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= 017897
(364 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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 8/81 (9%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQV----VDC-RICGDPNSVLRFAFVEFTDEEGARA 233
R++YV ++D T E+L F CG V + C + G P FA++EF+D+E R
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKESVRT 62
Query: 234 ALSLAGTMLGFYPVRVLPSKT 254
+L+L ++ ++V+P +T
Sbjct: 63 SLALDESLFRGRQIKVIPKRT 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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 175 EVIRRTVYVSDIDQQVTEEQLATLFLTCGQV----VDC-RICGDPNSVLRFAFVEFTDEE 229
E R++YV ++D T E+L F CG V + C + G P FA++EF+D+E
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKE 59
Query: 230 GARAALSLAGTMLGFYPVRVLPSKT 254
R +L+L ++ ++V+P +T
Sbjct: 60 SVRTSLALDESLFRGRQIKVIPKRT 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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 3/88 (3%)
Query: 267 SEDEREMCSRTIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGD--YQHSTRIAFVEFA 324
+E+++E+ R++Y N+D T D++ F S CG + R+ +L D H A++EFA
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS-CGSINRITILCDKFSGHPKGYAYIEFA 86
Query: 325 MAESAIAALNCSGAVLGSLPIRVSPSKT 352
S AA+ V I+V P +T
Sbjct: 87 ERNSVDAAVAMDETVFRGRTIKVLPKRT 114
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 52/99 (52%), Gaps = 8/99 (8%)
Query: 169 SNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQV----VDC-RICGDPNSVLRFAFV 223
S ++ E+ +R+VYV ++D T + L F +CG + + C + G P +A++
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG---YAYI 83
Query: 224 EFTDEEGARAALSLAGTMLGFYPVRVLPSKTAIAPVNPT 262
EF + AA+++ T+ ++VLP +T + ++ T
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISST 122
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 58/209 (27%), Positives = 95/209 (45%), Gaps = 21/209 (10%)
Query: 160 GKRRMNCRTSNAQQDEV--IRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSV 217
G ++M R S AQ+ I VYV I ++ E+ + F G + + D ++
Sbjct: 9 GGQQMG-RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTM 67
Query: 218 LR--FAFVEFTDEEGARAAL-SLAGTMLGFYPVRV-LPSKTAIAPVNPTFLPRSEDEREM 273
FAFVE+ E A+ AL + MLG ++V PS I P +E+ R
Sbjct: 68 KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN--IGQAQPIIDQLAEEARAF 125
Query: 274 CSRTIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGD---YQHSTRIAFVEFAMAES-- 328
IY ++ + ++ DIK FE+ G+++ L D +H F+E+ A+S
Sbjct: 126 --NRIYVASVHQDLSDDDIKSVFEA-FGKIKSATLARDPTTGKHKG-YGFIEYEKAQSSQ 181
Query: 329 -AIAALNCSGAVLGSLPIRVSPSKTPVRP 356
A++++N LG +RV + TP P
Sbjct: 182 DAVSSMNLFD--LGGQYLRVGKAVTPPMP 208
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALSLA 238
+YV+ + Q ++++ + ++F G++ + DP + + F+E+ + ++ A+S
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 239 GTM-LGFYPVRVLPSKTAIAPVNPTFLP 265
LG +RV A+ P P P
Sbjct: 188 NLFDLGGQYLRV---GKAVTPPMPLLTP 212
>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 = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 70/166 (42%), Gaps = 20/166 (12%)
Query: 180 TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEFTDEEGARAAL-S 236
++YV D+ VTE L F G ++ R+C D L +A+V F A AL +
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFF 296
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 77 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 121
Query: 297 E--SVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNCSGAVL 340
+ S G + +++ D S FV F E+A A+ +L
Sbjct: 122 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGML 167
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 166 CRTSNAQQDEVIRRT----VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFA 221
R +Q+D +R++ +++ ++D+ + + L F G ++ C++ D N +
Sbjct: 87 VRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYG 146
Query: 222 FVEFTDEEGARAALSLAGTML 242
FV F +E A A+ ML
Sbjct: 147 FVHFETQEAAERAIEKMNGML 167
