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= 014839
(417 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 = 144 bits (363), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 72/167 (43%), Positives = 106/167 (63%), Gaps = 4/167 (2%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI--KKDKS-SYGFVDYFDRRSAALAIVT 104
R +YVGN+ +T +L++ F GP+ K++ K +K+ +Y FV+Y A +A+ T
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 105 LNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARV 164
LNG+ I +K+NWA+ SQ+ + FN+FVGDL+ V D TL F FP+ V
Sbjct: 61 LNGKQIENNIVKINWAF-QSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 165 MWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAK 211
MWD +TG SRG+GFVSF +Q+DAQ+A++ + G+ L R +R NWAAK
Sbjct: 120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 44/199 (22%), Positives = 84/199 (42%), Gaps = 42/199 (21%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG+L +T+ L F V ++ ++M D K ++ + FV + DA A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 195 NGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPENN 254
NGK + N ++ NWA + Q+ S++D
Sbjct: 62 NGKQIENNIVKINWAFQ------------------------------SQQSSSDDT---- 87
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHA----LCVGTIEDVRVQRDKGFGFVRYSTHPEAAL 310
++VG+L+ V L F L + D++ +G+GFV +++ +A
Sbjct: 88 ---FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 311 AIQMGNARILCGKPIKCSW 329
A+ + L G+P++ +W
Sbjct: 145 AMDSMQGQDLNGRPLRINW 163
>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 = 112 bits (281), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 51/90 (56%), Positives = 68/90 (75%)
Query: 122 ASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
+S Q++DTS HF+VFVGDLSPE+T + A F+ F SDARV+ D TG+S+G+GFVSF
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 182 RNQEDAQSAINDLNGKWLGNRQIRCNWAAK 211
N+ DA++AI + G+WLG RQIR NWA +
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQIRTNWATR 94
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 48/90 (53%), Gaps = 4/90 (4%)
Query: 35 SGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKK----DKSSYGFV 90
SG+ + D S V+VG++ P++T ++ F+ G + +++K YGFV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 91 DYFDRRSAALAIVTLNGRHIFGQPIKVNWA 120
+F++ A AI + G+ + G+ I+ NWA
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
V+VG+LS E+T+ D+ F G I D RV +D KG+GFV + +A AIQ
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPF--GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 314 MGNARILCGKPIKCSW 329
+ L G+ I+ +W
Sbjct: 76 QMGGQWLGGRQIRTNW 91
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 111 bits (278), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 50/90 (55%), Positives = 68/90 (75%)
Query: 122 ASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
+S Q++DTS HF+VFVGDLSPE+T + + F+ F SDARV+ D TG+S+G+GFVSF
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 182 RNQEDAQSAINDLNGKWLGNRQIRCNWAAK 211
N+ DA++AI + G+WLG RQIR NWA +
Sbjct: 65 YNKLDAENAIVHMGGQWLGGRQIRTNWATR 94
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 4/90 (4%)
Query: 35 SGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKK----DKSSYGFV 90
SG+ + D S V+VG++ P++T ++ F+ G + +++K YGFV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFV 62
Query: 91 DYFDRRSAALAIVTLNGRHIFGQPIKVNWA 120
++++ A AIV + G+ + G+ I+ NWA
Sbjct: 63 SFYNKLDAENAIVHMGGQWLGGRQIRTNWA 92
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
V+VG+LS E+T+ D+ F G I D RV +D KG+GFV + +A AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPF--GKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 314 MGNARILCGKPIKCSW 329
+ L G+ I+ +W
Sbjct: 76 HMGGQWLGGRQIRTNW 91
>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 = 98.2 bits (243), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 57/176 (32%), Positives = 95/176 (53%), Gaps = 13/176 (7%)
Query: 36 GNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCK----LIKKDKSSYGFVD 91
G++ P + S+YVG++HP VT A+L E FS GP+ + +I + Y +V+
Sbjct: 4 GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 92 YFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDT---SGHFNVFVGDLSPEVTDAT 148
+ A A+ T+N I G+P+++ W SQR+ + SG N+F+ +L + +
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKA 119
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQI 204
L+ FS F +V+ D+ S+G+GFV F QE A+ AI +NG L +R++
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 62.0 bits (149), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 50/196 (25%), Positives = 83/196 (42%), Gaps = 43/196 (21%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+++VGDL P+VT+A L+ FS RV D T RS G+ +V+F+ DA+ A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
+N + + +R W+ ++ S KS V
Sbjct: 77 MNFDVIKGKPVRIMWS--------QRDPSLRKSGV------------------------- 103
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD----KGFGFVRYSTHPEAA 309
+++ NL + + L+ F A G I +V D KG+GFV + T A
Sbjct: 104 ----GNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAE 157
Query: 310 LAIQMGNARILCGKPI 325
AI+ N +L + +
Sbjct: 158 RAIEKMNGMLLNDRKV 173
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 255 PQY--TTVYVGNLSSEVTSVDLHRHFHA----LCVGTIEDVRVQRDKGFGFVRYSTHPEA 308
P Y ++YVG+L +VT L+ F L + D+ +R G+ +V + +A
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 309 ALAIQMGNARILCGKPIKCSW 329
A+ N ++ GKP++ W
Sbjct: 71 ERALDTMNFDVIKGKPVRIMW 91
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
Query: 40 PRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRS 97
P S ++++ N+ + N L + FS+ G + CK++ + S YGFV + + +
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 155
Query: 98 AALAIVTLNGRHIFGQPIKVNWAYASSQREDTSG 131
A AI +NG + + + V + +RE G
Sbjct: 156 AERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189
>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 = 97.1 bits (240), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 55/163 (33%), Positives = 90/163 (55%), Gaps = 13/163 (7%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCK----LIKKDKSSYGFVDYFDRRSAALAIVT 104
S+YVG++HP VT A+L E FS GP+ + +I + Y +V++ A A+ T
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 105 LNGRHIFGQPIKVNWAYASSQREDT---SGHFNVFVGDLSPEVTDATLFACFSVFPTCSD 161
+N I G+P+++ W SQR+ + SG N+F+ +L + + L+ FS F
Sbjct: 72 MNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 162 ARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQI 204
+V+ D+ S+G+GFV F QE A+ AI +NG L +R++
Sbjct: 128 CKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 61.6 bits (148), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 50/196 (25%), Positives = 83/196 (42%), Gaps = 43/196 (21%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+++VGDL P+VT+A L+ FS RV D T RS G+ +V+F+ DA+ A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
+N + + +R W+ ++ S KS V
Sbjct: 72 MNFDVIKGKPVRIMWS--------QRDPSLRKSGV------------------------- 98
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD----KGFGFVRYSTHPEAA 309
+++ NL + + L+ F A G I +V D KG+GFV + T A
Sbjct: 99 ----GNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAE 152
Query: 310 LAIQMGNARILCGKPI 325
AI+ N +L + +
Sbjct: 153 RAIEKMNGMLLNDRKV 168
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 255 PQY--TTVYVGNLSSEVTSVDLHRHFHA----LCVGTIEDVRVQRDKGFGFVRYSTHPEA 308
P Y ++YVG+L +VT L+ F L + D+ +R G+ +V + +A
Sbjct: 6 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 65
Query: 309 ALAIQMGNARILCGKPIKCSW 329
A+ N ++ GKP++ W
Sbjct: 66 ERALDTMNFDVIKGKPVRIMW 86
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
Query: 40 PRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRS 97
P S ++++ N+ + N L + FS+ G + CK++ + S YGFV + + +
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 150
Query: 98 AALAIVTLNGRHIFGQPIKVNWAYASSQREDTSG 131
A AI +NG + + + V + +RE G
Sbjct: 151 AERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 184
>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 = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 47/80 (58%), Positives = 61/80 (76%)
Query: 132 HFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
HF+VFVGDLSPE+T A + A F+ F SDARV+ D TG+S+G+GFVSF N+ DA++AI
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 192 NDLNGKWLGNRQIRCNWAAK 211
+ G+WLG RQIR NWA +
Sbjct: 66 QQMGGQWLGGRQIRTNWATR 85
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKK----DKSSYGFVDYFDRRSAALAIVTL 105
V+VG++ P++T A + F+ G + +++K YGFV +F++ A AI +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 106 NGRHIFGQPIKVNWA 120
G+ + G+ I+ NWA
Sbjct: 69 GGQWLGGRQIRTNWA 83
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
V+VG+LS E+T+ + F G I D RV +D KG+GFV + +A AIQ
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPF--GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 314 MGNARILCGKPIKCSW 329
+ L G+ I+ +W
Sbjct: 67 QMGGQWLGGRQIRTNW 82
>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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 42/79 (53%), Positives = 55/79 (69%)
Query: 133 FNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
FN+FVGDL+ V D TL F FP+ VMWD +TG SRG+GFVSF +Q+DAQ+A++
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 193 DLNGKWLGNRQIRCNWAAK 211
+ G+ L R +R NWAAK
Sbjct: 62 SMQGQDLNGRPLRINWAAK 80
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 49 SVYVGNIHPQVTNALLQEVFSS-TGPLEGCKLIKKDKSS---YGFVDYFDRRSAALAIVT 104
+++VG+++ V + L+ F L G + S YGFV + + A A+ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 105 LNGRHIFGQPIKVNWA 120
+ G+ + G+P+++NWA
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHA----LCVGTIEDVRVQRDKGFGFVRYSTHPEAALAIQM 314
++VG+L+ V L F L + D++ +G+GFV +++ +A A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 315 GNARILCGKPIKCSW 329
+ L G+P++ +W
Sbjct: 63 MQGQDLNGRPLRINW 77
>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 = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 56/150 (37%), Positives = 82/150 (54%), Gaps = 10/150 (6%)
Query: 54 NIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALAIVTLNG 107
N PQ +T + +F S G +E CKL++ DK + YGFV+Y D + A AI TLNG
Sbjct: 8 NYLPQNMTQEEFRSLFGSIGEIESCKLVR-DKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 108 RHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWD 167
+ + IKV++A SS + N++V L +T L FS + +R++ D
Sbjct: 67 LRLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD 123
Query: 168 QKTGRSRGFGFVSFRNQEDAQSAINDLNGK 197
Q TG SRG GF+ F + +A+ AI LNG+
Sbjct: 124 QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 49/204 (24%), Positives = 80/204 (39%), Gaps = 49/204 (24%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L +T + F +++ D+ TG+S G+GFV++ + +DA+ AIN
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
LNG L + I+ ++A + S DA
Sbjct: 64 LNGLRLQTKTIKVSYARPSSA-------------------------------SIRDA--- 89
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPE 307
+YV L +T +L + F G I R+ D +G GF+R+ E
Sbjct: 90 -----NLYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIE 142
Query: 308 AALAIQMGNARILCG--KPIKCSW 329
A AI+ N + G +PI +
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKF 166
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T + V L +T + F + +G IE ++ RDK G+GFV Y +A A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGS--IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 312 IQMGNARILCGKPIKCSW 329
I N L K IK S+
Sbjct: 61 INTLNGLRLQTKTIKVSY 78
>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 = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 56/155 (36%), Positives = 83/155 (53%), Gaps = 10/155 (6%)
Query: 48 RSVYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALA 101
R+ + N PQ +T L+ +FSS G +E KLI+ DK + YGFV+Y + A A
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERA 60
Query: 102 IVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSD 161
I TLNG + + IKV++A SS+ N+++ L +T + FS F +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 162 ARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNG 196
+RV+ DQ TG SRG F+ F + +A+ AI NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%)
Query: 131 GHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSA 190
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 191 INDLNGKWLGNRQIRCNWA 209
IN LNG L ++ I+ ++A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T + V L +T +L F + +G +E ++ RDK G+GFV Y T +A A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSS--IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 312 IQMGNARILCGKPIKCSW 329
I N L K IK S+
Sbjct: 61 INTLNGLRLQSKTIKVSY 78
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 56/155 (36%), Positives = 83/155 (53%), Gaps = 10/155 (6%)
Query: 48 RSVYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALA 101
R+ + N PQ +T L+ +FSS G +E KLI+ DK + YGFV+Y + A A
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERA 60
Query: 102 IVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSD 161
I TLNG + + IKV++A SS+ N+++ L +T + FS F +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 162 ARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNG 196
+RV+ DQ TG SRG F+ F + +A+ AI NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%)
Query: 131 GHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSA 190
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 191 INDLNGKWLGNRQIRCNWA 209
IN LNG L ++ I+ ++A
Sbjct: 61 INTLNGLRLQSKTIKVSYA 79
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T + V L +T +L F + +G +E ++ RDK G+GFV Y T +A A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSS--IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 312 IQMGNARILCGKPIKCSW 329
I N L K IK S+
Sbjct: 61 INTLNGLRLQSKTIKVSY 78
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 57/154 (37%), Positives = 83/154 (53%), Gaps = 11/154 (7%)
Query: 54 NIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALAIVTLNG 107
N PQ +T + +F S G +E CKL++ DK + YGFV+Y D A AI TLNG
Sbjct: 10 NYLPQNMTQDEFKSLFGSIGDIESCKLVR-DKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Query: 108 RHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWD 167
