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= 013503
(442 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 8/81 (9%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQV----VDC-RICGDPNSVLRFAFIEFTDEEGARA 311
R++YV ++D T E+L A F GCG V + C + G P FA+IEF+D+E R
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKESVRT 62
Query: 312 ALNLAGTMLGFYPVRVLPSKT 332
+L L ++ ++V+P +T
Sbjct: 63 SLALDESLFRGRQIKVIPKRT 83
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 350 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 407
E AR+IY N+D T +++ F CG V R+ +L D H A++EF ES
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 408 IAALNCSGVVLGSLPIRVSPSKT 430
+L + I+V P +T
Sbjct: 61 RTSLALDESLFRGRQIKVIPKRT 83
>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 = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 8/81 (9%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQV----VDC-RICGDPNSVLRFAFIEFTDEEGARA 311
R++YV ++D T E+L A F GCG V + C + G P FA+IEF+D+E R
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKESVRT 63
Query: 312 ALNLAGTMLGFYPVRVLPSKT 332
+L L ++ ++V+P +T
Sbjct: 64 SLALDESLFRGRQIKVIPKRT 84
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 350 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 407
E AR+IY N+D T +++ F CG V R+ +L D H A++EF ES
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
Query: 408 IAALNCSGVVLGSLPIRVSPSKT 430
+L + I+V P +T
Sbjct: 62 RTSLALDESLFRGRQIKVIPKRT 84
>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 = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 52/99 (52%), Gaps = 8/99 (8%)
Query: 247 SLAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQV----VDC-RICGDPNSVLRFAFI 301
S +++EI +R+VYV ++D T + L A F CG + + C + G P +A+I
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG---YAYI 83
Query: 302 EFTDEEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPT 340
EF + AA+ + T+ ++VLP +T + ++ T
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISST 122
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 346 EDEREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVM 403
E+++E+ R++Y N+D T D++ F S CG + R+ +L D H A++EF
Sbjct: 29 EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS-CGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 404 AESAIAALNCSGVVLGSLPIRVSPSKT 430
S AA+ V I+V P +T
Sbjct: 88 RNSVDAAVAMDETVFRGRTIKVLPKRT 114
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 80/187 (42%), Gaps = 29/187 (15%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL 313
+ + V+ + Q +T+++ +LF G + C++ D L + F+ ++D A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 314 N-LAGTMLGFYPVRVL---PSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 369
N L G L ++V PS +I N +Y + + K ++Q +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMSQKE 106
Query: 370 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 424
++ F S G + R+L D S + F+ F + AE AI LN + + PI
Sbjct: 107 MEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPIT 165
Query: 425 VSPSKTP 431
V + P
Sbjct: 166 VKFANNP 172
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 21/179 (11%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAALN- 314
++YV D+ VTE L F G ++ R+C D L +A++ F A AL+
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFF 374
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 72 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 116
Query: 375 E--SVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAAL-NCSGVVLGSLPIRVSPSKT 430
+ S G + +++ D + S FV F E+A A+ +G++L + V K+
Sbjct: 117 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 245 RTSLAQREEIIRRT----VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAF 300
R +QR+ +R++ +++ ++D+ + + L F G ++ C++ D N + F
Sbjct: 83 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 142
Query: 301 IEFTDEEGARAALNLAGTML 320
+ F +E A A+ ML
Sbjct: 143 VHFETQEAAERAIEKMNGML 162
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 74/167 (44%), Gaps = 21/167 (12%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAALN- 314
++YV D+ VTE L F G ++ R+C D L +A++ F A AL+
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFF 374
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 77 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 121
Query: 375 E--SVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAAL-NCSGVVL 418
+ S G + +++ D + S FV F E+A A+ +G++L
Sbjct: 122 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL 168
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 245 RTSLAQREEIIRRT----VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAF 300