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 51/88 (57%), Gaps = 5/88 (5%)
Query: 267 SEDEREMCSRTIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDY--QHSTRIAFVEFA 324
S +ER+ +RT++C + ++ D++ FF +V G+V+ +R++ D + S IA+VEF
Sbjct: 19 SPEERD--ARTVFCMQLAARIRPRDLEDFFSAV-GKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 325 MAESAIAALNCSGAVLGSLPIRVSPSKT 352
+S A+ +G L +PI V S+
Sbjct: 76 EIQSVPLAIGLTGQRLLGVPIIVQASQA 103
Score = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 2/78 (2%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
RTV+ + ++ L F G+V D RI D NS A+VEF + + A+
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 237 LAGTMLGFYPVRVLPSKT 254
L G L P+ V S+
Sbjct: 86 LTGQRLLGVPIIVQASQA 103
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 70/166 (42%), Gaps = 20/166 (12%)
Query: 180 TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEFTDEEGARAAL-S 236
++YV D+ VTE L F G ++ R+C D L +A+V F A AL +
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFF 296
+ ++ PVR++ S+ R R+ I+ N+DK + D K +
Sbjct: 72 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSI---DNKALY 116
Query: 297 E--SVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNCSGAVL 340
+ S G + +++ D S FV F E+A A+ +L
Sbjct: 117 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGML 162
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 167 RTSNAQQDEVIRRT----VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAF 222
R +Q+D +R++ +++ ++D+ + + L F G ++ C++ D N + F
Sbjct: 83 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 142
Query: 223 VEFTDEEGARAALSLAGTML 242
V F +E A A+ ML
Sbjct: 143 VHFETQEAAERAIEKMNGML 162
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 50/185 (27%), Positives = 83/185 (44%), Gaps = 16/185 (8%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL-SL 237
VYV I ++ E+ + F G + + D ++ FAFVE+ E A+ AL +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 238 AGTMLGFYPVRV-LPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFF 296
MLG ++V PS I P +E+ R IY ++ + ++ DIK F
Sbjct: 76 NSVMLGGRNIKVGRPSN--IGQAQPIIDQLAEEARAF--NRIYVASVHQDLSDDDIKSVF 131
Query: 297 ESVCGEVQRLRLLGDYQHSTR--IAFVEFAMAES---AIAALNCSGAVLGSLPIRVSPSK 351
E+ G+++ L D F+E+ A+S A++++N LG +RV +
Sbjct: 132 EAF-GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFD--LGGQYLRVGKAV 188
Query: 352 TPVRP 356
TP P
Sbjct: 189 TPPMP 193
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 6/88 (6%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALSLA 238
+YV+ + Q ++++ + ++F G++ C + DP + + F+E+ + ++ A+S
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 239 GTM-LGFYPVRVLPSKTAIAPVNPTFLP 265
LG +RV A+ P P P
Sbjct: 173 NLFDLGGQYLRV---GKAVTPPMPLLTP 197
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 73/177 (41%), Gaps = 18/177 (10%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSV-LRFAFVEFTDEEGARAAL-S 236
R +YV ++D+ +TE+ L F G + + +I D N+ + +AFVE+ A AL +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTI--YCTNIDKKVTQGDIKL 294
L G + + I +N F + + + + N+D + + K
Sbjct: 61 LNGKQI----------ENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 295 FFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNC-SGAVLGSLPIRVSPS 350
F + G V G S FV F + A A++ G L P+R++ +
Sbjct: 111 FPSYLSGHVMWDMQTG---SSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 31/200 (15%)
Query: 180 TVYVSDID-QQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALS-L 237
+ VS+++ ++VT + L LF G V +I + A V+ D A+ A+S L
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN---ALVQMADGNQAQLAMSHL 61
Query: 238 AGTMLGFYPVRVLPSKT-------------------AIAPVNPTFLPRSEDEREMC--SR 276
G L P+R+ SK +P++ P S++ + + S
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Query: 277 TIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAAL-NC 335
T++ +NI V++ D+K+ F S G V+ + +Q ++A ++ E A+ AL +