+ + IKV++A SS + N++V L ++ + FS + +R++ D
Sbjct: 69 LKLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD 125
Query: 168 QKTGRSRGFGFVSFRNQEDAQSAINDLNG-KWLG 200
Q TG SRG GF+ F + +A+ AI LNG K LG
Sbjct: 126 QATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLG 159
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 42/82 (51%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L +T + F +++ D+ TG+S G+GFV++ + DA AIN
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 194 LNGKWLGNRQIRCNWAAKGATS 215
LNG L + I+ ++A + S
Sbjct: 66 LNGLKLQTKTIKVSYARPSSAS 87
Score = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T + V L +T + F + +G IE ++ RDK G+GFV YS +A A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGS--IGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 312 IQMGNARILCGKPIKCSW 329
I N L K IK S+
Sbjct: 63 INTLNGLKLQTKTIKVSY 80
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 74.3 bits (181), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 46/150 (30%), Positives = 79/150 (52%), Gaps = 10/150 (6%)
Query: 52 VGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSAALAIVTLN 106
+ N PQ +T+ L +F + GP+ C++++ K+ Y FVD+ + AI LN
Sbjct: 7 IVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN 66
Query: 107 GRHIFGQPIKVNWAYASSQR-EDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVM 165
G + + +KV++A + +DT N++V +L +TD L F + + ++
Sbjct: 67 GITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 166 WDQKTGRSRGFGFVSFRNQEDAQSAINDLN 195
D+ TGR RG FV + +E+AQ AI+ LN
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 53/189 (28%), Positives = 76/189 (40%), Gaps = 47/189 (24%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L ++TD L+A F + R+M D KTG S G+ FV F ++ D+Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
LNG + N++++ ++A G S +
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 89
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPE 307
T +YV NL +T L F G+I + RDK G FVRY+ E
Sbjct: 90 ----TNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREE 143
Query: 308 AALAIQMGN 316
A AI N
Sbjct: 144 AQEAISALN 152
>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 = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 47/159 (29%), Positives = 79/159 (49%), Gaps = 10/159 (6%)
Query: 43 DASTCRSVYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRS 97
D + + N PQ T+ L +F + GP+ C++ + K+ Y FVD+
Sbjct: 9 DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 98 AALAIVTLNGRHIFGQPIKVNWAYASSQR-EDTSGHFNVFVGDLSPEVTDATLFACFSVF 156
+ AI LNG + + +KV++A + +DT N++V +L +TD L F +
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKY 124
Query: 157 PTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLN 195
+ ++ D+ TGR RG FV + +E+AQ AI+ LN
Sbjct: 125 GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 54/195 (27%), Positives = 76/195 (38%), Gaps = 47/195 (24%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L + TD L+A F + R+ D KTG S G+ FV F ++ D+Q AI
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
LNG + N++++ ++A G S +
Sbjct: 76 LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 100
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPE 307
T +YV NL +T L F G+I + RDK G FVRY+ E
Sbjct: 101 ----TNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREE 154
Query: 308 AALAIQMGNARILCG 322
A AI N I G
Sbjct: 155 AQEAISALNNVIPEG 169
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 68.6 bits (166), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 34/77 (44%), Positives = 50/77 (64%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FVG LS + + +L FS + S+ V+ D++T RSRGFGFV+F N +DA+ A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 195 NGKWLGNRQIRCNWAAK 211
NGK + RQIR + A K
Sbjct: 75 NGKSVDGRQIRVDQAGK 91
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSAA 99
AS ++VG + L++VFS G + ++K ++ +GFV + + A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 100 LAIVTLNGRHIFGQPIKVNWAYASS 124
A++ +NG+ + G+ I+V+ A SS
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSS 93
Score = 35.0 bits (79), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALC----VGTIEDVRVQRDKGFGFVRYSTHPEAALAIQMG 315
++VG LS + L + F V ++D QR +GFGFV + +A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 316 NARILCGKPIKC 327
N + + G+ I+
Sbjct: 75 NGKSVDGRQIRV 86
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 68.2 bits (165), Expect = 9e-12, Method: Composition-based stats.
Identities = 38/91 (41%), Positives = 57/91 (62%), Gaps = 3/91 (3%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRSAAL 100
D R++YVGN+ VT L+ ++FS GP + CK+I + S+ Y FV++++ R AA
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70
Query: 101 AIVTLNGRHIFGQPIKVNWAYA-SSQREDTS 130
A+ +NGR I G+ +KVNWA SSQ+ S
Sbjct: 71 ALAAMNGRKILGKEVKVNWATTPSSQKSGPS 101
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 122 ASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
+S ED ++VG+LS +VT+ + FS C +++ + + + FV F
Sbjct: 5 SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEF 62
Query: 182 RNQEDAQSAINDLNGKWLGNRQIRCNWA 209
DA +A+ +NG+ + ++++ NWA
Sbjct: 63 YEHRDAAAALAAMNGRKILGKEVKVNWA 90
Score = 35.4 bits (80), Expect = 0.064, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 252 ENNPQYTTVYVGNLSSEVTSVDLHRHFHAL--CVGTIEDVRVQRDKGFGFVRYSTHPEAA 309
E++ Q T+YVGNLS +VT V + + F + C + + FV + H +AA
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 69
Query: 310 LAIQMGNARILCGKPIKCSW 329
A+ N R + GK +K +W
Sbjct: 70 AALAAMNGRKILGKEVKVNW 89
>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 = 65.9 bits (159), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 85/172 (49%), Gaps = 12/172 (6%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKL----IKKDKSSYGFVDYFDRRSAALAI--- 102
VYVG+I+ ++ +++ F+ GP++ + + + FV+Y +A LA+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 103 --VTLNGRHI-FGQPIKVNWAYAS-SQREDTSGHFN-VFVGDLSPEVTDATLFACFSVFP 157
V L GR+I G+P + A Q + + FN ++V + +++D + + F F
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 158 TCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWA 209
A + D TG+ +G+GF+ + + +Q A++ +N LG + +R A
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSA 98
+A +YV ++H +++ ++ VF + G ++ L + + YGF++Y +S+
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 99 ALAIVTLNGRHIFGQPIKVNWA 120
A+ ++N + GQ ++V A
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKA 202
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALA 311
+ VYVG++ E+ + + F G I+ + + D KGF FV Y A LA
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPF--GPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 312 IQMGNARILCGKPIKC 327
++ N+ +L G+ IK
Sbjct: 87 LEQMNSVMLGGRNIKV 102
>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 = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 48/181 (26%), Positives = 91/181 (50%), Gaps = 19/181 (10%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----IKKDKSSYGFVDYFDRRSAA 99
A CR VYVG+I+ ++ +++ F+ GP++ + + + FV+Y +A
Sbjct: 11 AIMCR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 69
Query: 100 LAI-----VTLNGRHI-FGQPIKVNWAYAS-SQREDTSGHFN-VFVGDLSPEVTD---AT 148
LA+ V L GR+I G+P + A Q + + FN ++V + +++D +
Sbjct: 70 LALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS 129
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNW 208
+F F +C+ AR D TG+ +G+GF+ + + +Q A++ +N LG + +R
Sbjct: 130 VFEAFGKIKSCTLAR---DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK 186
Query: 209 A 209
A
Sbjct: 187 A 187
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSA 98
+A +YV ++H +++ ++ VF + G ++ C L + + YGF++Y +S+
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 99 ALAIVTLNGRHIFGQPIKVNWA 120
A+ ++N + GQ ++V A
Sbjct: 166 QDAVSSMNLFDLGGQYLRVGKA 187
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
VYVG++ E+ + + F G I+ + + D KGF FV Y A LA++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPF--GPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 314 MGNARILCGKPIKC 327
N+ +L G+ IK
Sbjct: 74 QMNSVMLGGRNIKV 87
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 53/89 (59%), Gaps = 1/89 (1%)
Query: 129 TSGHFNVFVGDLSPEVTDATLFACFSVFPTC-SDARVMWDQKTGRSRGFGFVSFRNQEDA 187
+SG +F+G+L PE+ + L+ FS F ++M D TG S+G+ F++F + + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 188 QSAINDLNGKWLGNRQIRCNWAAKGATSG 216
+AI +NG++L NR I ++A K + G
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKG 90
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 51/93 (54%), Gaps = 9/93 (9%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSA 98
+S +++GN+ P++ LL + FS+ G + I +D + Y F+++ ++
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 99 ALAIVTLNGRHIFGQPIKVNWAYASSQREDTSG 131
AI +NG+++ +PI V++A+ ++D+ G
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAF----KKDSKG 90
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
+++GNL E+ L+ F A V ++ ++ RD KG+ F+ +++ + AI+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGV-ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 314 MGNARILCGKPIKCSW 329
N + LC +PI S+
Sbjct: 67 AMNGQYLCNRPITVSY 82
>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 = 61.6 bits (148), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 85/178 (47%), Gaps = 13/178 (7%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----IKKDKSSYGFVDYFDRRSAA 99
A CR VYVG+I+ ++ +++ F+ GP++ + + FV+Y +A
Sbjct: 10 AIXCR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQ 68
Query: 100 LAI-----VTLNGRHI-FGQPIKVNWAYAS-SQREDTSGHFN-VFVGDLSPEVTDATLFA 151
LA+ V L GR+I G+P + A Q + + FN ++V + +++D + +
Sbjct: 69 LALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 152 CFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWA 209
F F + D TG+ +G+GF+ + + +Q A++ N LG + +R A
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 44/199 (22%), Positives = 79/199 (39%), Gaps = 36/199 (18%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+VG + E+ + T+ F+ F WD T + +GF FV + E AQ A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 195 NGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPENN 254
N LG R I+ G ++ +++ AE+ +
Sbjct: 75 NSVXLGGRNIKV---------GRPSNIGQAQPIIDQ-------LAEEARA---------- 108
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEA 308
+ +YV ++ +++ D+ F A G I+ + RD KG+GF+ Y +
Sbjct: 109 --FNRIYVASVHQDLSDDDIKSVFEAF--GKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 309 ALAIQMGNARILCGKPIKC 327
A+ N L G+ ++
Sbjct: 165 QDAVSSXNLFDLGGQYLRV 183
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSA 98
+A +YV ++H +++ ++ VF + G ++ C L + + YGF++Y +S+
Sbjct: 105 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 99 ALAIVTLNGRHIFGQPIKVNWA 120
A+ + N + GQ ++V A
Sbjct: 165 QDAVSSXNLFDLGGQYLRVGKA 186
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG L+ EV D L A F F +D ++ D +T + RGF FV F EDA +AI+++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 195 NGKWLGNRQIRCNWA 209
N L R IR N A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----IKKDKSSYGFVDYFDRRSAA 99
A+T R +YVG + +V + +L F G + ++ + + FV++ AA
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 100 LAIVTLNGRHIFGQPIKVNWA 120
AI +N +FG+ I+VN A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAI 312
+YVG L+ EV LH F + G I D+++ ++ +GF FV + +AA AI
Sbjct: 65 VLYVGGLAEEVDDKVLHAAF--IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 313 QMGNARILCGKPIK 326
N L G+ I+
Sbjct: 123 DNMNESELFGRTIR 136
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 59.3 bits (142), Expect = 4e-09, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 47/82 (57%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L ++TD L+A F + R+M D KTG S G+ FV F ++ D+Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 194 LNGKWLGNRQIRCNWAAKGATS 215
LNG + N++++ ++A G S
Sbjct: 65 LNGITVRNKRLKVSYARPGGES 86
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 54 NIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSAALAIVTLNGR 108
N PQ +T+ L +F + GP+ C++++ K+ Y FVD+ + AI LNG
Sbjct: 9 NYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI 68
Query: 109 HIFGQPIKVNWA 120
+ + +KV++A
Sbjct: 69 TVRNKRLKVSYA 80
>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 = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG L+ EV D L A F F +D ++ D +T + RGF FV F EDA +AI+++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 195 NGKWLGNRQIRCNWA 209
N L R IR N A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAIQ 313
+YVG L+ EV LH F + G I D+++ ++ +GF FV + +AA AI
Sbjct: 5 LYVGGLAEEVDDKVLHAAF--IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 314 MGNARILCGKPIK 326
N L G+ I+
Sbjct: 63 NMNESELFGRTIR 75
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSAALAIV 103
R +YVG + +V + +L F G + ++ + + FV++ AA AI
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 104 TLNGRHIFGQPIKVNWA 120
+N +FG+ I+VN A
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG L+ EV D L A F F +D ++ D +T + RGF FV F EDA +AI+++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 195 NGKWLGNRQIRCNWA 209
N L R IR N A
Sbjct: 68 NESELFGRTIRVNLA 82
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAIQ 313
+YVG L+ EV LH F + G I D+++ ++ +GF FV + +AA AI
Sbjct: 8 LYVGGLAEEVDDKVLHAAF--IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 314 MGNARILCGKPIK 326
N L G+ I+
Sbjct: 66 NMNESELFGRTIR 78
Score = 35.8 bits (81), Expect = 0.048, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSAA 99
++T R +YVG + +V + +L F G + ++ + + FV++ AA
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 100 LAIVTLNGRHIFGQPIKVNWA 120
AI +N +FG+ I+VN A
Sbjct: 62 AAIDNMNESELFGRTIRVNLA 82
>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 = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG L+ EV D L A F F +D ++ D +T + RGF FV F EDA +AI+++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 195 NGKWLGNRQIRCNWA 209
N L R IR N A
Sbjct: 70 NESELFGRTIRVNLA 84
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAIQ 313
+YVG L+ EV LH F + G I D+++ ++ +GF FV + +AA AI
Sbjct: 10 LYVGGLAEEVDDKVLHAAF--IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 314 MGNARILCGKPIK 326
N L G+ I+
Sbjct: 68 NMNESELFGRTIR 80