R +QR+ +R++ +++ ++D+ + + L F G ++ C++ D N + F
Sbjct: 88 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 147
Query: 301 IEFTDEEGARAALNLAGTML 320
+ F +E A A+ ML
Sbjct: 148 VHFETQEAAERAIEKMNGML 167
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 74/168 (44%), Gaps = 29/168 (17%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL 313
+ + V+ + Q +T+E+ +LF G++ C++ D L + F+ + D + A A+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 314 N-LAGTMLGFYPVRVL---PSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 369
N L G L ++V PS +I N +Y + + K +TQ +
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMTQKE 104
Query: 370 VKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEF---VMAESAIAALN 412
++ F S G + R+L D S + F+ F + AE AI LN
Sbjct: 105 LEQLF-SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 350 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 407
E ART++C + ++ D++ FF +V G+V +R++ D + S IA+VEF +S
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAV-GKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 408 IAALNCSGVVLGSLPIRVSPSKT 430
A+ +G L +PI V S+
Sbjct: 81 PLAIGLTGQRLLGVPIIVQASQA 103
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 2/83 (2%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGA 309
EE RTV+ + ++ L F G+V D RI D NS A++EF + +
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 310 RAALNLAGTMLGFYPVRVLPSKT 332
A+ L G L P+ V S+
Sbjct: 81 PLAIGLTGQRLLGVPIIVQASQA 103
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD-EEGARAAL 313
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D E A A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 314 NLAGTMLG 321
NL G LG
Sbjct: 64 NLNGYQLG 71
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 22/120 (18%)
Query: 283 VVDCRICGDPNSVLRFAFIEFTDEEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTFL 342
VVD RI +F +++F E AL L G ++V ++ +
Sbjct: 39 VVDVRI----GMTRKFGYVDFESAEDLEKALELTG-------LKVFGNEIKLEK------ 81
Query: 343 PRTED-EREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEF 401
P+ +D ++E ART+ N+ KVTQ ++K FE +RL+ S IA++EF
Sbjct: 82 PKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAA----EIRLVSKDGKSKGIAYIEF 137
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD-EEGARAAL 313
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D E A A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 314 NLAGTMLG 321
NL G LG
Sbjct: 63 NLNGYQLG 70
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAALNL 315
TVYV +D++V+E L LF+ G VV+ + D + F+EF EE A A+ +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 316 AGTMLGFY--PVRV 327
M+ Y P+RV
Sbjct: 77 M-DMIKLYGKPIRV 89
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD-EEGARAAL 313
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D E A A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 314 NLAGTMLG 321
NL G LG
Sbjct: 65 NLNGYQLG 72
>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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 47/181 (25%), Positives = 76/181 (41%), Gaps = 29/181 (16%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL 313
R + V+ + Q +T+++L +LF G+V ++ D L + F+ + + A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 314 N-LAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 369
N L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 370 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 424
V+ F S G + R+L D S +AF+ F AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 425 V 425
V
Sbjct: 164 V 164
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 47/181 (25%), Positives = 76/181 (41%), Gaps = 29/181 (16%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL 313
R + V+ + Q +T+++L +LF G+V ++ D L + F+ + + A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 314 N-LAGTMLGFYPVRVL---PSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 369
N L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 370 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 424
V+ F S G + R+L D S +AF+ F AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 425 V 425
V
Sbjct: 164 V 164
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 48/174 (27%), Positives = 75/174 (43%), Gaps = 25/174 (14%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRF--AFIEFTDEEGARAALNLAGT 318
V+ + Q T+ +L ALF G + CRI D + F AF++FT E ++ A+
Sbjct: 19 VNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK---- 74
Query: 319 MLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFES-- 376
+L VR K + A P E ++ +Y TN+ + +T + F
