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= 013446
(443 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 20/179 (11%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAALN 315
++YV D+ VTE L F G ++ R+C D L +A++ F A+ RA
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 316 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFF 375
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 72 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 116
Query: 376 E--SVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAAL-NCSGVVLGSLPIRVSPSKT 431
+ S G + +++ D + S FV F E+A A+ +G++L + V K+
Sbjct: 117 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 15/116 (12%)
Query: 245 RTSLAQREEIIRRT----VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAF 300
R +QR+ +R++ +++ ++D+ + + L F G ++ C++ D N + F
Sbjct: 83 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 142
Query: 301 IEFTDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCART 356
+ F + RA + G +L V V F R E E E+ AR
Sbjct: 143 VHFETQEAAERAIEKMNGMLLNDRKVFV-----------GRFKSRKEREAELGARA 187
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 74/167 (44%), Gaps = 20/167 (11%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAALN 315
++YV D+ VTE L F G ++ R+C D L +A++ F A+ RA
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 316 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFF 375
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 77 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 121
Query: 376 E--SVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAAL-NCSGVVL 419
+ S G + +++ D + S FV F E+A A+ +G++L
Sbjct: 122 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL 168
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/81 (20%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 245 RTSLAQREEIIRRT----VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAF 300
R +QR+ +R++ +++ ++D+ + + L F G ++ C++ D N + F
Sbjct: 88 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 147
Query: 301 IEFTDEAEGARAALNLAGTML 321
+ F + RA + G +L
Sbjct: 148 VHFETQEAAERAIEKMNGMLL 168
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 9/82 (10%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQV----VDC-RICGDPNSVLRFAFIEFTDEAEGAR 311
R++YV ++D T E+L A F GCG V + C + G P FA+IEF+D+ E R
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDK-ESVR 61
Query: 312 AALNLAGTMLGFYPVRVLPSKT 333
+L L ++ ++V+P +T
Sbjct: 62 TSLALDESLFRGRQIKVIPKRT 83
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 351 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 408
E AR+IY N+D T +++ F CG V R+ +L D H A++EF ES
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 409 IAALNCSGVVLGSLPIRVSPSKT 431
+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 = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 9/82 (10%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQV----VDC-RICGDPNSVLRFAFIEFTDEAEGAR 311
R++YV ++D T E+L A F GCG V + C + G P FA+IEF+D+ E R
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDK-ESVR 62
Query: 312 AALNLAGTMLGFYPVRVLPSKT 333
+L L ++ ++V+P +T
Sbjct: 63 TSLALDESLFRGRQIKVIPKRT 84
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 351 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 408
E AR+IY N+D T +++ F CG V R+ +L D H A++EF ES
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
Query: 409 IAALNCSGVVLGSLPIRVSPSKT 431
+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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 52/100 (52%), Gaps = 9/100 (9%)
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 EFTDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPT 341
EF E AA+ + T+ ++VLP +T + ++ T
Sbjct: 84 EFA-ERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISST 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: 347 EDEREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVM 404
E+++E+ R++Y N+D T D++ F S CG + R+ +L D H A++EF
Sbjct: 29 EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS-CGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 405 AESAIAALNCSGVVLGSLPIRVSPSKT 431
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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/187 (22%), Positives = 79/187 (42%), Gaps = 28/187 (14%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAA 313
+ + V+ + Q +T+++ +LF G + C++ D L + F+ ++D + +A
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 314 LNLAGTMLGFYPVRVL---PSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 370