Score = 37.0 bits (84), Expect = 0.021, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSAA 99
A+T R +YVG + +V + +L F G + ++ + + FV++ AA
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 100 LAIVTLNGRHIFGQPIKVNWA 120
AI +N +FG+ I+VN A
Sbjct: 64 AAIDNMNESELFGRTIRVNLA 84
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 54/84 (64%), Gaps = 3/84 (3%)
Query: 133 FNVFVGDLSPEVTDATLFACF-SVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+++FVGDL+P+V D L+ F V+P+C +V+ DQ TG S+G+GFV F ++ + + A+
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRAL 68
Query: 192 NDLNGK-WLGNRQIRCNWAAKGAT 214
+ G LG++ +R + A A+
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKAS 92
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGP-LEGCKLIKKD---KSSYGFVDYFDRRSAALAIVT 104
S++VG++ P V + +L E F P G K++ YGFV + D A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 105 LNGRHIFG-QPIKVNWAYASSQR 126
G G +P++++ A + R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 58.9 bits (141), Expect = 6e-09, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 53/83 (63%), Gaps = 2/83 (2%)
Query: 135 VFVGDLSPEVTDATLF-ACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
V++G + + T+ + C +V P + ++M+D +TGRS+G+ F+ FR+ E + SA+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 194 LNGKWLGNRQIRCNWAAKGATSG 216
LNG LG+R ++C +++ SG
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISG 86
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIV 103
R VY+G+I T + ++ S+ GP+ K++ ++ Y F+++ D S+A A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 104 TLNGRHIFGQPIKVNWAYASSQREDTSG 131
LNG + + +K + S D SG
Sbjct: 63 NLNGYQLGSRFLKCGY----SSNSDISG 86
>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 = 58.2 bits (139), Expect = 8e-09, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 53/83 (63%), Gaps = 2/83 (2%)
Query: 135 VFVGDLSPEVTDATLF-ACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
V++G + + T+ + C +V P + ++M+D +TGRS+G+ F+ FR+ E + SA+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 194 LNGKWLGNRQIRCNWAAKGATSG 216
LNG LG+R ++C +++ SG
Sbjct: 65 LNGYQLGSRFLKCGYSSNSDISG 87
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIV 103
R VY+G+I T + ++ S+ GP+ K++ ++ Y F+++ D S+A A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 104 TLNGRHIFGQPIKVNWAYASSQREDTSG 131
LNG + + +K + S D SG
Sbjct: 64 NLNGYQLGSRFLKCGY----SSNSDISG 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 58.2 bits (139), Expect = 8e-09, Method: Composition-based stats.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 6/94 (6%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+VFVG++ E T+ L FS R+++D++TG+ +G+GF +++QE A SA+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSV 227
LNG+ R +R + AA EK + KS+
Sbjct: 70 LNGREFSGRALRVDNAAS------EKNKEELKSL 97
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 32/93 (34%), Positives = 53/93 (56%), Gaps = 5/93 (5%)
Query: 40 PRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDR 95
P D S RSV+VGNI + T L+++FS GP+ +L+ ++ YGF +Y D+
Sbjct: 2 PAVDRSL-RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 96 RSAALAIVTLNGRHIFGQPIKVNWAYASSQRED 128
+A A+ LNGR G+ ++V+ A + +E+
Sbjct: 61 ETALSAMRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYST 304
P + +V+VGN+ E T L F VG + R+ D KG+GF Y
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSE--VGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 305 HPEAALAIQMGNARILCGKPIK 326
A A++ N R G+ ++
Sbjct: 60 QETALSAMRNLNGREFSGRALR 81
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG L+ EV D L A F F +D ++ D +T + RGF FV F EDA +AI+++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 195 NGKWLGNRQIRCNWA 209
N L R IR N A
Sbjct: 75 NESELFGRTIRVNLA 89
Score = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAIQ 313
+YVG L+ EV LH F + G I D+++ ++ +GF FV + +AA AI
Sbjct: 15 LYVGGLAEEVDDKVLHAAF--IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 314 MGNARILCGKPIK 326
N L G+ I+
Sbjct: 73 NMNESELFGRTIR 85
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSAA 99
A+T R +YVG + +V + +L F G + ++ + + FV++ AA
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 100 LAIVTLNGRHIFGQPIKVNWA 120
AI +N +FG+ I+VN A
Sbjct: 69 AAIDNMNESELFGRTIRVNLA 89
>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 = 2e-08, Method: Compositional matrix adjust.
Identities = 41/142 (28%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 45 STCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAAL 100
+C+ +++G ++ T L+E F G + K++K + +GF+ F++ S+
Sbjct: 2 ESCK-MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS-FEKPSSVD 59
Query: 101 AIVTLNGRHIF-GQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTC 159
+V +HI G+ I A +++ T +FVG + P+V FS + T
Sbjct: 60 EVVKT--QHILDGKVIDPKRAIPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 160 SDARVMWDQKTGRSRGFGFVSF 181
DA++M D+ TG+SRGFGFV++
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTY 136
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 70/180 (38%), Gaps = 55/180 (30%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G L+ + T+ L F + T +D ++M D TGRSRGFGF+SF +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 194 ---LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDA 250
L+GK + D K + D Q+K+ +
Sbjct: 65 QHILDGKVI-----------------------DPKRAI----------PRDEQDKTGK-- 89
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYST 304
++VG + +V + F GTI D ++ DK GFGFV Y +
Sbjct: 90 ---------IFVGGIGPDVRPKEFEEFFSQW--GTIIDAQLMLDKDTGQSRGFGFVTYDS 138
>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 = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 51/77 (66%), Gaps = 2/77 (2%)
Query: 135 VFVGDLSPEVTDATLF-ACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
V++G + + T+ + C +V P + ++M+D +TGRS+G+ F+ FR+ E + SA+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 194 LNGKWLGNRQIRCNWAA 210
LNG LG+R ++C +++
Sbjct: 66 LNGYQLGSRFLKCGYSS 82
Score = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIV 103
R VY+G+I T + ++ S+ GP+ K++ ++ Y F+++ D S+A A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 104 TLNGRHIFGQPIKVNWAYAS 123
LNG + + +K ++ S
Sbjct: 65 NLNGYQLGSRFLKCGYSSNS 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 46/80 (57%)
Query: 126 REDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQE 185
++ ++G ++VG L +T+ L F F ++M D +TGRS+G+GF++F + E
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 186 DAQSAINDLNGKWLGNRQIR 205
A+ A+ LNG L R ++
Sbjct: 80 CAKKALEQLNGFELAGRPMK 99
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIVTL 105
+YVG++H +T +L+ +F G +E +L+ ++ YGF+ + D A A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 106 NGRHIFGQPIKV 117
NG + G+P+KV
Sbjct: 89 NGFELAGRPMKV 100
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQ------RDKGFGFVRYSTHPEAALAIQ 313
+YVG+L +T L F G IE +++ R KG+GF+ +S A A++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPF--GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 314 MGNARILCGKPIK 326
N L G+P+K
Sbjct: 87 QLNGFELAGRPMK 99
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 252 ENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALA 311
+++P+ TVY G ++S +T + + F G I ++RV +KG+ FVR+STH AA A
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPEKGYSFVRFSTHESAAHA 77
Query: 312 IQMGNARILCGKPIKCSW 329
I N + G +KC W
Sbjct: 78 IVSVNGTTIEGHVVKCYW 95
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGR 108
+VY G I +T+ L+++ FS G + ++ + Y FV + SAA AIV++NG
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK--GYSFVRFSTHESAAHAIVSVNGT 84
Query: 109 HIFGQPIKVNWAYAS 123
I G +K W S
Sbjct: 85 TIEGHVVKCYWGKES 99
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+ G ++ +TD + FS F + RV + +G+ FV F E A AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 195 NGKWLGNRQIRCNWAAK 211
NG + ++C W +
Sbjct: 82 NGTTIEGHVVKCYWGKE 98
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 42/72 (58%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+F+ L E TD L + F F A+V D++T S+ FGFVSF N + AQ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 194 LNGKWLGNRQIR 205
+NG +G ++++
Sbjct: 102 MNGFQVGTKRLK 113
>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 = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 7/101 (6%)
Query: 122 ASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
A SQ+E G N+F+ L E D L F F A+V D++T S+ FGFVS+
Sbjct: 16 AGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Query: 182 RNQEDAQSAINDLNGKWLGNRQIRC------NWAAKGATSG 216
N AQ+AI +NG +G ++++ N + G +SG
Sbjct: 75 DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.7 bits (130), Expect = 1e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 43/77 (55%)
Query: 129 TSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQ 188
+SG ++VG L +T+ L F F + +M D TGRS+G+GF++F + E A+
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 189 SAINDLNGKWLGNRQIR 205
A+ LNG L R +R
Sbjct: 62 RALEQLNGFELAGRPMR 78
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAA 99
+S +YVG++H +T +L+ +F G ++ L+K + YGF+ + D A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 100 LAIVTLNGRHIFGQPIKV 117
A+ LNG + G+P++V
Sbjct: 62 RALEQLNGFELAGRPMRV 79
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAIQ 313
+YVG+L +T L F G I+++ + +D KG+GF+ +S A A++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPF--GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 314 MGNARILCGKPIK 326
N L G+P++
Sbjct: 66 QLNGFELAGRPMR 78
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 75 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 100
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 71
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 72 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 11/79 (13%)
Query: 246 SNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGF 299
S ++P+ Q +++G LS E T L HF GT+ D V RD +GFGF
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGF 59
Query: 300 VRYSTHPEAALAIQMGNAR 318
V Y+T E A+ NAR
Sbjct: 60 VTYATVEEVDAAM---NAR 75
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 74 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 99
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 100 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 155
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 70
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 71 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 129
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 130 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 11/79 (13%)
Query: 246 SNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGF 299
S ++P+ Q +++G LS E T L HF GT+ D V RD +GFGF
Sbjct: 1 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGF 58
Query: 300 VRYSTHPEAALAIQMGNAR 318
V Y+T E A+ NAR
Sbjct: 59 VTYATVEEVDAAM---NAR 74
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 76 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 101
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 102 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 157
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 72
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 73 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 131
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 132 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 11/79 (13%)
Query: 246 SNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGF 299
S ++P+ Q +++G LS E T L HF GT+ D V RD +GFGF
Sbjct: 3 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGF 60
Query: 300 VRYSTHPEAALAIQMGNAR 318
V Y+T E A+ NAR
Sbjct: 61 VTYATVEEVDAAM---NAR 76
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 68 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 93
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 94 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 149
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 64
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 65 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 34/69 (49%), Gaps = 11/69 (15%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAA 309
Q +++G LS E T L HF GT+ D V RD +GFGFV Y+T E
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 310 LAIQMGNAR 318
A+ NAR
Sbjct: 63 AAM---NAR 68
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 75 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 100
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 101 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 71
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 72 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 11/79 (13%)
Query: 246 SNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGF 299
S ++P+ Q +++G LS E T L HF GT+ D V RD +GFGF
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGF 59
Query: 300 VRYSTHPEAALAIQMGNAR 318
V Y+T E A+ NAR
Sbjct: 60 VTYATVEEVDAAM---NAR 75
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 49/178 (27%), Positives = 71/178 (39%), Gaps = 42/178 (23%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+F+G LS E TD +L + F + T +D VM D T RSRGFGFV++ E+ +A+N
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPEN 253
K G VVE +S ED Q P
Sbjct: 73 RPHKVDGR-------------------------VVEPKRAVS---REDSQR------PGA 98
Query: 254 NPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTH 305
+ ++VG + + L +F G IE + + D +GF FV + H
Sbjct: 99 HLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDH 154
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 12/153 (7%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAALAIV 103
R +++G + + T+ L+ F G L C +++ K +GFV Y A
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-- 69
Query: 104 TLNGR--HIFGQPIKVNWAYASSQREDTSGHFNV---FVGDLSPEVTDATLFACFSVFPT 158
+N R + G+ ++ A + + H V FVG + + + L F +
Sbjct: 70 -MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+M D+ +G+ RGF FV+F + + +
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 38/76 (50%), Gaps = 11/76 (14%)
Query: 249 DAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRY 302
++P+ Q +++G LS E T L HF GT+ D V RD +GFGFV Y