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF---FQKDRKMALIQMGSVEEAVQALIDL 178
Query: 336 SGAVLG-SLPIRVSPSKTPV 354
LG + +RVS SK+ +
Sbjct: 179 HNHDLGENHHLRVSFSKSTI 198
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 31/200 (15%)
Query: 180 TVYVSDID-QQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALS-L 237
+ VS+++ ++VT + L LF G V +I + A V+ D A+ A+S L
Sbjct: 36 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN---ALVQMADGNQAQLAMSHL 92
Query: 238 AGTMLGFYPVRVLPSKT-------------------AIAPVNPTFLPRSEDEREMC--SR 276
G L P+R+ SK +P++ P S++ + + S
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152
Query: 277 TIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAAL-NC 335
T++ +NI V++ D+K+ F S G V+ + +Q ++A ++ E A+ AL +
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF---FQKDRKMALIQMGSVEEAVQALIDL 209
Query: 336 SGAVLG-SLPIRVSPSKTPV 354
LG + +RVS SK+ +
Sbjct: 210 HNHDLGENHHLRVSFSKSTI 229
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 22/120 (18%)
Query: 205 VVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAGTMLGFYPVRVLPSKTAIAPVNPTFL 264
VVD RI +F +V+F E AL L G ++V ++ +
Sbjct: 39 VVDVRI----GMTRKFGYVDFESAEDLEKALELTG-------LKVFGNEIKLEK------ 81
Query: 265 PRSED-EREMCSRTIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEF 323
P+ +D ++E +RT+ N+ KVTQ ++K FE +RL+ S IA++EF
Sbjct: 82 PKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAA----EIRLVSKDGKSKGIAYIEF 137
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 48/171 (28%), Positives = 73/171 (42%), Gaps = 19/171 (11%)
Query: 183 VSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRF--AFVEFTDEEGARAALSLAGT 240
V+ + Q T+ +L LF G + CRI D + F AFV+FT E ++ A+
Sbjct: 19 VNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK---- 74
Query: 241 MLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFFESVC 300
+L VR K + A P E ++ +Y TN+ + +T + F
Sbjct: 75 VLNGITVRNKRLKVSYA------RPGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYG 125
Query: 301 GEVQRLRLLGDYQHSTR-IAFVEFAM---AESAIAALNCSGAVLGSLPIRV 347
VQ+ L R +AFV + A+ AI+ALN GS P+ V
Sbjct: 126 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 155 NGYSQGKRRMNCRTSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDC-----R 209
NG + +R+ + + + +YV+++ + +T++QL T+F G +V +
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 136
Query: 210 ICGDPNSVLRFAFVEFTDEEGARAALS 236
+ G P V AFV + E A+ A+S
Sbjct: 137 LTGRPRGV---AFVRYNKREEAQEAIS 160
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 80/187 (42%), Gaps = 29/187 (15%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTDEEGARAAL 235
+ + V+ + Q +T+++ +LF + G + C++ D L + FV ++D A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 236 -SLAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGD 291
+L G L ++V PS +I N +Y + + K ++Q +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMSQKE 106
Query: 292 IKLFFESVCGEVQRLRLLGDYQH--STRIAFVEFAM---AESAIAALNCSGAVLGSLPIR 346
++ F S G + R+L D S + F+ F AE AI LN + + PI
Sbjct: 107 MEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPIT 165
Query: 347 VSPSKTP 353
V + P
Sbjct: 166 VKFANNP 172
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 76/176 (43%), Gaps = 29/176 (16%)
Query: 183 VSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTDEEGARAAL-SLAG 239
V+ + Q +T+E+ +LF + G++ C++ D L + FV + D + A A+ +L G
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66
Query: 240 TMLGFYPVRV---LPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFF 296
L ++V PS +I N +Y + + K +TQ +++ F
Sbjct: 67 LRLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMTQKELEQLF 109
Query: 297 ESVCGEVQRLRLLGDYQH--STRIAFVEF---AMAESAIAALNCSGAVLGSLPIRV 347
S G + R+L D S + F+ F AE AI LN + PI V
Sbjct: 110 -SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
>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: Composition-based stats.
Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 180 TVYVSDIDQQVTEEQLATLFLTCGQVVDC-----RICGDPNSVLRFAFVEFTDEEGARAA 234
TVYV +D++V+E L LFL G VV+ R+ G + FVEF EE A A
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG---YGFVEFLSEEDADYA 73
Query: 235 LSLAGTMLGFY--PVRV 249
+ + M+ Y P+RV
Sbjct: 74 IKIM-DMIKLYGKPIRV 89
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/181 (25%), Positives = 79/181 (43%), Gaps = 29/181 (16%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEF-TDEEGARAA 234
R + V+ + Q +T+++L +LF + G+V ++ D L + FV + T ++ RA
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 235 LSLAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGD 291
+L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 292 IKLFFESVCGEVQRLRLLGDYQH--STRIAFVEF---AMAESAIAALNCSGAVLGSLPIR 346
++ F S G + R+L D S +AF+ F + AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 347 V 347
V
Sbjct: 164 V 164
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 175 EVIR-RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGA 231
EVI+ +Y+S + + +T++ + +F G++++ R+ D + L AF+ F A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 232 RAALS 236
A++
Sbjct: 144 EEAIT 148
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/181 (25%), Positives = 79/181 (43%), Gaps = 29/181 (16%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEF-TDEEGARAA 234
R + V+ + Q +T+++L +LF + G+V ++ D L + FV + T ++ RA
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 235 LSLAGTMLGFYPVRV---LPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGD 291
+L G L ++V PS I N +Y + + + +TQ D
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDAN-----------------LYISGLPRTMTQKD 104
Query: 292 IKLFFESVCGEVQRLRLLGDYQH--STRIAFVEF---AMAESAIAALNCSGAVLGSLPIR 346
++ F S G + R+L D S +AF+ F + AE AI + N S PI
Sbjct: 105 VEDMF-SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPIT 163
Query: 347 V 347
V
Sbjct: 164 V 164
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 175 EVIR-RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGA 231
EVI+ +Y+S + + +T++ + +F G++++ R+ D + L AF+ F A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 232 RAALS 236
A++
Sbjct: 144 EEAIT 148
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNS--VLRFAFVEFTD-EEGARAAL 235
R VY+ I TEEQ+ L G V++ ++ DP + +AF+EF D E A A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 236 SLAGTMLG 243
+L G LG
Sbjct: 65 NLNGYQLG 72
>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 = 0.005, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRIC-----GDPNSVLRFAFVEFTDEEGARA 233
R+V+V +I + TEEQL +F G VV R+ G P + F E+ D+E A +
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG---YGFCEYQDQETALS 65
Query: 234 AL 235
A+
Sbjct: 66 AM 67
>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 = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTD-EEGARAAL 235
R VY+ I TEEQ+ L G V++ ++ DP + +AF+EF D E A A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 236 SLAGTMLG 243
+L G LG
Sbjct: 64 NLNGYQLG 71
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTD-EEGARAAL 235
R VY+ I TEEQ+ L G V++ ++ DP + +AF+EF D E A A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 236 SLAGTMLG 243
+L G LG
Sbjct: 63 NLNGYQLG 70
>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 = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 12/104 (11%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGA-RAALSLAG 239
+++ ++D+ + + L F G ++ C++ D N + FV F +E A RA + G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 240 TMLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNI 283
+L V V F R E E E+ +R TN+
Sbjct: 68 MLLNDRKVFV-----------GRFKSRKEREAELGARAKEFTNV 100
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 169 SNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR-FAFVEFTD 227
+NA +D R +++ I ++ TE + +F + GQ+ +CRI P+ + R AFV FT
Sbjct: 90 NNAVED----RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT 145
Query: 228 EEGARAALSL---AGTMLG 243
A+ A+ A TM G
Sbjct: 146 RAMAQTAIKAMHQAQTMEG 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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 169 SNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR-FAFVEFTD 227
+NA +D R +++ I ++ TE + +F + GQ+ +CRI P+ + R AFV FT
Sbjct: 102 NNAVED----RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT 157
Query: 228 EEGARAALSL---AGTMLG 243
A+ A+ A TM G
Sbjct: 158 RAMAQTAIKAMHQAQTMEG 176
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRIC----GDPNSVLRFAFVEFTDEEGARAA 234
RTV+V +++ +V EE L LFL G + IC G P S F FV F E A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS---FGFVCFKHPESVSYA 73
Query: 235 LSL 237
++L
Sbjct: 74 IAL 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 = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR-FAFVEFTDEEGARAAL 235
R +++ I ++ TE + F + GQ+ +CRI P+ + R AFV FT A+ A+
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 75 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 122