L G L ++V PS +I N +Y + + K ++Q +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMSQKE 106
Query: 371 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 425
++ F S G + R+L D S + F+ F + AE AI LN + + PI
Sbjct: 107 MEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPIT 165
Query: 426 VSPSKTP 432
V + P
Sbjct: 166 VKFANNP 172
>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: 351 EMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYH--HSTRIAFVEFVMAESA 408
E ART++C + ++ D++ FF +V G+V +R++ D + S IA+VEF +S
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAV-GKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 409 IAALNCSGVVLGSLPIRVSPSKT 431
A+ +G L +PI V S+
Sbjct: 81 PLAIGLTGQRLLGVPIIVQASQA 103
Score = 31.6 bits (70), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 3/84 (3%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEG 309
EE RTV+ + ++ L F G+V D RI D NS A++EF E +
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC-EIQS 79
Query: 310 ARAALNLAGTMLGFYPVRVLPSKT 333
A+ L G L P+ V S+
Sbjct: 80 VPLAIGLTGQRLLGVPIIVQASQA 103
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 40/168 (23%), Positives = 72/168 (42%), Gaps = 28/168 (16%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAA 313
+ + V+ + Q +T+E+ +LF G++ C++ D L + F+ + D + +A
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 314 LNLAGTMLGFYPVRVL---PSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 370
L G L ++V PS +I N +Y + + K +TQ +
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMTQKE 104
Query: 371 VKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEF---VMAESAIAALN 413
++ F S G + R+L D S + F+ F + AE AI LN
Sbjct: 105 LEQLF-SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 46/175 (26%), Positives = 73/175 (41%), Gaps = 26/175 (14%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRF--AFIEFTDEAEGARAALNLAG 318
V+ + Q T+ +L ALF G + CRI D + F AF++FT E + RA L G
Sbjct: 19 VNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNG 78
Query: 319 TMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFES- 377
+ ++V ++ + T +Y TN+ + +T + F
Sbjct: 79 ITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITDDQLDTIFGKY 124
Query: 378 ---VCGEVYRLRLLGDYHHSTRIAFVEFVM---AESAIAALNCSGVVLGSLPIRV 426
V + R +L G +AFV + A+ AI+ALN GS P+ V
Sbjct: 125 GSIVQKNILRDKLTG---RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFT-- 304
E I +YV+++ + +T++QL +F G +V I G P V AF+ +
Sbjct: 96 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 152
Query: 305 DEAEGARAALN 315
+EA+ A +ALN
Sbjct: 153 EEAQEAISALN 163
>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 = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D A A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 315 NLAGTMLG 322
NL G LG
Sbjct: 64 NLNGYQLG 71
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D A A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 315 NLAGTMLG 322
NL G LG
Sbjct: 63 NLNGYQLG 70
>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 = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R VY+ I TEEQ+ L G V++ ++ DP + +AFIEF D A A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 315 NLAGTMLG 322
NL G LG
Sbjct: 65 NLNGYQLG 72
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/175 (25%), Positives = 74/175 (42%), Gaps = 26/175 (14%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAALNLAG 318
V+ + Q +T+ +L ALF G + CRI D + +AF++FT E + RA L G
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
Query: 319 TMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFES- 377
+ ++V ++ + T +Y TN+ + +T + F
Sbjct: 68 ITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITDDQLDTIFGKY 113
Query: 378 ---VCGEVYRLRLLGDYHHSTRIAFVEFVM---AESAIAALNCSGVVLGSLPIRV 426
V + R +L G +AFV + A+ AI+ALN GS P+ V
Sbjct: 114 GSIVQKNILRDKLTG---RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 10/71 (14%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFT-- 304
E I +YV+++ + +T++QL +F G +V I G P V AF+ +
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 141
Query: 305 DEAEGARAALN 315
+EA+ A +ALN
Sbjct: 142 EEAQEAISALN 152
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/181 (25%), Positives = 74/181 (40%), Gaps = 28/181 (15%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAA 313
R + V+ + Q +T+++L +LF G+V ++ D L + F+ + + RA
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 314 LNLAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 370