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGFVTY 60
Query: 303 STHPEAALAIQMGNAR 318
+T E A+ NAR
Sbjct: 61 ATVEEVDAAM---NAR 73
>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 = 2e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 140 LSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
LS T+ L FS + +D +++DQ++ RSRGF FV F N +DA+ A NG L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 200 GNRQIRCNWA 209
R+IR +++
Sbjct: 83 DGRRIRVDFS 92
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSA 98
D + C V+ +++ T L+EVFS GP+ ++ +S + FV + + A
Sbjct: 13 DPNCCLGVFGLSLY--TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 99 ALAIVTLNGRHIFGQPIKVNWA 120
A NG + G+ I+V+++
Sbjct: 71 KEAKERANGMELDGRRIRVDFS 92
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 6/91 (6%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N++V +L + D L FS F T + A+VM + GRS+GFGFV F + E+A A+ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74
Query: 194 LNGKWLGNRQIRCNWAAKGATSGDEKQSSDS 224
+NG+ + + + A + +E+QS S
Sbjct: 75 MNGRIVATKPLYVALAQR----KEERQSGPS 101
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQ----RDKGFGFVRYSTHPEAALA 311
Q +YV NL + L + F GTI +V R KGFGFV +S+ EA A
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPF--GTITSAKVMMEGGRSKGFGFVCFSSPEEATKA 71
Query: 312 IQMGNARILCGKPI 325
+ N RI+ KP+
Sbjct: 72 VTEMNGRIVATKPL 85
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 35 SGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDY 92
SG+ R ++YV N+ + + L++ FS G + K++ + S +GFV +
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCF 62
Query: 93 FDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQRE 127
A A+ +NGR + +P+ V A +R+
Sbjct: 63 SSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 78/184 (42%), Gaps = 11/184 (5%)
Query: 34 LSGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGF 89
LS L P DA C V N+ P +T +E+ G LE C L+ +++ YGF
Sbjct: 87 LSVQLQPT-DALLC----VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 141
Query: 90 VDYFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDA-T 148
+Y + SAA A L G+ + + + V+W A + V L P D
Sbjct: 142 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 201
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNW 208
L S + + ++ Q G+ +GF + + E A+ A +G LG +R ++
Sbjct: 202 LCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Query: 209 AAKG 212
A G
Sbjct: 261 CAPG 264
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 41/73 (56%)
Query: 140 LSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
LS T+ L FS + +D +++DQ++ RSRGF FV F N +DA+ A NG L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 200 GNRQIRCNWAAKG 212
R+IR + + G
Sbjct: 83 DGRRIRVSGPSSG 95
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 140 LSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
LS T+ L FS + +D +++DQ++ RSRGF FV F N +DA+ A NG L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 200 GNRQIRCNWA 209
R+IR +++
Sbjct: 80 DGRRIRVDFS 89
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 78/184 (42%), Gaps = 11/184 (5%)
Query: 34 LSGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGF 89
LS L P DA C V N+ P +T +E+ G LE C L+ +++ YGF
Sbjct: 87 LSVQLQPT-DALLC----VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 141
Query: 90 VDYFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDA-T 148
+Y + SAA A L G+ + + + V+W A + V L P D
Sbjct: 142 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 201
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNW 208
L S + + ++ Q G+ +GF + + E A+ A +G LG +R ++
Sbjct: 202 LCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Query: 209 AAKG 212
A G
Sbjct: 261 CAPG 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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 78/184 (42%), Gaps = 11/184 (5%)
Query: 34 LSGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGF 89
LS L P DA C V N+ P +T +E+ G LE C L+ +++ YGF
Sbjct: 85 LSVQLQPT-DALLC----VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 139
Query: 90 VDYFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDA-T 148
+Y + SAA A L G+ + + + V+W A + V L P D
Sbjct: 140 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 199
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNW 208
L S + + ++ Q G+ +GF + + E A+ A +G LG +R ++
Sbjct: 200 LCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 258
Query: 209 AAKG 212
A G
Sbjct: 259 CAPG 262
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 130 SGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQS 189
SG N+F+ +L + + L+ FS F +V+ D+ S+G+GFV F QE A+
Sbjct: 9 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 66
Query: 190 AINDLNGKWLGNRQI 204
AI +NG L +R++
Sbjct: 67 AIEKMNGMLLNDRKV 81
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 40 PRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRS 97
P S ++++ N+ + N L + FS+ G + CK++ + S YGFV + + +
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 63
Query: 98 AALAIVTLNGRHIFGQPIKVNWAYASSQRE 127
A AI +NG + + + V + +RE
Sbjct: 64 AERAIEKMNGMLLNDRKVFVGRFKSRKERE 93
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD----KGFGFVRYSTHPEAALAIQMG 315
+++ NL + + L+ F A G I +V D KG+GFV + T A AI+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 71
Query: 316 NARIL 320
N +L
Sbjct: 72 NGMLL 76
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 140 LSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
LS T+ L FS + +D +++DQ++ RSRGF FV F N +DA+ A NG L
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 200 GNRQIRCNWA 209
R+IR +++
Sbjct: 114 DGRRIRVDFS 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 = 5e-07, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEG---CKLIKKDKSSYGFVDYFDRRSAALAIVT 104
R+V+VGN+ +V +L E+F GPL CK + S+GFV + S + AI
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 105 LNGRHIFGQPIKVN 118
LNG ++G+PI V+
Sbjct: 77 LNGIRLYGRPINVS 90
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
VFVG+L V + L+ F + + D++ G+ + FGFV F++ E AI L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 195 NGKWLGNRQIRCNWAAKG 212
NG L R I + + G
Sbjct: 78 NGIRLYGRPINVSGPSSG 95
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 30/84 (35%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD-----KGFGFVRYSTH 305
P TV+VGNL + V L+ F L G + V + +D K FGFV + H
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELF--LQAGPLTKVTICKDREGKPKSFGFVCFK-H 66
Query: 306 PEA-ALAIQMGNARILCGKPIKCS 328
PE+ + AI + N L G+PI S
Sbjct: 67 PESVSYAIALLNGIRLYGRPINVS 90
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+FVG L TDA+L F F +A V+ D++TG+SRG+GFV+ ++ A+ A D
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 194 LNGKWLGNRQIRCNWAAKGA 213
N + R+ N A GA
Sbjct: 79 PN-PIIDGRKANVNLAYLGA 97
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+F+G L+ E + L A F S+ ++ D +T +SRGF F++F N DA++A D+
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 195 NGKWLGNRQIRCNWAAK 211
NGK L + I+ A K
Sbjct: 69 NGKSLHGKAIKVEQAKK 85
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIVTL 105
+++G ++ + +L+ VF GP+ LI KD++S + F+ + + A A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLI-KDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 106 NGRHIFGQPIKVNWAYASS 124
NG+ + G+ IKV A S
Sbjct: 69 NGKSLHGKAIKVEQAKKPS 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 68/146 (46%), Gaps = 13/146 (8%)
Query: 47 CRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLN 106
CR ++VGN+ +T + +F G E ++ +GF+ R A +A L+
Sbjct: 23 CR-LFVGNLPTDITEEDFKRLFERYG--EPSEVFINRDRGFGFIRLESRTLAEIAKAELD 79
Query: 107 GRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMW 166
G + +P+++ +A + + V +LSP V++ L FS F A V+
Sbjct: 80 GTILKSRPLRIRFATHGA---------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAIN 192
D + GR+ G GFV F + A+ A+
Sbjct: 131 DDR-GRATGKGFVEFAAKPPARKALE 155
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALAIQMG 315
Q ++VGNL +++T D R F G +V + RD+GFGF+R + A +A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFER--YGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 78
Query: 316 NARILCGKPIKCSW 329
+ IL +P++ +
Sbjct: 79 DGTILKSRPLRIRF 92
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+FVG+L ++T+ F + S+ + R RGFGF+ ++ A+ A +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 194 LNGKWLGNRQIRCNWAAKGA 213
L+G L +R +R +A GA
Sbjct: 78 LDGTILKSRPLRIRFATHGA 97
>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 = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 131 GHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSA 190
G N+F+ +L + + L+ FS F +V+ D+ S+G+GFV F QE A+ A
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
Query: 191 INDLNGKWLGNRQI 204
I +NG L +R++
Sbjct: 62 IEKMNGMLLNDRKV 75
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 27/106 (25%), Positives = 51/106 (48%), Gaps = 7/106 (6%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRSAALAIVTLN 106
++++ N+ + N L + FS+ G + CK++ + S YGFV + + +A AI +N
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 107 GRHIFGQPIKVNWAYASSQREDTSG-----HFNVFVGDLSPEVTDA 147
G + + + V + +RE G NV++ + P T A
Sbjct: 67 GMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD----KGFGFVRYSTHPEAALAIQMG 315
+++ NL + + L+ F A G I +V D KG+GFV + T A AI+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65
Query: 316 NARIL 320
N +L
Sbjct: 66 NGMLL 70
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 43/85 (50%)
Query: 128 DTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDA 187
D G ++ V +L+ + TL F + D + D+ T SRGF FV F ++ DA
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 188 QSAINDLNGKWLGNRQIRCNWAAKG 212
+ A++ ++G L R++R A G
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T++ V NL+ + L R F G + DV + RD+ GF FVR+ +A A
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKY--GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 312 IQMGNARILCGKPIKC 327
+ + +L G+ ++
Sbjct: 129 MDAMDGAVLDGRELRV 144
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V + V + L F + +++ D++T +SRG+GFV F++ AQ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 194 LNGKWLGNRQIRCNWAAKG 212
LNG + N++++ AA G
Sbjct: 104 LNGFNILNKRLKVALAASG 122
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 44/93 (47%), Gaps = 4/93 (4%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSA 98
+ R++ V I V L+++F GP+E K++ + YGFV + SA
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 99 ALAIVTLNGRHIFGQPIKVNWAYASSQREDTSG 131
AI LNG +I + +KV A + QR +G
Sbjct: 98 QQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%)
Query: 131 GHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSA 190
G N+ V L +T L + FS A+++ D+ G S G+GFV++ +DA+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 191 INDLNGKWLGNRQIRCNWA 209
IN LNG L ++ I+ ++A
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 33/82 (40%), Positives = 47/82 (57%), Gaps = 7/82 (8%)
Query: 48 RSVYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALA 101
R+ + N PQ +T L+ +FSS G +E KLI+ DK + YGFV+Y + A A
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERA 62
Query: 102 IVTLNGRHIFGQPIKVNWAYAS 123
I TLNG + + IKV++A S
Sbjct: 63 INTLNGLRLQSKTIKVSYARPS 84
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEA 308
P T + V L +T +L F + +G +E ++ RDK G+GFV Y T +A
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSS--IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 59
Query: 309 ALAIQMGNARILCGKPIKCSW 329
AI N L K IK S+
Sbjct: 60 ERAINTLNGLRLQSKTIKVSY 80
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 6/87 (6%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKK----DKSSYGFVDYFDRRSAALAIVT 104
+VYVG + +V+ LL E+F GP+ + K YGFV++ A AI
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 105 LNGRHIFGQPIKVNWAYASSQREDTSG 131
++ ++G+PI+VN AS+ ++ SG
Sbjct: 77 MDMIKLYGKPIRVN--KASAHNKNLSG 101
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 42/76 (55%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+VG L +V++ L+ F + + D+ TG+ +G+GFV F ++EDA AI +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 195 NGKWLGNRQIRCNWAA 210
+ L + IR N A+
Sbjct: 78 DMIKLYGKPIRVNKAS 93
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAA 309
Q TVYVG L +V+ L F L G + + + +D+ G+GFV + + +A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELF--LQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71
Query: 310 LAIQMGNARILCGKPIKCS 328
AI++ + L GKPI+ +
Sbjct: 72 YAIKIMDMIKLYGKPIRVN 90
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FVG LS T + F F DA +M+D+ T R RGFGFV+F + ED + ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 195 NGKWLGNRQIRCNWA 209
+ + N+ + C A
Sbjct: 61 HFHEINNKMVECKKA 75
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 42/76 (55%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L T L + FS A+++ D+ G S G+GFV++ +DA+ AIN
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 194 LNGKWLGNRQIRCNWA 209
LNG L ++ I+ ++A
Sbjct: 81 LNGLRLQSKTIKVSYA 96
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 7/76 (9%)
Query: 54 NIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALAIVTLNG 107
N PQ T L+ +FSS G +E KLI +DK + YGFV+Y + A AI TLNG
Sbjct: 25 NYLPQNXTQDELRSLFSSIGEVESAKLI-RDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
Query: 108 RHIFGQPIKVNWAYAS 123
+ + IKV++A S
Sbjct: 84 LRLQSKTIKVSYARPS 99
Score = 35.4 bits (80), Expect = 0.059, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAA 309
Q T + V L T +L F + +G +E ++ RDK G+GFV Y T +A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSS--IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 75
Query: 310 LAIQMGNARILCGKPIKCSW 329
AI N L K IK S+
Sbjct: 76 RAINTLNGLRLQSKTIKVSY 95
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 43/85 (50%)
Query: 128 DTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDA 187
D G ++ V +L+ + TL F + D + D+ T SRGF FV F ++ DA
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 188 QSAINDLNGKWLGNRQIRCNWAAKG 212
+ A++ ++G L R++R A G
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYG 127
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYST 304
P + T++ V NL+ + L R F G + DV + RD+ GF FVR+