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +FE G+++ + ++ D + AFV F
Sbjct: 123 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 154
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 30/62 (48%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAGT 240
+++ ++D+ + + L F G ++ C++ D N + FV F +E A A+
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 241 ML 242
ML
Sbjct: 74 ML 75
>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 = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 74 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +FE G+++ + ++ D + AFV F
Sbjct: 122 RDYFEQY-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 = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 73 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 120
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +FE G+++ + ++ D + AFV F
Sbjct: 121 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 152
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 74 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +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 = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 53/120 (44%), Gaps = 22/120 (18%)
Query: 205 VVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAGTMLGFYPVRVLPSKTAIAPVNPTFL 264
VVD R + +F +V+F E AL L G ++V ++ +
Sbjct: 45 VVDVRTGTNR----KFGYVDFESAEDLEKALELTG-------LKVFGNEIKLEK------ 87
Query: 265 PRSEDEREM-CSRTIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEF 323
P+ D +++ +RT+ N+ +T+ ++K FE +RL+ S IA++EF
Sbjct: 88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL----EIRLVSQDGKSKGIAYIEF 143
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 72 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 119
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +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 = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 21/153 (13%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALS 236
R +++ + + T+E L + F G + DC + DPN+ F FV + E AA++
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 237 LAGTMLGFYPVRVLPSKTAIAPVNPTFLPRSEDER----EMCSRTIYCTNIDKKVTQGDI 292
P K V P ED + + + I+ I + + +
Sbjct: 67 ------------ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 114
Query: 293 KLFFESVCGEVQRLRLLGDYQHSTR--IAFVEF 323
+ +FE G+++ + ++ D + AFV F
Sbjct: 115 RDYFEQY-GKIEVIEIMTDRGSGKKRGFAFVTF 146
>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 = 0.045, Method: Compositional matrix adjust.
Identities = 30/151 (19%), Positives = 58/151 (38%), Gaps = 22/151 (14%)
Query: 180 TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAG 239
TV V ++ + + ++ F CG ++ + RFA +EF +GA AA++
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102
Query: 240 TMLGFYPVRVLPSKTAIAPVNPTFLPRSEDEREMCSRTIYCTNIDKKVTQGDIKLFFESV 299
++G + V + T++ TN TQ +I+ + +
Sbjct: 103 KVVGQNEIIV---------------------SHLTECTLWXTNFPPSYTQRNIRDLLQDI 141
Query: 300 CGEVQRLRLLG-DYQHSTRIAFVEFAMAESA 329
+RL + S R A+++ E A
Sbjct: 142 NVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Score = 34.3 bits (77), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 277 TIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNCS 336
T+ N+ K Q + +F+ CG + + + + + R A +EFA + A+AA+ +
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 337 GAVLGSLPIRVS 348
V+G I VS
Sbjct: 102 HKVVGQNEIIVS 113
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.4 bits (80), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 155 NGYSQGKRRMNCRTSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDC-----R 209
NG + +R+ + + + +YV+++ + +T++QL T+F G +V +
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125
Query: 210 ICGDPNSVLRFAFVEFTDEEGARAALS 236
+ G P V AFV + E A+ A+S
Sbjct: 126 LTGRPRGV---AFVRYNKREEAQEAIS 149
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 31/64 (48%)
Query: 180 TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAG 239
TV V ++ + + ++ F CG ++ + RFA +EF +GA AA++
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 240 TMLG 243
++G
Sbjct: 66 KVVG 69
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 277 TIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNCS 336
T+ N+ K Q + +F+ CG + + + + + R A +EFA + A+AA+ +
Sbjct: 6 TVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 64
Query: 337 GAVLGSLPIRVS 348
V+G I VS
Sbjct: 65 HKVVGQNEIIVS 76
>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 = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 9/68 (13%)
Query: 175 EVIRRT-VYVSDIDQQVTEEQLATLFLTCGQVVDC-----RICGDPNSVLRFAFVEFTDE 228
E I+ T +YV+++ + +T++QL T+F G +V ++ G P V AFV +
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV---AFVRYNKR 65
Query: 229 EGARAALS 236
E A+ A+S
Sbjct: 66 EEAQEAIS 73
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTD 227
++V +D T+E L + F G+VVDC I D N F FV+F D
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 6/88 (6%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAALSLA 238
+YV+ + Q ++++ + ++F G++ C + DP + + F+E+ + ++ A+S