L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 371 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 425
V+ F S G + R+L D S +AF+ F AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 426 V 426
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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/181 (25%), Positives = 74/181 (40%), Gaps = 28/181 (15%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAA 313
R + V+ + Q +T+++L +LF G+V ++ D L + F+ + + RA
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 314 LNLAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQAD 370
L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 371 VKLFFESVCGEVYRLRLLGDYHH--STRIAFVEF---VMAESAIAALNCSGVVLGSLPIR 425
V+ F S G + R+L D S +AF+ F AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 426 V 426
V
Sbjct: 164 V 164
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 57/121 (47%), Gaps = 23/121 (19%)
Query: 283 VVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTF 342
VVD RI +F +++F + AE AL L G ++V ++ +
Sbjct: 39 VVDVRI----GMTRKFGYVDF-ESAEDLEKALELTG-------LKVFGNEIKLEK----- 81
Query: 343 LPRTED-EREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVE 401
P+ +D ++E ART+ N+ KVTQ ++K FE +RL+ S IA++E
Sbjct: 82 -PKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAA----EIRLVSKDGKSKGIAYIE 136
Query: 402 F 402
F
Sbjct: 137 F 137
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDE--AEGARAA 313
R +++ I ++ TE + +F GQ+ +CRI P+ + R AF+ FT A+ A A
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 314 LNLAGTMLG 322
++ A TM G
Sbjct: 156 MHQAQTMEG 164
>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 = 24/104 (23%), Positives = 43/104 (41%), Gaps = 11/104 (10%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAG 318
+++ ++D+ + + L F G ++ C++ D N + F+ F + RA + G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 319 TMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNI 362
+L V V F R E E E+ AR TN+
Sbjct: 68 MLLNDRKVFV-----------GRFKSRKEREAELGARAKEFTNV 100
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDE--AEGARAA 313
R +++ I ++ TE + +F GQ+ +CRI P+ + R AF+ FT A+ A A
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 314 LNLAGTMLG 322
++ A TM G
Sbjct: 168 MHQAQTMEG 176
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 39/176 (22%), Positives = 72/176 (40%), Gaps = 19/176 (10%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSV-LRFAFIEFTDEAEGARAALN 315
R +YV ++D+ +TE+ L F G + + +I D N+ + +AF+E+ + A
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 316 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPR---TEDEREMCARTIYCTNIDKKVTQADVK 372
L G + + I +N F + ++D + + N+D + + K
Sbjct: 61 LNGKQI----------ENNIVKINWAFQSQQSSSDDTFNLFVGDL-NVNVDDETLRNAFK 109
Query: 373 LFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNC-SGVVLGSLPIRVS 427
F + G V G S FV F + A A++ G L P+R++
Sbjct: 110 DFPSYLSGHVMWDMQTG---SSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRI-----CGDPNSVLRFAFIEFTDEAEGAR 311
R+V+V +I + TEEQL +F G VV R+ G P + F E+ D+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG---YGFCEYQDQETALS 65
Query: 312 AALNLAGTMLGFYPVRV 328
A NL G +RV
Sbjct: 66 AMRNLNGREFSGRALRV 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAALNL 316
V+V D+ ++T E + + F G++ D R+ D + F+ F ++ + A +++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 317 AGTMLGFYPVRV-LPSKTAIAPVNPT 341
G LG +R ++ AP P+
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPSGPS 103
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAALN 315
TVYV +D++V+E L LF+ G VV+ + D + F+EF E E A A+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE-EDADYAIK 75
Query: 316 LAGTMLGFY--PVRV 328
+ M+ Y P+RV
Sbjct: 76 IM-DMIKLYGKPIRV 89
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.4 bits (80), Expect = 0.070, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 261 VSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAALNLAG 318
V+ + Q +T+ +L ALF G + CRI D + +AF++FT E + RA L G
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.0 bits (79), Expect = 0.078, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEAEGARAALNL 316
++V +D T+E L + F G+VVDC I D N F F++F D N
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP--------NC 70
Query: 317 AGTMLGFYP 325
GT+L P
Sbjct: 71 VGTVLASRP 79
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.0 bits (79), Expect = 0.087, Method: Composition-based stats.