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY--GRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 305 HPEAALAIQMGNARILCGKPIK 326
+A A+ + +L G+ ++
Sbjct: 99 KRDAEDAMDAMDGAVLDGRELR 120
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV LS + T+ TL F AR++ D++TG S+GFGFV F ++EDA++A +
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 195 NGKWLGNRQIRCNWA 209
+ ++ +WA
Sbjct: 75 EDGEIDGNKVTLDWA 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 32/77 (41%), Positives = 44/77 (57%), Gaps = 7/77 (9%)
Query: 54 NIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSS-----YGFVDYFDRRSAALAIVTLNG 107
N PQ +T + +F S G +E CKL+ +DK + YGFV+Y D A AI TLNG
Sbjct: 10 NYLPQNMTQDEFKSLFGSIGDIESCKLV-RDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Query: 108 RHIFGQPIKVNWAYASS 124
+ + IKV++A SS
Sbjct: 69 LKLQTKTIKVSYARPSS 85
Score = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 42/82 (51%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N+ V L +T + F +++ D+ TG+S G+GFV++ + DA AIN
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 194 LNGKWLGNRQIRCNWAAKGATS 215
LNG L + I+ ++A + S
Sbjct: 66 LNGLKLQTKTIKVSYARPSSAS 87
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------GFGFVRYSTHPEAALA 311
T + V L +T + F + +G IE ++ RDK G+GFV YS +A A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGS--IGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 312 IQMGNARILCGKPIKCSW 329
I N L K IK S+
Sbjct: 63 INTLNGLKLQTKTIKVSY 80
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 77/177 (43%), Gaps = 19/177 (10%)
Query: 46 TCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----------IKKDKSSYGFVDY--F 93
+ R +YVGNI +T + + F++ L G I +DK+ + F+++
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-FAFLEFRSV 63
Query: 94 DRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACF 153
D + A+A +G GQ +K+ + + G +F+G L + D +
Sbjct: 64 DETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKELL 117
Query: 154 SVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAA 210
+ F ++ D TG S+G+ F + + AI LNG LG++++ A+
Sbjct: 118 TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 77/177 (43%), Gaps = 19/177 (10%)
Query: 46 TCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----------IKKDKSSYGFVDY--F 93
+ R +YVGNI +T + + F++ L G I +DK+ + F+++
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-FAFLEFRSV 61
Query: 94 DRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACF 153
D + A+A +G GQ +K+ + + G +F+G L + D +
Sbjct: 62 DETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKELL 115
Query: 154 SVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAA 210
+ F ++ D TG S+G+ F + + AI LNG LG++++ A+
Sbjct: 116 TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>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 = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 27/67 (40%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND- 193
+F+G LS + T L FS F D + D TGRSRGFGFV F+ E ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 194 ---LNGK 197
LNGK
Sbjct: 62 EHKLNGK 68
>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 = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 35/62 (56%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N++V +L +TD L F + + ++ D+ TGR RG FV + +E+AQ AI+
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 194 LN 195
LN
Sbjct: 75 LN 76
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 36/64 (56%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N++V L ++ + FS + +R++ DQ TG SRG GF+ F + +A+ AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 194 LNGK 197
LNG+
Sbjct: 63 LNGQ 66
>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 = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 133 FNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
FN+F+G+L+P + A L S +D V+ D +TG +R FG+V F + ED + A+
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE 72
Query: 193 DLNGKWLGN 201
K GN
Sbjct: 73 LTGLKVFGN 81
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/173 (19%), Positives = 79/173 (45%), Gaps = 12/173 (6%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQ----EVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSA 98
+++T ++++GN++P + A L+ E+F+ L + +G+VD+
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKN-DLAVVDVRTGTNRKFGYVDFESAEDL 67
Query: 99 ALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPT 158
A+ L G +FG IK+ ++ + + +LS +T+ L VF
Sbjct: 68 EKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR-TLLAKNLSFNITEDELK---EVFED 122
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAK 211
+ R++ + G+S+G ++ F+++ DA+ + + G + R + + +
Sbjct: 123 ALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 107 GRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMW 166
G H+ P+ + +++ FN+F+G+L+P + A L S +D V+
Sbjct: 1 GSHMLEDPV---------EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV- 50
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGN 201
D +TG +R FG+V F + ED + A+ K GN
Sbjct: 51 DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGN 85
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 33/90 (36%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTG-PLEGCKLIKKDKSSYGFVDYFDRRSAALAI 102
+S +Y+GN+ P VT L+++F PL G L+K S Y FVDY D+ A AI
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK---SGYAFVDYPDQNWAIRAI 61
Query: 103 VTLNGR-HIFGQPIKVNWAYASSQREDTSG 131
TL+G+ + G+ ++V+ Y+ S++ +SG
Sbjct: 62 ETLSGKVELHGKIMEVD--YSVSKKLRSSG 89
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 129 TSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQ 188
+SG +++G+LSP VT L F D ++ + G+ FV + +Q A
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAI 58
Query: 189 SAINDLNGK 197
AI L+GK
Sbjct: 59 RAIETLSGK 67
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+ V +LS + + L F F + S + D+ TG+S+GF F+SF +EDA AI +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 195 NGKWLGNRQIRCNWAAKGATSG 216
+G + + WA SG
Sbjct: 78 SGFGYDHLILNVEWAKPSTNSG 99
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 12/77 (15%)
Query: 242 GQEKSNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK------ 295
G N A +N T+ V NLS + DL F G+I + + +DK
Sbjct: 4 GSSGPNRRADDN----ATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKTTGQSK 57
Query: 296 GFGFVRYSTHPEAALAI 312
GF F+ + +AA AI
Sbjct: 58 GFAFISFHRREDAARAI 74
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 35 SGNLPPRFDASTCRSVYVGNIHPQVTN-ALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYF 93
SG PR S V++GN++ V + ++ +FS G + GC + K + FV Y
Sbjct: 6 SGKTDPR---SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK----GFAFVQYV 58
Query: 94 DRRSAALAIVTLNGRHIFGQPIKVNWA 120
+ R+A A+ +GR I GQ + +N A
Sbjct: 59 NERNARAAVAGEDGRMIAGQVLDINLA 85
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 243 QEKSNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KG 296
++ +E P+ + + ++V + E T D+H F G I+++ + D KG
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKG 65
Query: 297 FGFVRYSTHPEAALAIQMGNARILCGKPIKCSW 329
+ V Y T+ EA A++ N + L G+PI W
Sbjct: 66 YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 85 NGQDLMGQPISVDWCF 100
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 85 NGQDLMGQPISVDW 98
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 243 QEKSNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KG 296
++ +E P+ + + ++V + E T D+H F G I+++ + D KG
Sbjct: 9 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKG 66
Query: 297 FGFVRYSTHPEAALAIQMGNARILCGKPIKCSW 329
+ V Y T+ EA A++ N + L G+PI W
Sbjct: 67 YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 86 NGQDLMGQPISVDWCF 101
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 86 NGQDLMGQPISVDW 99
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 50 VYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGR 108
V++GN++ V + ++ +FS G + GC + K Y FV Y + R A A++ NGR
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK----GYAFVQYSNERHARAAVLGENGR 85
Query: 109 HIFGQPIKVNWA 120
+ GQ + +N A
Sbjct: 86 VLAGQTLDINMA 97
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 21/101 (20%), Positives = 47/101 (46%), Gaps = 15/101 (14%)
Query: 115 IKVNWAYASSQREDTSGHFNVFVGDLSPEVTDA----TLFACFSVFPTCSDARVMWDQKT 170
+K+ + +++ + S + VF+G+L+ + T+F+ + CS
Sbjct: 10 LKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---------- 59
Query: 171 GRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAK 211
+G+ FV + N+ A++A+ NG+ L + + N A +
Sbjct: 60 -VHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 252 ENNPQY--TTVYVGNLSSE-VTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEA 308
+N+P+ + V++GNL++ V D+ F G + V KG+ FV+YS A
Sbjct: 20 KNDPKSINSRVFIGNLNTALVKKSDVETIFSKY--GRVAGCSVH--KGYAFVQYSNERHA 75
Query: 309 ALAIQMGNARILCGKPI 325
A+ N R+L G+ +
Sbjct: 76 RAAVLGENGRVLAGQTL 92
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/164 (25%), Positives = 76/164 (46%), Gaps = 13/164 (7%)
Query: 40 PRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS-----SYG--FVDY 92
P DA ++VG + + L+E+F G + +++ D+S S G FV +
Sbjct: 11 PDLDAI---KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTF 66
Query: 93 FDRRSAALAIVTLNGRHIF-GQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFA 151
+ R++A A L+ + G + A S++ + +F+G +S + T+ +
Sbjct: 67 YTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 126
Query: 152 CFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLN 195
FS F + R++ G SRG FV+F + AQ+AI ++
Sbjct: 127 MFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMH 169
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 73/154 (47%), Gaps = 10/154 (6%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS-----SYG--FVDYFDRRSAALAI 102
++VG + + L+E+F G + +++ D+S S G FV ++ R++A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 103 VTLNGRHIF-GQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSD 161
L+ + G + A S++ + +F+G +S + T+ + FS F +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 162 ARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLN 195
R++ G SRG FV+F + AQ+AI ++
Sbjct: 125 CRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK-KDKSSYG--FVDYFDRRSAALAIVT 104
R +++G I + T ++ +FSS G +E C++++ D S G FV + R A AI
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 105 LN 106
++
Sbjct: 156 MH 157
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLE----GCKLIKKDKSSYGFVDYFDRRSAALAIVT 104
++YVGN+ T + E+FS +G ++ G +KK + FV+Y+ R A A+
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 105 LNGRHIFGQPIKVNW 119
+NG + + I+ +W
Sbjct: 101 INGTRLDDRIIRTDW 115
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
++VG+LS T+ ++ FS + D+ + GF FV + ++ DA++A+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 195 NGKWLGNRQIRCNWAA 210
NG L +R IR +W A
Sbjct: 102 NGTRLDDRIIRTDWDA 117
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 49/112 (43%), Gaps = 13/112 (11%)
Query: 224 SKSVVELTNGISVLFAEDGQEKSNEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCV 283
S S VEL+ F D NE+ + + T+YVGNLS T ++ F
Sbjct: 11 SDSYVELSQYRDQHFRGD-----NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK--S 63
Query: 284 GTIEDVRVQRDK------GFGFVRYSTHPEAALAIQMGNARILCGKPIKCSW 329
G I+ + + DK GF FV Y + +A A++ N L + I+ W
Sbjct: 64 GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW 115
>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 = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 123 SSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFR 182
+S+ E+ +G FVG LS + + L F+ F D + D TGRSRGFGF+ F+
Sbjct: 4 ASKNEEDAG--KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 183 NQEDAQSAIN 192
+ + ++
Sbjct: 62 DAASVEKVLD 71
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 39/70 (55%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV ++ + T++ L F V+ +++ +++G+ RG+ F+ + ++ D SA
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 195 NGKWLGNRQI 204
+GK + R++
Sbjct: 165 DGKKIDGRRV 174
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 44/201 (21%), Positives = 83/201 (41%), Gaps = 33/201 (16%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL----------IKKDKSSYGFVDY- 92
+ R +YVGNI +T + + F++ L G I +DK+ + F+++
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-FAFLEFR 59
Query: 93 -FDRRSAALAIVTLNGRHIFGQPIKV----NWAYASSQREDTSGHF-------------N 134
D + A+A +G GQ +K+ ++ E+ S +
Sbjct: 60 SVDETTQAMA---FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+F+G L + D + + F ++ D TG S+G+ F + + AI L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 195 NGKWLGNRQIRCNWAAKGATS 215
NG LG++++ A+ GA +
Sbjct: 177 NGMQLGDKKLLVQRASVGAKN 197
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 70/150 (46%), Gaps = 10/150 (6%)
Query: 51 YVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS-----SYG--FVDYFDRRSAALAIV 103
+VG + + L+E+F G + +++ D+S S G FV ++ R++A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 104 TLNGRHIF-GQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDA 162
L+ + G + A S++ + +F+G +S + T+ + FS F +
Sbjct: 66 ALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEEC 125
Query: 163 RVMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
R++ G SRG FV+F + AQ+AI
Sbjct: 126 RILRG-PDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK-KDKSSYG--FVDYFDRRSAALAI 102
R +++G I + T ++ FSS G +E C++++ D S G FV + R A AI
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRN 183
+FVG L T TL + FS + D +M D+ T +SRGFGFV F++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALA-IQM 314
Q + ++VGNL ++T ++ + F G +V + +DKGFGF+R T A +A +++
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEK--YGKAGEVFIHKDKGFGFIRLETRTLAEIAKVEL 78
Query: 315 GNARILCGKPIKCSW 329
N L GK ++ +
Sbjct: 79 DNM-PLRGKQLRVRF 92
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+FVG+L P++T+ + F + + + D +GFGF+ + A+ A +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 194 LNGKWLGNRQIRCNWAAKGAT 214
L+ L +Q+R +A A+
Sbjct: 78 LDNMPLRGKQLRVRFACHSAS 98
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 32 PILSGNLPPRFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDK---SSYG 88
P+ L RF A S+ V N+ V+N LL+E FS G +E +I D+ S G