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 239 GTM-LGFYPVRVLPSKTAIAPVNPTFLP 265
LG +RV A+ P P P
Sbjct: 172 NLFDLGGQYLRV---GKAVTPPXPLLTP 196
>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 = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 170 NAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTD 227
NA ++E +V + +++ L F G+VVDC I DPN+ F F+ F D
Sbjct: 3 NASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Query: 228 EEGARAAL 235
L
Sbjct: 63 AASVEKVL 70
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 30/71 (42%)
Query: 277 TIYCTNIDKKVTQGDIKLFFESVCGEVQRLRLLGDYQHSTRIAFVEFAMAESAIAALNCS 336
T Y N+ QGDI F+ + RL D +VEF +S AL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD 76
Query: 337 GAVLGSLPIRV 347
GA+LG +RV
Sbjct: 77 GALLGDRSLRV 87
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALS 236
++V ++ T ++L +LF G+V++C + D +AFV E A+AA++
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD------YAFVHMEKEADAKAAIA 61
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 168 TSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEF 225
+S +D+ RT+YV ++ + VTE + LF G C++ + S + FVEF
Sbjct: 5 SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF 62
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFT 226
R +++ + + TEE L + G++ DC + DP S F FV F+
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAALSLAGT 240
V+V + +T E+L F G+VVD I P FAFV F D+ + A SL G
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFI---PKPFRAFAFVTFADD---KVAQSLCGE 67
Query: 241 ML 242
L
Sbjct: 68 DL 69
>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 = 0.31, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 6/86 (6%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSV-----LRFAFVEFTDEEGARAAL 235
+++ +++ TEE L +F G + C I N + F FVE+ E A+ AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 236 -SLAGTMLGFYPVRVLPSKTAIAPVN 260
L G + + + V S+ A P +
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPAS 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.7 bits (73), Expect = 0.31, Method: Composition-based stats.
Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 4/99 (4%)
Query: 168 TSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEF 225
+S ++D V+V D+ ++T E + + F G++ D R+ D + FV F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 226 TDE-EGARAALSLAGTMLGFYPVRV-LPSKTAIAPVNPT 262
++ + A + + G LG +R ++ AP P+
Sbjct: 65 YNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPSGPS 103
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 168 TSNAQQDEVIRRTV---YVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVE 224
+S + D + R V YV ++D + +E+L F G + ++ + F FV
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVC 61
Query: 225 FTD-EEGARAALSLAGTMLGFYPVRV 249
F+ EE +A + G ++ P+ V
Sbjct: 62 FSSPEEATKAVTEMNGRIVATKPLYV 87
>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 = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL 235
+R +YV + ++V ++ L F+ G + D +I D + FAFVEF E A AA+
Sbjct: 2 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL 235
+R +YV + ++V ++ L F+ G + D +I D + FAFVEF E A AA+
Sbjct: 5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
>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 = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL 235
+R +YV + ++V ++ L F+ G + D +I D + FAFVEF E A AA+
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
>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 = 32.0 bits (71), Expect = 0.52, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 167 RTSNAQQDEVIRR--TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP-NSVLRFAFV 223
R N +Q++++++ T+YV ++ TEEQ+ LF G + + D + F FV
Sbjct: 5 RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFV 64
Query: 224 EFTDEEGARAALS-LAGTML 242
E+ A A+ + GT L
Sbjct: 65 EYYSRADAENAMRYINGTRL 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL 235
+R +YV + ++V ++ L F+ G + D +I D + FAFVEF E A AA+
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 158 SQGKRRMNCRTSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSV 217
S G + + A+Q E +Y+S++ + E++L + GQV+ RI D +
Sbjct: 5 SSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64
Query: 218 LR---FAFVEFTDE 228
R FA +E T++
Sbjct: 65 SRGVGFARMESTEK 78
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.0 bits (71), Expect = 0.58, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGARAAL 235
+R +YV + ++V ++ L F+ G + D +I D + FAFVEF E A AA+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 301 GEVQRLRLLGDYQHSTR--IAFVEFAMAESAIAAL-NCSGAVLGSLPIRVSPSKTPVRPR 357
G++ +++ DY+ AFVEF +AE A AA+ N + + L IRV+ +K P+R +
Sbjct: 37 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK-PMRIK 95
Query: 358 APRP 361
P
Sbjct: 96 ESGP 99
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 32.0 bits (71), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSV--LRFAFVEFTDEEGARAALS 236
R +YV ++ T EQ+ LF G+V + ++ D + F FVE +E + A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 237 LAGT 240