Sbjct: 75 VLNGITVRNKRLKVSYA------RPGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYG 125
Query: 377 --VCGEVYRLRLLGDYHHSTRIAFVEFVM---AESAIAALNCSGVVLGSLPIRV 425
V + R +L G +AFV + A+ AI+ALN GS P+ V
Sbjct: 126 SIVQKNILRDKLTG---RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFTDE 306
E I +YV+++ + +T++QL +F G +V I G P V AF+ +
Sbjct: 96 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 152
Query: 307 EGARAAL 313
E A+ A+
Sbjct: 153 EEAQEAI 159
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFTDEEGARA 311
R+V+V +I + TEEQL +F G VV R+ G P + F E+ D+E A +
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG---YGFCEYQDQETALS 65
Query: 312 AL-NLAGTMLGFYPVRV 327
A+ NL G +RV
Sbjct: 66 AMRNLNGREFSGRALRV 82
>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 = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 12/104 (11%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGA-RAALNLAG 317
+++ ++D+ + + L F G ++ C++ D N + F+ F +E A RA + G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 318 TMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNI 361
+L V V F R E E E+ AR TN+
Sbjct: 68 MLLNDRKVFV-----------GRFKSRKEREAELGARAKEFTNV 100
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 41/176 (23%), Positives = 73/176 (41%), Gaps = 20/176 (11%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSV-LRFAFIEFTDEEGARAAL-N 314
R +YV ++D+ +TE+ L F G + + +I D N+ + +AF+E+ A AL
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPR---TEDEREMCARTIYCTNIDKKVTQADVK 371
L G + + I +N F + ++D + + N+D + + K
Sbjct: 61 LNGKQI----------ENNIVKINWAFQSQQSSSDDTFNLFVGDL-NVNVDDETLRNAFK 109
Query: 372 LFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNC-SGVVLGSLPIRVS 426
F + G V G S FV F + A A++ G L P+R++
Sbjct: 110 DFPSYLSGHVMWDMQTG---SSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 76/174 (43%), Gaps = 25/174 (14%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALNLAGT 318
V+ + Q +T+ +L ALF G + CRI D + +AF++FT E ++ A+ +
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV--- 64
Query: 319 MLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFES-- 376
L VR K + A P E ++ +Y TN+ + +T + F
Sbjct: 65 -LNGITVRNKRLKVSYAR------PGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYG 114
Query: 377 --VCGEVYRLRLLGDYHHSTRIAFVEFVM---AESAIAALNCSGVVLGSLPIRV 425
V + R +L G +AFV + A+ AI+ALN GS P+ V
Sbjct: 115 SIVQKNILRDKLTG---RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFTDE 306
E I +YV+++ + +T++QL +F G +V I G P V AF+ +
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 141
Query: 307 EGARAAL 313
E A+ A+
Sbjct: 142 EEAQEAI 148
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARA---A 312
R +++ I ++ TE + +F GQ+ +CRI P+ + R AF+ FT A+ A
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 313 LNLAGTMLG 321
++ A TM G
Sbjct: 156 MHQAQTMEG 164
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARA---A 312
R +++ I ++ TE + +F GQ+ +CRI P+ + R AF+ FT A+ A
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 313 LNLAGTMLG 321
++ A TM G
Sbjct: 168 MHQAQTMEG 176
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 14/62 (22%), Positives = 30/62 (48%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALNLAGT 318
+++ ++D+ + + L F G ++ C++ D N + F+ F +E A A+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 319 ML 320
ML
Sbjct: 74 ML 75
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.2 bits (82), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 75 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 122
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 123 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARAAL 313
R +++ I ++ TE + F GQ+ +CRI P+ + R AF+ FT A+ A+
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>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 = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 73 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 120
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 121 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 152
>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 = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 74 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 122 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAALNLA 316
++V +D T+E L + F G+VVDC I D N F F++F D N
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP-------NCV 71
Query: 317 GTMLGFYP 324
GT+L P
Sbjct: 72 GTVLASRP 79
