
Sbjct: 91 IYN 93
>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 = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 12/78 (15%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
++YVGN+ T +L HFH G G + V + D KGF ++ +S ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFH--GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 318 QMGNTTQSSYLFGKQMKV 335
+ S G+Q+KV
Sbjct: 66 AL----DESLFRGRQIKV 79
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
+I+VG++ T L A F S + ++ D+ +G +GF ++ F +++ ++++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66
Query: 203 LTGKWLGSRQIR 214
L RQI+
Sbjct: 67 LDESLFRGRQIK 78
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEG----CKLIRKDKSSYGFIHYFDRRSAAMAIL 112
RS+YVGN+ T L+ F G V C + +I + D+ S + L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-L 65
Query: 113 SLNGRHLFGQPIKV 126
+L+ G+ IKV
Sbjct: 66 ALDESLFRGRQIKV 79
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
+ R+M ++ +G+SRGF FV F + QDA
Sbjct: 29 AREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
F +++ L E + + F D+ + G++ G GFV FRN+ D ++A+
Sbjct: 26 FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85
Query: 202 DLTGKWLGSRQIRCNWATK 220
+++G+R I+ + TK
Sbjct: 86 RHK-QYMGNRFIQVHPITK 103
>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 = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEG----CKLIRKDKSSYGFIHYFDRRSAAMAIL 112
RSVYVGN+ T L+ FSS G + C Y +I + +R S A+
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV- 95
Query: 113 SLNGRHLFGQPIKV 126
+++ G+ IKV
Sbjct: 96 AMDETVFRGRTIKV 109
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
+VYVGN+ T DL HF S G+ I + + D KG+ ++ ++ A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGS--INRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 318 QMGNTTQSSYLFGKQMKV 335
M T G+ +KV
Sbjct: 96 AMDETV----FRGRTIKV 109
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF--RNQQDAQSAI 200
+++VG++ T L A FS S + ++ D+ +G +G+ ++ F RN DA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 201 ND 202
++
Sbjct: 98 DE 99
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 31.2 bits (69), Expect = 0.83, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCS--DARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
I + +++P ++ S Y S + + R++ D++T ++RGF FV + DA +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 202 DL 203
L
Sbjct: 72 IL 73
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 126 VNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGF 185
V A Q +D + N+++ +L + + L + R++ D +G SRG
Sbjct: 13 VQAQMAKQQEQDPT---NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGV 68
Query: 186 GFVSFRNQQDAQSAINDLTGKWL 208
GF + + ++ I GK++
Sbjct: 69 GFARMESTEKCEAVIGHFNGKFI 91
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
D++TG+ +G VSF + A++AI+ GK I+ ++AT+ A
Sbjct: 50 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 43 PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI-RKDKSSYGFIHY 101
P+GN + CR +YVGN+ + +++VF G + L R+ + F+ +
Sbjct: 17 PAGN-------NDCR-IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 68
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNW 128
D R A A+ +G G ++V +
Sbjct: 69 EDPRDAEDAVYGRDGYDYDGYRLRVEF 95
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG---FGFVRYSTHAEAALAI 317
+YVGNL P++ D+ F+ GA I ++ ++ +G F FV + +A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGA--IRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 5/88 (5%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRS-RGFGFVSFRNQQDAQSAIND 202
I+VG+L P++ + F Y + D D K R F FV F + +DA+ A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDI----DLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQS 230
G ++R + G G S
Sbjct: 81 RDGYDYDGYRLRVEFPRSGRGTGSGPSS 108
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 9/75 (12%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGR-----SRGFGFVSFRNQQDAQS 198
+ +G L+ VT + FS Y M D R S+G+ +V F N +A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIK----MIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 199 AINDLTGKWLGSRQI 213
A+ + G + ++I
Sbjct: 63 ALKHMDGGQIDGQEI 77
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 187 FVSFRNQQDAQSAINDLTGKWLGSRQI 213
+V FR ++DA+ A+ DL +W + I
Sbjct: 72 YVKFRREEDAEKAVIDLNNRWFNGQPI 98
>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 = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
D++TG+ +G VSF + A++AI+ GK I+ ++AT
Sbjct: 56 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99
>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 = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 63 SSATNALR---SMQGFPFYDKPMRI 84
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
D+ TG+++GF FV + DA+ I GK L
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>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 = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 62 SSATNALR---SMQGFPFYDKPMRI 83
>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 = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 62 SSATNALR---SMQGFPFYDKPMRI 83