L T
Sbjct: 62 LDNT 65
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 162 RRMNCRTSNAQQDEVIRR--TVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSV 217
R + R N +Q++++++ T+YV ++ TEEQ+ LF G + + D +
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80
Query: 218 LRFAFVEFTDEEGARAALS-LAGTML 242
F FVE+ A A+ + GT L
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRL 106
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 31.2 bits (69), Expect = 0.90, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTDEEGARAALS 236
+++ + Q T+E L F G+V +C + DP F FV F D+ G L+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 169 SNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNS--VLRFAFVEFT 226
+N Q+ +YV + +TE+ L +F G++ ++ D + + F+ F+
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 227 DEEGARAAL-SLAGTMLGFYPVRV 249
D E A+ AL L G L P++V
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKV 100
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 169 SNAQQDEVIRRTVYVSDIDQQ-VTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTD 227
+N + I V++ +++ V + + T+F G+V C + +AFV++++
Sbjct: 18 TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG------YAFVQYSN 71
Query: 228 EEGARAAL 235
E ARAA+
Sbjct: 72 ERHARAAV 79
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTDEEGARAALS 236
+++ + Q T+E L F G+V +C + DP F FV F D+ G L+
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR-FAFVEFTDEEGARAAL 235
R ++V +++Q +EE + LF G + +C + P+ + AFV+F+ A+AA+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAI 73
>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 = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 168 TSNAQQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEF 225
+S ++D V+V D+ ++T E + F G++ D R+ D + FV F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 226 TDEEGARAAL-SLAGTMLGFYPVR 248
++ A A+ + G LG +R
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQIR 88
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 13/55 (23%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 181 VYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGARAAL 235
+++ ++ ++ TE+++ +LF G+V++C I + + FV D+ A A+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDI------IKNYGFVHIEDKTAAEDAI 59
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRF-AFVEFTDEEGARAALSL 237
R ++V + +Q T+E + +F G + +C + P+ + AFV+F A+AA++
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINT 72
Query: 238 AGTMLGFYPVRVLPSKTA 255
+ R LP ++
Sbjct: 73 ------LHSSRTLPGASS 84
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 26/104 (25%), Positives = 48/104 (46%), Gaps = 19/104 (18%)
Query: 140 GTANTNGHTTTRRKRNGYSQGKRRMNCRTSNAQQDEVIRRTVYVSDIDQQVTEEQLATLF 199
G++ ++G+T R + +Q + NC TVY I +T++ + F
Sbjct: 1 GSSGSSGNTKQLRFEDVVNQSSPK-NC-------------TVYCGGIASGLTDQLMRQTF 46
Query: 200 LTCGQVVDCRICGDPNSVLRFAFVEF-TDEEGARAALSLAGTML 242
GQ+++ R+ + ++FV F T E A A +S+ GT +
Sbjct: 47 SPFGQIMEIRVFPEKG----YSFVRFSTHESAAHAIVSVNGTTI 86
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 19/85 (22%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDP--NSVLRFAFVEFTDEEGARAAL 235
+ + V+ + Q +T+++ +LF + G + C++ D L + FV ++D A A+
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 236 -SLAGTMLGFYPVRVLPSKTAIAPV 259
+L G L ++V ++ + A +
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASI 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.5 bits (62), Expect = 6.4, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 179 RTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGD--PNSVLRFAFVEFTDEEGARAA 234
+T++V + + TEE L F V RI D S F FV+F EE A+AA
Sbjct: 16 KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 28.5 bits (62), Expect = 6.5, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 178 RRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLR--FAFVEFTDEEGAR 232
+ TVYVS++ +T L +F G+VV I D ++ AF+ F D++ A+
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.1 bits (61), Expect = 8.1, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 172 QQDEVIRRTVYVSDIDQQVTEEQLATLFLTCGQVVDCRICGDPNSVLRFAFVEFTDEEGA 231
Q+ E+ ++V V E +L +F G + + +I FAFVEF + E A
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------FAFVEFEEAESA 78
Query: 232 RAAL-SLAGTMLGFYPVRVLPSK 253
A+ + G P+ V+ SK
Sbjct: 79 AKAIEEVHGKSFANQPLEVVYSK 101
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
0.319 0.132 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,454,927
Number of Sequences: 62578
Number of extensions: 291903
Number of successful extensions: 659
Number of sequences better than 100.0: 76
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 99
length of query: 364
length of database: 14,973,337
effective HSP length: 100
effective length of query: 264
effective length of database: 8,715,537
effective search space: 2300901768
effective search space used: 2300901768
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: 52 (24.6 bits)