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.8 bits (81), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 74 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 122 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 35.4 bits (80), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 53/120 (44%), Gaps = 22/120 (18%)
Query: 283 VVDCRICGDPNSVLRFAFIEFTDEEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTFL 342
VVD R + +F +++F E AL L G ++V ++ +
Sbjct: 45 VVDVRTGTNR----KFGYVDFESAEDLEKALELTG-------LKVFGNEIKLEK------ 87
Query: 343 PRTEDEREM-CARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEF 401
P+ D +++ ART+ N+ +T+ ++K FE +RL+ S IA++EF
Sbjct: 88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL----EIRLVSQDGKSKGIAYIEF 143
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 30/151 (19%), Positives = 58/151 (38%), Gaps = 22/151 (14%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALNLAG 317
TV V ++ + + ++ F CG ++ + RFA IEF +GA AA+
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102
Query: 318 TMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFESV 377
++G + V + T++ TN TQ +++ + +
Sbjct: 103 KVVGQNEIIV---------------------SHLTECTLWXTNFPPSYTQRNIRDLLQDI 141
Query: 378 CGEVYRLRLLG-DYHHSTRIAFVEFVMAESA 407
+RL ++ S R A+++ E A
Sbjct: 142 NVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 355 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 414
T+ N+ K Q V +F+ CG + + + + R A +EF + A+AA+ +
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 415 GVVLGSLPIRVS 426
V+G I VS
Sbjct: 102 HKVVGQNEIIVS 113
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 72 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 119
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 120 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 151
>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 = 35.4 bits (80), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 61/153 (39%), Gaps = 21/153 (13%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+N
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 315 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQADV 370
P K V P ED + + + I+ I + + +
Sbjct: 67 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 114
Query: 371 KLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 401
+ +FE G++ + ++ D + AFV F
Sbjct: 115 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 35.0 bits (79), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRIC----GDPNSVLRFAFIEFTDEEGARAA 312
RTV+V +++ +V EE L LF+ G + IC G P S F F+ F E A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS---FGFVCFKHPESVSYA 73
Query: 313 LNL 315
+ L
Sbjct: 74 IAL 76
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALNLAG 317
TV V ++ + + ++ F CG ++ + RFA IEF +GA AA+
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 318 TMLG 321
++G
Sbjct: 66 KVVG 69
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 355 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 414
T+ N+ K Q V +F+ CG + + + + R A +EF + A+AA+ +
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 64
Query: 415 GVVLGSLPIRVS 426
V+G I VS
Sbjct: 65 HKVVGQNEIIVS 76
>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 = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 48/101 (47%), Gaps = 7/101 (6%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD 305
LA+ R +YV+ + Q ++++ + ++F G++ C + DP + + FIE+
Sbjct: 102 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEK 160
Query: 306 EEGARAALNLAGTM-LGFYPVRVLPSKTAIAPVNPTFLPRT 345
+ ++ A++ LG +RV A+ P P P T
Sbjct: 161 AQSSQDAVSSXNLFDLGGQYLRV---GKAVTPPXPLLTPAT 198
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL 313
+R +YV + ++V ++ L A F+ G + D +I D + FAF+EF E A AA+
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 314 N 314
+
Sbjct: 65 D 65
>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 = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL 313
+R +YV + ++V ++ L A F+ G + D +I D + FAF+EF E A AA+
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 314 N 314
+
Sbjct: 67 D 67
>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 = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL 313
+R +YV + ++V ++ L A F+ G + D +I D + FAF+EF E A AA+
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 314 N 314
+
Sbjct: 62 D 62
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 48/101 (47%), Gaps = 7/101 (6%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD 305
LA+ R +YV+ + Q ++++ + ++F G++ C + DP + + FIE+
Sbjct: 103 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEK 161
Query: 306 EEGARAALNLAGTM-LGFYPVRVLPSKTAIAPVNPTFLPRT 345