Sbjct: 82 PLRGKQLRVRF-ACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKG 140
Query: 89 FVDYFDRRSAALAI 102
V++ + +A A+
Sbjct: 141 IVEFSGKPAARKAL 154
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+++ +LSP VT+ L + F+ F + + TGR RG F++F N+E A A++ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 195 NG 196
NG
Sbjct: 88 NG 89
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+V +L +T+ L+ FS + +M D+ T +S+G F+ F +++ AQ+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 195 NGKWLGNRQIRCNWA 209
N K L R I+ + A
Sbjct: 79 NNKQLFGRVIKASIA 93
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHF----HALCVGTIEDVRVQRDKGFGFVRYSTHPEAAL 310
P +TVYV NL +T+ DL+R F + V ++D ++ KG F+ + A
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 311 AIQMGNARILCGKPIKCS 328
+ N + L G+ IK S
Sbjct: 74 CTRAINNKQLFGRVIKAS 91
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK----KDKSSYGFVDYFDRRSAA 99
A + +VYV N+ +TN L +FS G + ++K + F+ + D+ SA
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 100 LAIVTLNGRHIFGQPIKVNWA 120
+N + +FG+ IK + A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 34/57 (59%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
+F+G LS E T+ +L + + +D VM D + RSRGFGFV+F + + +A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 35.0 bits (79), Expect = 0.073, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 242 GQEKSNEDAP-----ENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD-- 294
G EK+ E P Q+ +++G LS E T L ++ G + D V RD
Sbjct: 7 GMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQW--GKLTDCVVMRDPA 64
Query: 295 ----KGFGFVRYSTHPEAALAI 312
+GFGFV +S+ E A+
Sbjct: 65 SKRSRGFGFVTFSSMAEVDAAM 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 = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 39/70 (55%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV ++ + T++ L F V+ +++ +++G+ RG+ F+ + ++ D SA
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 195 NGKWLGNRQI 204
+GK + R++
Sbjct: 165 DGKKIDGRRV 174
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQ 184
+F+G LS + T L F F + VM D T RSRGFGFV+F +Q
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQ 184
+F+G LS + T L F F + VM D T RSRGFGFV+F +Q
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
N++VG+L T + FS F + ++++D++T + +GFGFV + +E AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 194 LNGKWLGNRQIRCNWA 209
L+ R IR A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI----KKDKSSYGFVDYFDRRSAALAIV 103
R++YVGN+ T+ ++E+FS G + KLI K +GFV+ S + AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 104 TLNGRHIFGQPIKVNWA 120
L+ G+ I+V A
Sbjct: 61 KLDNTDFMGRTIRVTEA 77
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYST 304
P+ + + ++V + E T D+H F G I+++ + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 305 HPEAALAIQMGNARILCGKPIKCSW 329
+ EA A++ N + L G+PI W
Sbjct: 59 YKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 70 NGQDLMGQPISVDWCF 85
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYST 304
P+ + + ++V + E T D+H F G I+++ + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 305 HPEAALAIQMGNARILCGKPIKCSW 329
+ EA A++ N + L G+PI W
Sbjct: 59 YKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 70 NGQDLMGQPISVDWCF 85
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 250 APENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYS 303
P+ + + ++V + E T D+H F G I+++ + D KG+ V Y
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYE 59
Query: 304 THPEAALAIQMGNARILCGKPIKCSW 329
T+ EA A++ N + L G+PI W
Sbjct: 60 TYKEAQAAMEGLNGQDLMGQPISVDW 85
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 72 NGQDLMGQPISVDWCF 87
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 72 NGQDLMGQPISVDW 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYST 304
P+ + + ++V + E T D+H F G I+++ + D KG+ V Y T
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 305 HPEAALAIQMGNARILCGKPIKCSW 329
+ EA A++ N + L G+PI W
Sbjct: 59 YKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSY----GFVDYFDRRSAALAIVTL 105
++V +H + T + + F+ G ++ L ++ Y V+Y + A A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 NGRHIFGQPIKVNWAY 121
NG+ + GQPI V+W +
Sbjct: 70 NGQDLMGQPISVDWCF 85
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E T+ + F+ + + + D++TG +G+ V + ++AQ+A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 195 NGKWLGNRQIRCNW 208
NG+ L + I +W
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 25/78 (32%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDAR--VMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
++VG+LS T+ ++ FS D + +M K + GF FV + ++ DA++A+
Sbjct: 21 LYVGNLSFYTTEEQIYELFS---KSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 193 DLNGKWLGNRQIRCNWAA 210
+NG L +R IR +W A
Sbjct: 78 YINGTRLDDRIIRTDWDA 95
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCKL-IKKDKSSYGF--VDYFDRRSAALAIVTL 105
++YVGN+ T + E+FS +G ++ + + K K++ GF V+Y+ R A A+ +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 106 NGRHIFGQPIKVNW 119
NG + + I+ +W
Sbjct: 80 NGTRLDDRIIRTDW 93
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 247 NEDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK-----GFGFVR 301
NE+ + + T+YVGNLS T ++ F G I+ + + DK GF FV
Sbjct: 8 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK--SGDIKKIIMGLDKMKTACGFCFVE 65
Query: 302 YSTHPEAALAIQMGNARILCGKPIKCSW 329
Y + +A A++ N L + I+ W
Sbjct: 66 YYSRADAENAMRYINGTRLDDRIIRTDW 93
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
VYVGN+ L+ F GPL + ++ + FV++ D R AA A+ L+GR
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV-WVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 110 IFGQPIKV 117
+ G ++V
Sbjct: 135 LCGCRVRV 142
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK-GFGFVRYSTHPEAALAIQ 313
P VYVGNL + +L R F G + V V R+ GF FV + +AA A++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYY--GPLRSVWVARNPPGFAFVEFEDPRDAADAVR 128
Query: 314 MGNARILCGKPIK 326
+ R LCG ++
Sbjct: 129 ELDGRTLCGCRVR 141
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+VG+L L F + R +W + GF FV F + DA A+ +L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYY---GPLRSVWVARN--PPGFAFVEFEDPRDAADAVREL 130
Query: 195 NGKWLGNRQIR 205
+G+ L ++R
Sbjct: 131 DGRTLCGCRVR 141
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIVTL 105
++V +IH + +QE F G ++ L ++ Y V+Y + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 106 NGRHIFGQPIKVNWAYAS 123
NG I GQ I+V+W +
Sbjct: 135 NGAEIMGQTIQVDWCFVK 152
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E + + F + + + D++TG S+G+ V + + A +A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 195 NGKWLGNRQIRCNW 208
NG + + I+ +W
Sbjct: 135 NGAEIMGQTIQVDW 148
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 14/95 (14%)
Query: 246 SNEDAPENNPQYTT----VYVGNLSSEVTSVDLHRHFHALC-VGTIEDVRVQRD------ 294
++D E PQ + ++V ++ E ++ F C G I+++ + D
Sbjct: 57 EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKF---CDYGEIKNIHLNLDRRTGFS 113
Query: 295 KGFGFVRYSTHPEAALAIQMGNARILCGKPIKCSW 329
KG+ V Y TH +A A + N + G+ I+ W
Sbjct: 114 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
VYVGN+ L+ F GPL + ++ + FV++ D R AA A+ L+GR
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV-WVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 110 IFGQPIKV 117
+ G ++V
Sbjct: 135 LCGCRVRV 142
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK-GFGFVRYSTHPEAALAIQ 313
P VYVGNL + +L R F G + V V R+ GF FV + +AA A++
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYY--GPLRSVWVARNPPGFAFVEFEDPRDAADAVR 128
Query: 314 MGNARILCGKPIK 326
+ R LCG ++
Sbjct: 129 DLDGRTLCGCRVR 141
Score = 31.6 bits (70), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+VG+L L F + R +W + GF FV F + DA A+ DL
Sbjct: 76 VYVGNLGNNGNKTELERAFGYY---GPLRSVWVARN--PPGFAFVEFEDPRDAADAVRDL 130
Query: 195 NGKWLGNRQIR 205
+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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQR-----DKGFGFVRYSTHPEAA 309
P + ++VG L+ + + D+ R F A G IE+ + R KG FV+YS+H EA
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAF--GNIEECTILRGPDGNSKGCAFVKYSSHAEAQ 70
Query: 310 LAI 312
AI
Sbjct: 71 AAI 73
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 132 HFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI 191
H +FVG L+ + ++ + F F + ++ G S+G FV + + +AQ+AI
Sbjct: 15 HRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAI 73
Query: 192 NDLNG 196
N L+G
Sbjct: 74 NALHG 78
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK-KDKSSYG--FVDYFDRRSAALAIVT 104
R ++VG ++ Q + ++ +F + G +E C +++ D +S G FV Y A AI
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 105 LNG 107
L+G
Sbjct: 76 LHG 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/133 (21%), Positives = 56/133 (42%), Gaps = 7/133 (5%)
Query: 86 SYGFVDYFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVT 145
+G+VD+ A+ L G +FG IK+ +++ + +L +VT
Sbjct: 49 KFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGKDSKKERDAR-TLLAKNLPYKVT 106
Query: 146 DATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIR 205
L VF ++ R++ K G+S+G ++ F+ + DA+ + G + R I
Sbjct: 107 QDELK---EVFEDAAEIRLV--SKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSIS 161
Query: 206 CNWAAKGATSGDE 218
+ + G E
Sbjct: 162 LYYTGEPKGEGLE 174
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 58/120 (48%), Gaps = 8/120 (6%)
Query: 133 FNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
FN+FVG+L+ + L S +D V+ D + G +R FG+V F + ED + A+
Sbjct: 8 FNLFVGNLNFNKSAPELKTGISDVFAKNDLAVV-DVRIGMTRKFGYVDFESAEDLEKALE 66
Query: 193 DLNGKWLGNRQIRCNWAAKGATSGDEKQSSDSKSVVELTNGISVLFAEDGQEKSNEDAPE 252
K GN +I+ KG D K+ D++++ L + +D ++ EDA E
Sbjct: 67 LTGLKVFGN-EIKLE-KPKGK---DSKKERDARTL--LAKNLPYKVTQDELKEVFEDAAE 119
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
VYVGN+ L+ FS GPL I ++ + FV++ D R A A+ L+G+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTV-WIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 110 IFGQPIKVNWAYASSQR 126
I G ++V + +R
Sbjct: 62 ICGSRVRVELSTGMPRR 78
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
V+VG+L L FS + R +W + GF FV F + DA+ A+ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYY---GPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGL 57
Query: 195 NGKWLGNRQIR 205
+GK + ++R
Sbjct: 58 DGKVICGSRVR 68
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDK-GFGFVRYSTHPEAALAIQMGNAR 318
VYVGNL + +L R F G + V + R+ GF FV + +A A++ + +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYY--GPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 319 ILCGKPIK 326
++CG ++
Sbjct: 61 VICGSRVR 68
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 4/79 (5%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNG 107
+ ++V N+ VT +L++ FS G LE K +K Y F+ + +R A A+ +NG
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK----DYAFIHFDERDGAVKAMEEMNG 67
Query: 108 RHIFGQPIKVNWAYASSQR 126
+ + G+ I++ +A Q+
Sbjct: 68 KDLEGENIEIVFAKPPDQK 86
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 255 PQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALAIQM 314
P+ TT Y+GN+ T DL F G I D + +KG F++Y TH +AA+ I
Sbjct: 25 PRVTTAYIGNIPHFATEADLIPLFQNF--GFILDFKHYPEKGCCFIKYDTHEQAAVCIVA 82
Query: 315 GNARILCGKPIKCSW 329
G+ ++ W
Sbjct: 83 LANFPFQGRNLRTGW 97
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN-- 192
+FVG + + L F F ++ +++D + R RGFGF++F +++ A+N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 193 --DLNGK 197
D+ GK
Sbjct: 73 FHDIMGK 79
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGT----IEDVRVQRDKGFGFVRYSTHPEAALAIQM 314
++VG + +L +F V T I D QR +GFGF+ + A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
VFV +L +V L FS+ A ++ D K G+SRG G V+F +A AI+
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 194 LNGKWLGNRQIRCNWAAKGATSGD 217
NG+ L +R + + GD
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGD 99
Score = 31.2 bits (69), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 49 SVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIK-KDKSSYGF--VDYFDRRSAALAIVTL 105
+V+V N+ +V L+EVFS G + +++ KD S G V + A AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 106 NGRHIFGQPIKVN 118
NG+ +F +P+ V
Sbjct: 77 NGQLLFDRPMHVK 89
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 40/91 (43%)
Query: 122 ASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
+ S D G + V +L+ + +L F + D + + T RGF FV F
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 182 RNQEDAQSAINDLNGKWLGNRQIRCNWAAKG 212
++ DAQ A ++G L R++R A G
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVARYG 93
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 256 QYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALA 311
Q + ++VGNL ++T ++ + F G +V + +DKGFGF+R T A +A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKDKGFGFIRLETRTLAEIA 67
Score = 35.4 bits (80), Expect = 0.057, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FVG+L P++T+ + F + + + D +GFGF+ + A+ A +L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 195 NGKWLGNRQIRCNWAAKGA--TSG 216
+ L +Q+R +A A TSG
Sbjct: 72 DNMPLRGKQLRVRFACHSASLTSG 95
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 258 TTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRDKGFGFVRYSTHPEAALAIQMG-N 316
TT+YVG L +T DL HF+ G I + V + + F++++T A +A + N
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQF--GEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFN 70
Query: 317 ARILCGKPIKCSW 329
I+ G+ + W
Sbjct: 71 KLIVNGRRLNVKW 83
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
++VGN+ T+ L+ +F G + C ++K Y FV A AI LNG+
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVK----DYAFVHMEKEADAKAAIAQLNGKE 67
Query: 110 IFGQPIKV 117
+ G+ I V
Sbjct: 68 VKGKRINV 75
Score = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 133 FNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN 192
+ +FVG++S T L + F + V+ D + FV + DA++AI
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIA 61
Query: 193 DLNGKWLGNRQIRCNWAAKG 212
LNGK + ++I + KG
Sbjct: 62 QLNGKEVKGKRINVELSTKG 81
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQE 185
+FVG LSP+ + + F F + D KT + RGF F++F+ +E