Identities = 13/63 (20%), Positives = 30/63 (47%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAG 318
+++ ++D+ + + L F G ++ C++ D N + F+ F + RA + G
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 319 TML 321
+L
Sbjct: 74 MLL 76
>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 = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEAEGARA 312
R +++ I ++ TE + F GQ+ +CRI P+ + R AF+ FT A A
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTA 152
>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 = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 50/103 (48%), Gaps = 10/103 (9%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEF-- 303
LA+ R +YV+ + Q ++++ + ++F G++ C + DP + + FIE+
Sbjct: 103 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEK 161
Query: 304 TDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRT 346
++ A +++NL LG +RV A+ P P P T
Sbjct: 162 AQSSQDAVSSMNLFD--LGGQYLRV---GKAVTPPMPLLTPAT 199
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRIC----GDPNSVLRFAFIEFTDEAEGARA 312
RTV+V +++ +V EE L LF+ G + IC G P S F F+ F + A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS---FGFVCFKHPESVSYA 73
Query: 313 ALNLAGTMLGFYPVRV 328
L G L P+ V
Sbjct: 74 IALLNGIRLYGRPINV 89
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 55/121 (45%), Gaps = 23/121 (19%)
Query: 283 VVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTF 342
VVD R + +F +++F + AE AL L G ++V ++ +
Sbjct: 45 VVDVRTGTNR----KFGYVDF-ESAEDLEKALELTG-------LKVFGNEIKLEK----- 87
Query: 343 LPRTEDEREM-CARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVE 401
P+ D +++ ART+ N+ +T+ ++K FE +RL+ S IA++E
Sbjct: 88 -PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL----EIRLVSQDGKSKGIAYIE 142
Query: 402 F 402
F
Sbjct: 143 F 143
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 250 QREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEA 307
+RE+ R +++ + + TEE L + G++ DC + DP S F F+ F+ A
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80
Query: 308 E 308
E
Sbjct: 81 E 81
>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 = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 51/102 (50%), Gaps = 8/102 (7%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTD 305
LA+ R +YV+ + Q ++++ + ++F G++ C + DP + + FIE+ +
Sbjct: 102 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY-E 159
Query: 306 EAEGARAALNLAGTM-LGFYPVRVLPSKTAIAPVNPTFLPRT 346
+A+ ++ A++ LG +RV A+ P P P T
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRV---GKAVTPPXPLLTPAT 198
>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 = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAALNL 316
V+V D+ ++T E + A F G++ D R+ D + F+ F ++ + A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 317 AGTMLGFYPVR 327
G LG +R
Sbjct: 78 GGQWLGGRQIR 88
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNL 316
+ ++VS+I + + L +F G+++D I + F F+ F + A+ RA L
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 317 AGTML 321
GT++
Sbjct: 90 HGTVV 94
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 73
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 74 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 121
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 122 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 154
>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 = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 72
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 73 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 121 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 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 = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 71
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 72 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 119
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 120 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 152
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNL 316
+ ++VS+I + + L +F G+++D I + F F+ F + A+ RA L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 317 AGTML 321
GT++
Sbjct: 76 HGTVV 80
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 72
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 73 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 121 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 260 YVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEA 307
+V + +++ L F G+VVDC I DPN+ F FI F D A
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAA 64
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 70
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 71 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 118
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 119 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 151
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.3 bits (72), Expect = 0.58, Method: Composition-based stats.