>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 = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
+Y+GNL T DL HSLG I E++ + KGF V + A + +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 319 M 319
+
Sbjct: 131 L 131
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
D+ TG+++GF FV + DA+ I GK L
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>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 = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 1 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 59
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 60 SSATNALR---SMQGFPFYDKPMRI 81
>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 = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 62 SSATNALR---SMQGFPFYDKPMRI 83
>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 = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYSTH 310
PE P +T +Y+ NL ++ + +L + H++ + G I ++ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
+ A A++ + Q + K M++
Sbjct: 63 SSATNALR---SMQGFPFYDKPMRI 84
>pdb|3R05|A Chain A, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), With
Splice Insert Ss3
pdb|3R05|B Chain B, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), With
Splice Insert Ss3
Length = 1254
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 119 LFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATL 158
LF ++ W +R D + +FVG L PE+ A L
Sbjct: 98 LFIDQVEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAAL 137
>pdb|3QCW|A Chain A, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), No
Splice Inserts
pdb|3QCW|B Chain B, Structure Of Neurexin 1 Alpha (Domains Lns1-Lns6), No
Splice Inserts
Length = 1245
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 119 LFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATL 158
LF ++ W +R D + +FVG L PE+ A L
Sbjct: 98 LFIDQVEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAAL 137
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
V+VG +TE L+E FS G V I K ++ F+ + D + A SL G
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDV-FIPKPFRAFAFVTFADDQIAQ----SLCGED 62
Query: 119 LFGQPIKVNWAYASGQREDTSG 140
L + I V+ + A + SG
Sbjct: 63 LIIKGISVHISNAEPKHNSNSG 84
>pdb|1ZXF|A Chain A, Solution Structure Of A Self-Sacrificing Resistance
Protein, Calc From Micromonospora Echinospora
pdb|2GKD|A Chain A, Structural Insight Into Self-Sacrifice Mechanism Of
Enediyne Resistance
pdb|2L65|A Chain A, Haddock Calculated Model Of The Complex Of The Resistance
Protein Calc And Calicheamicin-Gamma
Length = 155
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 256 PENNPQYTTVYVGNLAPEVTQLDL-HRHFHSLGAGVIEEVRVQRDKGF 302
P+N+ ++T +V + + T++D+ H HF +G + VR DKG+
Sbjct: 91 PDNSSEFTVTFVAD-GQKKTRVDVEHTHFDRMGTKHAKRVRNGMDKGW 137
>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 = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEA 313
+Y+GNL T DL HSLG I E++ + KGF V + A +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASS 58
>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 = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 26/44 (59%)
Query: 178 KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
+ G G V+F ++ +A +A+ DL + +GSR+++ + + G
Sbjct: 52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 24/53 (45%)
Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVR 306
EA N + TTV V NL Q ++++F G + +V K F F R
Sbjct: 33 EALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFAR 85
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 27.7 bits (60), Expect = 8.3, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
VYVGN+ L+ G V +L + F+HY D +A A+ L G
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLR 80
Query: 119 LFGQPIKVNWAYASGQRE 136
L ++V A A QR+
Sbjct: 81 LGTDTLRV--ALARQQRD 96
>pdb|2X5L|A Chain A, X-Ray Structure Of The Substrate-Free Mycobacterium
Tuberculosis Cytochrome P450 Cyp125, Alternative
Crystal Form
Length = 431
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 41 PIPSGNLPPGFD 52
P+PS NLPPGFD
Sbjct: 14 PMPSPNLPPGFD 25
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 27.7 bits (60), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVI----EEVRVQRDKGFGFVRY 307
+P YT ++GNL +VT+ + F L + E +R KGFG+ +
Sbjct: 13 SPPYT-AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 27.7 bits (60), Expect = 9.5, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 30/72 (41%), Gaps = 15/72 (20%)
Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
GSS + TE P T YVGNL Q D+ F L I VR+ RD
Sbjct: 1 GSSGSSGKELPTEPP------YTAYVGNLPFNTVQGDIDAIFKDLS---IRSVRLVRDKD 51
Query: 300 ----KGFGFVRY 307
KGF +V +
Sbjct: 52 TDKFKGFCYVEF 63
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
0.316 0.132 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,761,428
Number of Sequences: 62578
Number of extensions: 417246
Number of successful extensions: 1403
Number of sequences better than 100.0: 181
Number of HSP's better than 100.0 without gapping: 149
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 944
Number of HSP's gapped (non-prelim): 402
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)