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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQE 185
+FVG LSP+ + + F F + D KT + RGF F++F+ +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN-- 192
VFVG + + + + + F+ + + + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 193 -DLNGKWL 199
+ +GK L
Sbjct: 71 INFHGKKL 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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN-- 192
VFVG + + + + + F+ + + + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 193 -DLNGKWL 199
+ +GK L
Sbjct: 71 INFHGKKL 78
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIN-- 192
VFVG + + + + + F+ + + + +++ D +TG S+G+GFVSF N D Q +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 193 -DLNGKWL 199
+ +GK L
Sbjct: 72 INFHGKKL 79
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 127 EDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQED 186
E+ S + V ++ D L F F D ++++++ S+GFGFV+F N D
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSAD 81
Query: 187 AQSAINDLNGKWLGNRQIRCNWA 209
A A L+G + R+I N A
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNA 104
Score = 29.6 bits (65), Expect = 3.7, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 252 ENNPQYTTVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV----QRDKGFGFVRYSTHPE 307
EN Q ++V N+ DL + F G I DV + + KGFGFV + +
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTFENSAD 81
Query: 308 AALAIQMGNARILCGKPIK 326
A A + + ++ G+ I+
Sbjct: 82 ADRAREKLHGTVVEGRKIE 100
Score = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 43 DASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRSAAL 100
+ S + ++V NI + + L+++F G + ++I ++ S +GFV + + A
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84
Query: 101 AIVTLNGRHIFGQPIKVNWAYA 122
A L+G + G+ I+VN A A
Sbjct: 85 AREKLHGTVVEGRKIEVNNATA 106
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS----YGFVDYFDRRSAALAIVTL 105
++V +IH + +QE F G ++ L ++ Y V+Y + A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 106 NGRHIFGQPIKVNWAYASSQR 126
NG I GQ I+V+W + +
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPK 109
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 35/74 (47%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV + E + + F + + + D++TG S+G+ V + + A +A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 195 NGKWLGNRQIRCNW 208
NG + + I+ +W
Sbjct: 89 NGAEIMGQTIQVDW 102
Score = 32.0 bits (71), Expect = 0.69, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 10/89 (11%)
Query: 248 EDAPENNPQYTTVYVGNLSSEVTSVDLHRHFHALC-VGTIEDVRVQRD------KGFGFV 300
E P+ + + ++V ++ E ++ F C G I+++ + D KG+ V
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKF---CDYGEIKNIHLNLDRRTGFSKGYALV 73
Query: 301 RYSTHPEAALAIQMGNARILCGKPIKCSW 329
Y TH +A A + N + G+ I+ W
Sbjct: 74 EYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 129 TSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQ 188
+SG +++ L P TD L + + + D+ T + +G+GFV F + AQ
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 189 SAINDLN 195
A+ L
Sbjct: 62 KAVTALK 68
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 146 DATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIR 205
D L F F D ++++++ S+GFGFV+F N DA A L+G + R+I
Sbjct: 29 DPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
Query: 206 CNWA 209
N A
Sbjct: 87 VNNA 90
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 46 TCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS--YGFVDYFDRRSAALAIV 103
T + ++V NI + + L+++F G + ++I ++ S +GFV + + A A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73
Query: 104 TLNGRHIFGQPIKVNWAYA 122
L+G + G+ I+VN A A
Sbjct: 74 KLHGTVVEGRKIEVNNATA 92
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 59 VTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRHIFGQPIKVN 118
V + L E+F GP++ K++ + + FV++ + SAA AI ++G+ QP++V
Sbjct: 43 VQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
Query: 119 WAYASSQR 126
++ ++R
Sbjct: 99 YSKLPAKR 106
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 8/85 (9%)
Query: 120 AYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFV 179
++ ++E + +FV +V ++ L F F + +++ GF FV
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFV 70
Query: 180 SFRNQEDAQSAINDLNGKWLGNRQI 204
F E A AI +++GK N+ +
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPL 95
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 27/97 (27%), Positives = 44/97 (45%), Gaps = 9/97 (9%)
Query: 129 TSGHFNVFVGDLSPEVTDATLFACFS---VFPTCSDARVMWDQKTGRSRGFGFVSFRNQE 185
+SG +F+ +L+ T+ TL FS +C+ ++ S GFGFV ++ E
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 186 DAQSAINDLNGKWLGNRQI------RCNWAAKGATSG 216
AQ A+ L G + ++ R A G +SG
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98
Score = 35.0 bits (79), Expect = 0.083, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 44 ASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSS-------YGFVDYFDRR 96
+S +++ N++ T L+ VFS G ++ C + KK + +GFV+Y
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 97 SAALAIVTLNGRHIFGQPIKV 117
A A+ L G + G ++V
Sbjct: 62 QAQKALKQLQGHTVDGHKLEV 82
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 8/89 (8%)
Query: 45 STCRSVYVGNIHPQVTNALLQEVFSSTGP--LEGCKLIKKDKSSYGFVDYFDRRSAALAI 102
S+ + +YV N+ + ++++ F++ P +E K I+ Y FV + +R A A+
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAM 68
Query: 103 VTLNGRHIFGQPIKVNWAYASSQREDTSG 131
LNG+ + G PI+V A + D+SG
Sbjct: 69 KALNGKVLDGSPIEVTLAKPVDK--DSSG 95
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 168 QKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWA------AKGATSG 216
++ + R + FV F N+EDA A+ LNGK L I A + G +SG
Sbjct: 45 ERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 149 LFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL-NGKWLGNRQIRCN 207
LF+ F T + M TG RGFGFV F ++DA+ A N L + L R++
Sbjct: 35 LFSTFGELKTVRLPKKMTG--TGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE 92
Query: 208 WA 209
WA
Sbjct: 93 WA 94
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+FVG L + TD + F F T + V+ G S+G FV F+ +AQ+AIN
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 194 LN 195
L+
Sbjct: 73 LH 74
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQR-----DKGFGFVRYSTHPEAALAIQ- 313
++VG L + T D+ + F GTI++ V R KG FV++ TH EA AI
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPF--GTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 314 MGNARILCG 322
+ ++R L G
Sbjct: 73 LHSSRTLPG 81
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
++VGNI P TN L+ F GP+ C ++K Y FV A AI L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK----DYAFVHMERAEDAVEAIRGLDNTE 68
Query: 110 IFGQPIKVNWA 120
G+ + V +
Sbjct: 69 FQGKRMHVQLS 79
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 175 GFGFVSFRNQEDAQSAINDLNGKWLGNRQI 204
G VSFR+ E+A I L+G+W G RQI
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+ V +L V+DA + F+ F T A V +D ++GRS G V F + DA A+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 194 LNGKWLGNRQI 204
NG L R +
Sbjct: 89 YNGVPLDGRPM 99
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 117 VNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGF 176
V A Q +D + N+++ +L + + L F R++ D +G SRG
Sbjct: 13 VQAQMAKQQEQDPT---NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGV 68
Query: 177 GFVSFRNQEDAQSAINDLNGKWL 199
GF + E ++ I NGK++
Sbjct: 69 GFARMESTEKCEAVIGHFNGKFI 91
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 137 VGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNG 196
+ +LS T+ TL VF + +V +Q G+S+G+ F+ F + EDA+ A+N N
Sbjct: 20 LSNLSYSATEETLQ---EVFEKATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 197 KWLGNRQIR 205
+ + R IR
Sbjct: 76 REIEGRAIR 84
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.8 bits (81), Expect = 0.050, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 59 VTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRHIFGQPIKVN 118
V + L E+F GP++ K++ + + FV++ + SAA AI ++G+ QP++V
Sbjct: 16 VQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 71
Query: 119 WA 120
++
Sbjct: 72 YS 73
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV +V ++ L F F + +++ GF FV F E A AI ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 58
Query: 195 NGKWLGNRQI 204
+GK N+ +
Sbjct: 59 HGKSFANQPL 68
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 38/82 (46%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+F+G L + D + + F ++ D TG S+G+ F + + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 195 NGKWLGNRQIRCNWAAKGATSG 216
NG LG++++ A+ GA +
Sbjct: 64 NGMQLGDKKLLVQRASVGAKNA 85
Score = 32.0 bits (71), Expect = 0.62, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 4/80 (5%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKS----SYGFVDYFDRRSAALAIVTL 105
+++G + + + ++E+ +S GPL+ L+K + Y F +Y D AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 106 NGRHIFGQPIKVNWAYASSQ 125
NG + + + V A ++
Sbjct: 64 NGMQLGDKKLLVQRASVGAK 83
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.4 bits (80), Expect = 0.065, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNG 107
+ ++V N+ VT +L++ FS G LE K +K Y FV + DR +A A+ +NG
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK----DYAFVHFEDRGAAVKAMDEMNG 71
Query: 108 RHI 110
+ I
Sbjct: 72 KEI 74
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+ V +L V+DA + F+ F T A V +D ++GRS G V F + DA A
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 194 LNGKWLGNR 202
NG L R
Sbjct: 90 YNGVPLDGR 98
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 46/195 (23%), Positives = 79/195 (40%), Gaps = 41/195 (21%)
Query: 50 VYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGR 108
+ V N++P+ VT L +F G ++ K++ +K V D A LA+ LNG
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-NKKENALVQMADGNQAQLAMSHLNGH 95
Query: 109 HIFGQPIKVNWA--------------------YASS--QREDTSGHFNVFVGDLSPEVTD 146
+ G+PI++ + Y +S R G N F P T
Sbjct: 96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN-FQNIFPPSAT- 153
Query: 147 ATLFACFSVFPTCS--DARVMWDQKTGRSRGFGF---------VSFRNQEDAQSAINDLN 195
++ P+ S D +V++ G +GF F + + E+A A+ DL+
Sbjct: 154 ---LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 210
Query: 196 GKWLG-NRQIRCNWA 209
LG N +R +++
Sbjct: 211 NHDLGENHHLRVSFS 225
>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: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
++ V L + T+ L FS F +V D KTG S+GFGFV F E ++
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Query: 194 ---LNGKW 198
++G+W
Sbjct: 77 RHMIDGRW 84
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 46/195 (23%), Positives = 79/195 (40%), Gaps = 41/195 (21%)
Query: 50 VYVGNIHPQ-VTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGR 108
+ V N++P+ VT L +F G ++ K++ +K V D A LA+ LNG
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-NKKENALVQMADGNQAQLAMSHLNGH 64
Query: 109 HIFGQPIKVNWA--------------------YASS--QREDTSGHFNVFVGDLSPEVTD 146
+ G+PI++ + Y +S R G N F P T
Sbjct: 65 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN-FQNIFPPSAT- 122
Query: 147 ATLFACFSVFPTCS--DARVMWDQKTGRSRGFGF---------VSFRNQEDAQSAINDLN 195
++ P+ S D +V++ G +GF F + + E+A A+ DL+
Sbjct: 123 ---LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 179
Query: 196 GKWLG-NRQIRCNWA 209
LG N +R +++
Sbjct: 180 NHDLGENHHLRVSFS 194
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRV------QRDKGFGFVRYSTHPEAALAI 312
TV+ L++ + DL F A VG + DVR+ +R KG +V + LAI
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSA--VGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
Query: 313 QMGNARILCGKPI 325
+ R+L G PI
Sbjct: 85 GLTGQRLL-GVPI 96
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 137 VGDLSPEVTDATLFAC---------------FSVFPTCSDARVMWDQKTGRSRGFGFVSF 181
V +LSPE DA C FS D R++ D+ + RS+G +V F
Sbjct: 15 VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
Query: 182 RNQEDAQSAINDLNGKWLG 200
+ AI + LG
Sbjct: 75 CEIQSVPLAIGLTGQRLLG 93
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 178 FVSFRNQEDAQSAINDLNGKWLGNRQI 204
+V FR +EDA+ A+ DLN +W + I
Sbjct: 72 YVKFRREEDAEKAVIDLNNRWFNGQPI 98
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 123 SSQREDTSGHFNVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFR 182
S R F V++ L E + + F D+ + G++ G GFV FR
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75
Query: 183 NQEDAQSAINDLNGKWLGNRQIR 205
N+ D ++A+ + +++GNR I+
Sbjct: 76 NEADYKAALCR-HKQYMGNRFIQ 97
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQI--RCNWAAKGATSG 216
+ G+S+G G V F + E A+ A +NG L R+I R + A G +SG
Sbjct: 40 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 89
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 135 VFVGDLSPEVT-DATL--FACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQ 188
+ + +L+P T D+ L A ++V + S+ RV+ D++T +RGF F+ E AQ
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVL-SSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQ 81
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQI--RCNWAAKGATSG 216
+ G+S+G G V F + E A+ A +NG L R+I R + A G +SG
Sbjct: 43 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 47 CRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKLI-KKDKSSYGFVDYFDRRSAALAIVTL 105
CR +YVGN+ P + +++VF G + L ++ + FV++ D R A A+
Sbjct: 23 CR-IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 106 NGRHIFGQPIKVNWAYASSQREDTSG 131
+G G ++V + S R SG
Sbjct: 82 DGYDYDGYRLRVE--FPRSGRGTGSG 105
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDL 194
+FV +LS ++ L FS + S+ D T + +GF FV+F E A A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 195 NGKWLGNRQI 204
+G+ R +
Sbjct: 71 DGQVFQGRML 80
>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 = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQY 86
>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 = 32.7 bits (73), Expect = 0.44, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 1 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 59
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 60 SSATNALRSMQGFPFYDKPMRIQY 83
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQY 85