+ ++ A++ LG +RV A+ P P P T
Sbjct: 162 AQSSQDAVSSMNLFDLGGQYLRV---GKAVTPPMPLLTPAT 199
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL 313
+R +YV + ++V ++ L A F+ G + D +I D + FAF+EF E A AA+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 314 N 314
+
Sbjct: 72 D 72
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL 313
+R +YV + ++V ++ L A F+ G + D +I D + FAF+EF E A AA+
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 314 N 314
+
Sbjct: 123 D 123
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 6/86 (6%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSV-----LRFAFIEFTDEEGARAAL 313
+++ +++ TEE L +F G + C I N + F F+E+ E A+ AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 314 -NLAGTMLGFYPVRVLPSKTAIAPVN 338
L G + + + V S+ A P +
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPAS 93
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALNL 315
V+ + Q +T+ +L ALF G + CRI D + +AF++FT E ++ A+ +
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.3 bits (72), Expect = 0.54, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDE-EGARAALNL 315
V+V D+ ++T E + + F G++ D R+ D + F+ F ++ + A +++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 316 AGTMLGFYPVRV-LPSKTAIAPVNPT 340
G LG +R ++ AP P+
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
>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 = 32.0 bits (71), Expect = 0.72, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 260 YVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAALN 314
+V + +++ L F G+VVDC I DPN+ F FI F D L+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.0 bits (71), Expect = 0.80, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 6/55 (10%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAAL 313
++V ++ T ++L +LF G+V++C + D +AF+ E A+AA+
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD------YAFVHMEKEADAKAAI 60
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 250 QREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFT 304
+RE+ R +++ + + TEE L + G++ DC + DP S F F+ F+
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARAALNL 315
R ++V + +Q T+E + +F G + +C + P+ + AF++F A+AA+N
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 316 AGTMLGFYPVRVLPSKTA 333
+ R LP ++
Sbjct: 73 ------LHSSRTLPGASS 84
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEEGARAAL 313
+++ + Q T+E L F G+V +C + DP F F+ F D+ G L
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 361 IDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVMAESAIAALNC-SGVV 417
+ + +TQ +++ F S+ GEV +L+ D HS FV +V A+ A A+N +G+
Sbjct: 12 LPQNMTQDELRSLFSSI-GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR 70
Query: 418 LGSLPIRVSPSK 429
L S I+VS ++
Sbjct: 71 LQSKTIKVSYAR 82
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSV--LRFAFIEFTDEEGARAALN 314
R +YV ++ T EQ+ LF G+V + ++ D + F F+E +E + A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 315 LAGTMLGFYPVRV 327
L T +RV
Sbjct: 62 LDNTDFMGRTIRV 74
>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 = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/101 (22%), Positives = 47/101 (46%), Gaps = 7/101 (6%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD 305
LA+ R +YV+ + Q ++++ + ++F G++ + DP + + FIE+
Sbjct: 118 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK 176
Query: 306 EEGARAALNLAGTM-LGFYPVRVLPSKTAIAPVNPTFLPRT 345
+ ++ A++ LG +RV A+ P P P T
Sbjct: 177 AQSSQDAVSSMNLFDLGGQYLRV---GKAVTPPMPLLTPAT 214
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAA 312
+T++V + + TEE L F G V RI D S F F++F EE A+AA
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARA 311
V+V + +T E+L F G+VVD I P FAF+ F D++ A++
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFI---PKPFRAFAFVTFADDKVAQS 63
>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 = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 361 IDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVMAESAIAALNC-SGVV 417
+ + TQ +++ F S+ GEV +L+ D HS FV +V A+ A A+N +G+
Sbjct: 27 LPQNXTQDELRSLFSSI-GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR 85
Query: 418 LGSLPIRVSPSK 429
L S I+VS ++
Sbjct: 86 LQSKTIKVSYAR 97
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEF 303
RT+YV ++ + VTE + LF G C++ + S + F+EF
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF 62
>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 = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL-NL 315
V+V D+ ++T E + A F G++ D R+ D + F+ F ++ A A+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 316 AGTMLGFYPVR 326