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSV-----LRFAFIEFTDEAEGARAA 313
+++ +++ TEE L +F G + C I N + F F+E+ + +A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 314 LNLAGTMLGFYPVRVLPSKTAIAPVN 339
L G + + + V S+ A P +
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPAS 93
>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 = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAAL 314
R +++ + + T+E L + F G + DC + DPN+ F F+ + E AA+
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA-TVEEVDAAM 65
Query: 315 NLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDER----EMCARTIYCTNIDKKVTQAD 370
N P K V P ED + + + I+ I + +
Sbjct: 66 N------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 113
Query: 371 VKLFFESVCGEVYRLRLLGDYHHSTR--IAFVEF 402
++ +FE G++ + ++ D + AFV F
Sbjct: 114 LRDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 32.0 bits (71), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTDEAEGARAALN 315
R ++V + +Q T+E + +F G + +C + P+ + AF++F AE A+AA+N
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAE-AQAAIN 71
Query: 316 LAGTMLGFYPVRVLPSKTA 334
+ R LP ++
Sbjct: 72 T------LHSSRTLPGASS 84
>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 = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 30/152 (19%), Positives = 58/152 (38%), Gaps = 23/152 (15%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLA 317
TV V ++ + + ++ F CG ++ + RFA IEF +GA AA+
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFA-RYDGALAAITKT 101
Query: 318 GTMLGFYPVRVLPSKTAIAPVNPTFLPRTEDEREMCARTIYCTNIDKKVTQADVKLFFES 377
++G + V + T++ TN TQ +++ +
Sbjct: 102 HKVVGQNEIIV---------------------SHLTECTLWXTNFPPSYTQRNIRDLLQD 140
Query: 378 VCGEVYRLRLLG-DYHHSTRIAFVEFVMAESA 408
+ +RL ++ S R A+++ E A
Sbjct: 141 INVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 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: 356 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 415
T+ N+ K Q V +F+ CG + + + + R A +EF + A+AA+ +
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 416 GVVLGSLPIRVS 427
V+G I VS
Sbjct: 102 HKVVGQNEIIVS 113
>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 = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 250 QREEIIRR--TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP-NSVLRFAFIEFTDE 306
++E+++++ T+YV ++ TEEQ+ LF G + + D + F F+E+
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSR 69
Query: 307 AEGARAALNLAGTML 321
A+ A + GT L
Sbjct: 70 ADAENAMRYINGTRL 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 32/70 (45%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAG 318
+YV ++D + +E+L F G + ++ + F F+ F+ E +A + G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 319 TMLGFYPVRV 328
++ P+ V
Sbjct: 78 RIVATKPLYV 87
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (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 DEAEGARAALN 315
++ E N
Sbjct: 77 EKCEAVIGHFN 87
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAG 318
++V ++ T ++L +LF G+V++C + D +AF+ EA+ A L G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD------YAFVHMEKEADAKAAIAQLNG 65
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 10/103 (9%)
Query: 248 LAQREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEF-- 303
LA+ R +YV+ + Q ++++ + ++F G++ + DP + + FIE+
Sbjct: 118 LAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK 176
Query: 304 TDEAEGARAALNLAGTMLGFYPVRVLPSKTAIAPVNPTFLPRT 346
++ A +++NL LG +RV A+ P P P T
Sbjct: 177 AQSSQDAVSSMNLFD--LGGQYLRV---GKAVTPPMPLLTPAT 214
>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: 362 IDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVMAESAIAALNC-SGVV 418
+ + +TQ +++ F S+ GEV +L+ D HS FV +V A+ A A+N +G+
Sbjct: 12 LPQNMTQDELRSLFSSI-GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR 70
Query: 419 LGSLPIRVSPSK 430
L S I+VS ++
Sbjct: 71 LQSKTIKVSYAR 82
Score = 28.5 bits (62), Expect = 7.2, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSVLRFAFIEFTDEAEGARAA 313
R + V+ + Q +T+++L +LF G+V ++ D L + F+ + + RA
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 314 LNLAGTMLGFYPVRV 328
L G L ++V
Sbjct: 64 NTLNGLRLQSKTIKV 78
>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|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: 362 IDKKVTQADVKLFFESVCGEVYRLRLLGD--YHHSTRIAFVEFVMAESAIAALNC-SGVV 418
+ + TQ +++ F S+ GEV +L+ D HS FV +V A+ A A+N +G+
Sbjct: 27 LPQNXTQDELRSLFSSI-GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR 85
Query: 419 LGSLPIRVSPSK 430
L S I+VS ++
Sbjct: 86 LQSKTIKVSYAR 97
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLA 317
TV V ++ + + ++ F CG ++ + RFA IEF +GA AA+
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFA-RYDGALAAITKT 64
Query: 318 GTMLG 322
++G
Sbjct: 65 HKVVG 69
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 356 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 415
T+ N+ K Q V +F+ CG + + + + R A +EF + A+AA+ +
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 64
Query: 416 GVVLGSLPIRVS 427
V+G I VS
Sbjct: 65 HKVVGQNEIIVS 76
>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 = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 240 RRMNSRTSLAQREEIIRR--TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGD--PNSV 295
R + R ++E+++++ T+YV ++ TEEQ+ LF G + + D +
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80
Query: 296 LRFAFIEFTDEAEGARAALNLAGTML 321
F F+E+ A+ A + GT L
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRL 106
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 257 RTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR-FAFIEFTD--EAEGARAA 313
R ++V +++Q +EE + LF G + +C + P+ + AF++F+ EA+ A A
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 314 LNLAGTMLG 322
L+ + TM G
Sbjct: 76 LHGSQTMPG 84
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEA 307
+++ + Q T+E L F G+V +C + DP F F+ F D+A
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
>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 = 2.0, Method: Composition-based stats.
Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 256 RRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEAEGARAA 313
+ + V+ + Q +T+++ +LF G + C++ D L + F+ ++D + +A
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 314 LNLAGTMLGFYPVRVLPSKTAIAPV 338
L G L ++V ++ + A +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASI 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLR--FAFIEFTDEAEGARAALNL 316
+YV + +TE+ L +F G++ + + D ++ + FI F+D RA L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 317 AGTMLGFYPVRV 328
G L P+RV
Sbjct: 68 NGFELAGRPMRV 79
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLAG 318
V+V + +T E+L F G+VVD I P FAF+ F D+ + A +L G
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFI---PKPFRAFAFVTFADD----KVAQSLCG 66
Query: 319 TML 321
L
Sbjct: 67 EDL 69
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 6/83 (7%)
Query: 250 QREEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEG 309
Q E+ ++V V E +L +F G + + +I FAF+EF +
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESA 78
Query: 310 ARAALNLAGTMLGFYPVRVLPSK 332
A+A + G P+ V+ SK
Sbjct: 79 AKAIEEVHGKSFANQPLEVVYSK 101
>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 = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 10/71 (14%)
Query: 252 EEIIRRTVYVSDIDQQVTEEQLAALFVGCGQVVDC-----RICGDPNSVLRFAFIEFT-- 304
E I +YV+++ + +T++QL +F G +V ++ G P V AF+ +
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 65
Query: 305 DEAEGARAALN 315
+EA+ A +ALN
Sbjct: 66 EEAQEAISALN 76
>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 = 4.8, Method: Composition-based stats.
Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNL 316
+++ ++ ++ TE+++ +LF G+V++C I + + F+ D+ A NL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDI------IKNYGFVHIEDKTAAEDAIRNL 62
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 258 TVYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDPNSVLRFAFIEFTDEAEGARAALNLA 317
TVY I +T++ + F GQ+++ R+ + ++F+ F+ A A +++
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----YSFVRFSTHESAAHAIVSVN 82
Query: 318 GTMLGFYPVRVLPSK 332
GT + + V+ K
Sbjct: 83 GTTIEGHVVKCYWGK 97
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 259 VYVSDIDQQVTEEQLAALFVGCGQVVDCRICGDP--NSVLRFAFIEFTDEA 307
+++ + Q T+E L F G+V +C + DP F F+ F D+A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 53
>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: 346 TEDEREMCARTIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRI 397
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: 356 TIYCTNIDKKVTQADVKLFFESVCGEVYRLRLLGDYHHSTRIAFVEFVMAESAIAALNCS 415
T Y N+ Q D+ F+ + RL D +VEF +S AL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD 76
Query: 416 GVVLGSLPIRV 426
G +LG +RV
Sbjct: 77 GALLGDRSLRV 87
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 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,199,079
Number of Sequences: 62578
Number of extensions: 351765
Number of successful extensions: 830
Number of sequences better than 100.0: 70
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 776
Number of HSP's gapped (non-prelim): 87
length of query: 443
length of database: 14,973,337
effective HSP length: 102
effective length of query: 341
effective length of database: 8,590,381
effective search space: 2929319921
effective search space used: 2929319921
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)