>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 = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQY 86
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
+++GN+ + T ++ +F G + C +IK +YGFV D+ +A AI L+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK----NYGFVHIEDKTAAEDAIRNLHHYK 66
Query: 110 IFGQPIKVNWAYASSQREDTSG 131
+ G + +N + ++ + +SG
Sbjct: 67 LHG--VNINVEASKNKSKASSG 86
>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 = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQY 85
>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 = 32.3 bits (72), Expect = 0.46, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQY 85
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+FVG L+ + ++ + F F + V+ G S+G FV F + +AQ+AI+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 194 LNG 196
L+G
Sbjct: 76 LHG 78
Score = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 260 VYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQR-----DKGFGFVRYSTHPEAALAIQ 313
++VG L+ + + D+ R F G I++ V R KG FV++S+H EA AI
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPF--GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
>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 = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 48 RSVYVGNIHPQVTNALLQEVFSSTGPLEG----CKLIKKDKSSYGFVDYFDRRS--AALA 101
RSVYVGN+ T L+ FSS G + C Y ++++ +R S AA+A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 102 I--VTLNGRHIFGQPIKVNWAYASS 124
+ GR I P + N SS
Sbjct: 97 MDETVFRGRTIKVLPKRTNMPGISS 121
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAI 312
+VYVGN+ T+ DL HF + G+I + + D KG+ ++ ++ A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSS--CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 313 QMGNARILCGKPIK 326
M + + G+ IK
Sbjct: 96 AM-DETVFRGRTIK 108
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSF--RNQEDAQSAI 191
+V+VG++ T L A FS + + ++ D+ +G +G+ ++ F RN DA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 192 ND 193
++
Sbjct: 98 DE 99
>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 237
Score = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 41 RFDASTCRSVYVGNIHPQVTNALLQEVFSSTGPLEGCKL 79
R +TC +V +G +HP+ + ++ +V S G L C L
Sbjct: 98 RLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCL 136
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEV 61
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP + +
Sbjct: 62 SSATNALRSXQGFPFYDKPXRIQY 85
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEV 62
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP + +
Sbjct: 63 SSATNALRSXQGFPFYDKPXRIQY 86
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + +A+ G I D+ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQY 86
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 31.6 bits (70), Expect = 0.97, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 1 PETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEV 59
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP + +
Sbjct: 60 SSATNALRSXQGFPFYDKPXRIQY 83
>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 = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+++VG++ T L A F + + ++ D+ +G +GF ++ F ++E ++++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 65
Query: 194 LNGKWLGNRQIR 205
L+ RQI+
Sbjct: 66 LDESLFRGRQIK 77
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 9/74 (12%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYSTHPEAALAI 312
++YVGN+ T+ +L HFH G++ V + D KGF ++ +S ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHG--CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 313 QMGNARILCGKPIK 326
+ + + G+ IK
Sbjct: 65 ALDES-LFRGRQIK 77
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 159 CSDARVMWDQKTGRSRGFGFVSFRNQEDA 187
+ R+M ++ +G+SRGF FV F + +DA
Sbjct: 29 AREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 135 VFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGR-----SRGFGFVSFRNQEDAQS 189
V +G L+ VT + FS + M D R S+G+ +V F N ++A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIK----MIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 190 AINDLNGKWLGNRQI 204
A+ ++G + ++I
Sbjct: 63 ALKHMDGGQIDGQEI 77
>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 = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALCVGTIEDVRVQRD------KGFGFVRYS 303
++YVGN+ T+ +L HFH G++ V + D KGF ++ +S
Sbjct: 8 SIYVGNVDYGATAEELEAHFHG--CGSVNRVTILCDKFSGHPKGFAYIEFS 56
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAIND 193
+++VG++ T L A F + + ++ D+ +G +GF ++ F ++E ++++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66
Query: 194 LNGKWLGNRQIR 205
L+ RQI+
Sbjct: 67 LDESLFRGRQIK 78
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAKGA 213
D++TG+ +G VSF + A++AI+ +GK I+ ++A + A
Sbjct: 50 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 134 NVFVGDLSPEVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAI-- 191
VF+ +LS + + L F RV+ T S+G F F QE AQ +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 192 ----NDLNGKWLGNRQIRCNW------AAKGATSG 216
+ G L RQ++ + AA G +SG
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>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 = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 28/44 (63%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAKG 212
+ G G V+F ++++A +A+ DLN + +G+R+++ + + G
Sbjct: 52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95
>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 = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
D+ TG+++GF FV + DA+ I +GK L
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>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 = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWL 199
D+ TG+++GF FV + DA+ I +GK L
Sbjct: 47 DEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + +A+ G I D+ V R +G FV +
Sbjct: 4 PETRPNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQY 86
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 251 PENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTH 305
PE P +T +Y+ NL+ ++ +L + +A+ G I D+ V R +G FV +
Sbjct: 3 PETRPNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 306 PEAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQY 85
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 143 EVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNR 202
++T L FS F + D R FV++ E A A+ +LNG + +
Sbjct: 24 DMTPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESV 77
Query: 203 QIRCNWAAK 211
Q++ N A K
Sbjct: 78 QLKVNIARK 86
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAA-KGATSG 216
+ G+S+G ++ F+++ DA+ + + G + R + + KG T G
Sbjct: 48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 143 EVTDATLFACFSVFPTCSDARVMWDQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNR 202
++T L FS F + D R FV++ E A A+ +LNG + +
Sbjct: 48 DMTPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESV 101
Query: 203 QIRCNWAAK 211
Q++ N A K
Sbjct: 102 QLKVNIARK 110
>pdb|3PM9|A Chain A, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
pdb|3PM9|B Chain B, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
pdb|3PM9|C Chain C, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
pdb|3PM9|D Chain D, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
pdb|3PM9|E Chain E, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
pdb|3PM9|F Chain F, Crystal Structure Of A Putative Dehydrogenase (Rpa1076)
From Rhodopseudomonas Palustris Cga009 At 2.57 A
Resolution
Length = 476
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 21/49 (42%)
Query: 80 IKKDKSSYGFVDYFDRRSAALAIVTLNGRHIFGQPIKVNWAYASSQRED 128
+KKD + Y D F L I+T +F +P V A+ Q D
Sbjct: 194 LKKDNTGYDLRDLFIGAEGTLGIITAATLKLFPKPRAVETAFVGLQSPD 242
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 252 ENNPQYTTVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTHP 306
E P +T +Y+ NL+ ++ +L + HA+ G I D+ V R +G FV +
Sbjct: 1 ETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 59
Query: 307 EAALAIQMGNARILCGKPIKCSW 329
A A++ KP++ +
Sbjct: 60 SATNALRSMQGFPFYDKPMRIQY 82
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 28/44 (63%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAKG 212
+ G G V+F ++++A +A+ DLN + +G+R+++ + + G
Sbjct: 52 EKGXPTGEAXVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 169 KTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWAAKGATSG 216
+ G G V+F ++++A +A+ DLN + +G+R+++ + G +SG
Sbjct: 52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS-GPSSG 98
>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 = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 110 IFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATL 149
+F ++ W S+R D + +FVG L PE+ A L
Sbjct: 98 LFIDQVEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAAL 137
>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 = 4.3, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 110 IFGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATL 149
+F ++ W S+R D + +FVG L PE+ A L
Sbjct: 98 LFIDQVEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAAL 137
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 167 DQKTGRSRGFGFVSFRNQEDAQSAINDLNGKWLGNRQIRCNWA 209
D++TG+ +G VSF + A++AI+ +GK I+ ++A
Sbjct: 56 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 178 FVSFRNQEDAQSAINDLNGKWLGNRQIR 205
F+ F E A A+ DLNG++ G R ++
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVVK 87
>pdb|3NM1|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM1|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM1|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM1|D Chain D, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM1|E Chain E, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM1|F Chain F, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
Length = 540
Score = 28.9 bits (63), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 41 RFDASTCRSVYVGNIHPQVTNALLQEVFSSTGP--LEGCKLI----------KKDKSSYG 88
R +A CR+V +G +HP +L + SS G L+G ++ K K G
Sbjct: 168 RNNAHWCRTVGIGGLHPDNIERVLYQCVSSNGKRSLDGICVVSDIIASLDAAKSTKILRG 227
Query: 89 FVDYFDRRSAALAIVTLN 106
+D D + + + T N
Sbjct: 228 LIDKTDYKFVNIGLSTKN 245
>pdb|3NL2|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL2|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL2|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL2|D Chain D, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL2|E Chain E, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL2|F Chain F, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|D Chain D, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|E Chain E, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL3|F Chain F, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL5|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL5|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL5|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL6|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL6|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NL6|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|A Chain A, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|B Chain B, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|C Chain C, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|D Chain D, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|E Chain E, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
pdb|3NM3|F Chain F, The Crystal Structure Of Candida Glabrata Thi6, A
Bifunctional Enzyme Involved In Thiamin Biosyhthesis Of
Eukaryotes
Length = 540
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 41 RFDASTCRSVYVGNIHPQVTNALLQEVFSSTGP--LEGCKLI----------KKDKSSYG 88
R +A CR+V +G +HP +L + SS G L+G ++ K K G
Sbjct: 168 RNNAHWCRTVGIGGLHPDNIERVLYQCVSSNGKRSLDGICVVSDIIASLDAAKSTKILRG 227
Query: 89 FVDYFDRRSAALAIVTLN 106
+D D + + + T N
Sbjct: 228 LIDKTDYKFVNIGLSTKN 245
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 51/116 (43%), Gaps = 12/116 (10%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
+ V N+ VT +L ++FS G + K+ + Y D SA A ++L+G++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108
Query: 110 I----------FGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACFSV 155
I F + +N Y + + D + ++ GD P + D T+ A F +
Sbjct: 109 IYNACCTLRIDFSKLTSLNVKYNNDKSRDYT-RPDLPSGDSQPSL-DQTMAAAFGL 162
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTHPEAALAIQ 313
T+Y+ NL+ ++ +L + HA+ G I D+ V R +G FV + A A++
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64
Query: 314 MGNARILCGKPIKCSW 329
KP++ +
Sbjct: 65 SMQGFPFYDKPMRIQY 80
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 28.5 bits (62), Expect = 8.1, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 259 TVYVGNLSSEVTSVDLHRHFHALC--VGTIEDVRVQRD---KGFGFVRYSTHPEAALAIQ 313
T+Y+ NL+ ++ +L + HA+ G I D+ V R +G FV + A A++
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 65
Query: 314 MGNARILCGKPIKCSW 329
KP++ +
Sbjct: 66 SMQGFPFYDKPMRIQY 81
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 50/114 (43%), Gaps = 12/114 (10%)
Query: 50 VYVGNIHPQVTNALLQEVFSSTGPLEGCKLIKKDKSSYGFVDYFDRRSAALAIVTLNGRH 109
+ V N+ VT +L ++FS G + K+ + Y D SA A ++L+G++
Sbjct: 36 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 95
Query: 110 I----------FGQPIKVNWAYASSQREDTSGHFNVFVGDLSPEVTDATLFACF 153
I F + +N Y + + D + ++ GD P + D T+ A F
Sbjct: 96 IYNACCTLRIDFSKLTSLNVKYNNDKSRDYT-RPDLPSGDSQPSL-DQTMAAAF 147
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
0.318 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,802,937
Number of Sequences: 62578
Number of extensions: 417198
Number of successful extensions: 1814
Number of sequences better than 100.0: 195
Number of HSP's better than 100.0 without gapping: 158
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 1339
Number of HSP's gapped (non-prelim): 431
length of query: 417
length of database: 14,973,337
effective HSP length: 101
effective length of query: 316
effective length of database: 8,652,959
effective search space: 2734335044
effective search space used: 2734335044
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)