G LG +R
Sbjct: 78 GGQWLGGRQIR 88
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEEGARAAL 313
+ + V+ + Q +T+++ +LF G + C++ D L + F+ ++D A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 314 N-LAGTMLGFYPVRVLPSKTAIAPV 337
N L G L ++V ++ + A +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASI 88
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGARAAL-NL 315
+YV + +TE+ L +F G++ ++ D + + FI F+D E A+ AL L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 316 AGTMLGFYPVRV 327
G L P++V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTD-EEGARAALNLAG 317
+YV ++D + +E+L F G + ++ + F F+ F+ EE +A + G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 318 TMLGFYPVRV 327
++ P+ V
Sbjct: 78 RIVATKPLYV 87
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEEGARAAL 313
+++ + Q T+E L F G+V +C + DP F F+ F D+ G L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARAALN 314
R ++V +++Q +EE + LF G + +C + P+ + AF++F+ A+AA++
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 18/74 (24%)
Query: 240 RRMNSRTSLAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFA 299
R MNSR + ++ V + + A+F G++V C + FA
Sbjct: 12 RSMNSRVFIGNLNTLV------------VKKSDVEAIFSKYGKIVGCSVHKG------FA 53
Query: 300 FIEFTDEEGARAAL 313
F+++ +E ARAA+
Sbjct: 54 FVQYVNERNARAAV 67
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR---FAFIEFT 304
+A+++E +Y+S++ + E++L + GQV+ RI D + R FA +E T
Sbjct: 17 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMEST 76
Query: 305 DE 306
++
Sbjct: 77 EK 78
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEEGAR 310
+ TVYVS++ +T L +F G+VV I D ++ AFI F D++ A+
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 4.7, Method: Composition-based stats.
Identities = 12/55 (21%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAAL 313
+++ ++ ++ TE+++ +LF G+V++C I + + F+ D+ A A+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDI------IKNYGFVHIEDKTAAEDAI 59
>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 = 28.9 bits (63), Expect = 6.2, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 8/68 (11%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDC-----RICGDPNSVLRFAFIEFTDE 306
E I +YV+++ + +T++QL +F G +V ++ G P V AF+ +
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 65
Query: 307 EGARAALN 314
E A+ A++
Sbjct: 66 EEAQEAIS 73
>pdb|1DWN|A Chain A, Structure Of Bacteriophage Pp7 From Pseudomonas Aeruginosa
At 3.7 A Resolution
pdb|1DWN|B Chain B, Structure Of Bacteriophage Pp7 From Pseudomonas Aeruginosa
At 3.7 A Resolution
pdb|1DWN|C Chain C, Structure Of Bacteriophage Pp7 From Pseudomonas Aeruginosa
At 3.7 A Resolution
Length = 127
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 345 TEDEREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRI 396
T R+ A+T Y N+ K+ QADV SVCGE+ ++R + H I
Sbjct: 41 TASLRQNGAKTAYRVNL--KLDQADVVDCSTSVCGELPKVRYTQVWSHDVTI 90
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.5 bits (62), Expect = 8.0, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 28/71 (39%)
Query: 355 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 414
T Y N+ Q D+ F+ + RL D +VEF +S AL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD 76
Query: 415 GVVLGSLPIRV 425
G +LG +RV
Sbjct: 77 GALLGDRSLRV 87
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 250 QREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEEGA 309
Q E+ ++V V E +L +F G + + +I FAF+EF + E A
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESA 78
Query: 310 RAAL-NLAGTMLGFYPVRVLPSK 331
A+ + G P+ V+ SK
Sbjct: 79 AKAIEEVHGKSFANQPLEVVYSK 101
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.1 bits (61), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEF-TDEEGARAALNLA 316
TVY I +T++ + F GQ+++ R+ + ++F+ F T E A A +++
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----YSFVRFSTHESAAHAIVSVN 82
Query: 317 GTMLGFYPVRVLPSK 331
GT + + V+ K
Sbjct: 83 GTTIEGHVVKCYWGK 97
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,204,038
Number of Sequences: 62578
Number of extensions: 354133
Number of successful extensions: 860
Number of sequences better than 100.0: 76
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 49
Number of HSP's that attempted gapping in prelim test: 809
Number of HSP's gapped (non-prelim): 97
length of query: 442
length of database: 14,973,337
effective HSP length: 102
effective length of query: 340
effective length of database: 8,590,381
effective search space: 2920729540
effective search space used: 2920729540
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)