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= 008162
(575 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 = 168 bits (425), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 77/120 (64%), Positives = 99/120 (82%), Gaps = 1/120 (0%)
Query: 5 SSAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSF 64
+ A RALD +NF + K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+F
Sbjct: 63 ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 122
Query: 65 GNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 124
GNILSCK+ D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F ++ERE
Sbjct: 123 GNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181
Score = 102 bits (253), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 60/187 (32%), Positives = 104/187 (55%), Gaps = 6/187 (3%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 90
+PS ++++ +L + L++ FS G ILS ++ D + +S G+ +V F+
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 91 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 150
A+ A+D +N +I K V + +R+ K+ N+F+KNLD+S ++ L
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 151 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 210
F +G I S V+ D +G SK +GFV+FE + A +A+E +NG +DR+ +VG+ + +
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Query: 211 SEREQEL 217
ERE EL
Sbjct: 177 KEREAEL 183
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 69/194 (35%), Positives = 106/194 (54%), Gaps = 22/194 (11%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 192 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 249
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 72 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 113
Query: 250 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 309
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Query: 310 AQRKEERRARLQAQ 323
+ ++ER A L A+
Sbjct: 173 FKSRKEREAELGAR 186
>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 = 168 bits (425), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 77/120 (64%), Positives = 99/120 (82%), Gaps = 1/120 (0%)
Query: 5 SSAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSF 64
+ A RALD +NF + K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+F
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 65 GNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 124
GNILSCK+ D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F ++ERE
Sbjct: 128 GNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186
Score = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 62/204 (30%), Positives = 110/204 (53%), Gaps = 6/204 (2%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 90
+PS ++++ +L + L++ FS G ILS ++ D + +S G+ +V F+
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 91 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 150
A+ A+D +N +I K V + +R+ K+ N+F+KNLD+S ++ L
Sbjct: 67 PADAERALDTMNFDVIKGKPVRI----MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 151 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 210
F +G I S V+ D +G SK +GFV+FE + A +A+E +NG +DR+ +VG+ + +
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 211 SEREQELKGQFEQAMKETVDKFQG 234
ERE EL + ++ V + G
Sbjct: 182 KEREAELGARAKEFYPYDVPDYAG 205
Score = 92.8 bits (229), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 22/200 (11%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 192 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 249
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 77 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 118
Query: 250 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 309
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 310 AQRKEERRARLQAQFSQMRP 329
+ ++ER A L A+ + P
Sbjct: 178 FKSRKEREAELGARAKEFYP 197
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 139 bits (350), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 64/93 (68%), Positives = 81/93 (87%), Gaps = 1/93 (1%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENK 91
DPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+ D +G SKG+GFV FE +
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 92 ESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 124
E+A+ AI+K+NGML+ND++VFVG F ++ERE
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 94
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 39/83 (46%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 295
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 296 NGKMIVSKPLYVAVAQRKEERRA 318
NG ++ + ++V + ++ER A
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREA 94
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 57/89 (64%), Gaps = 1/89 (1%)
Query: 128 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
K+ N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQE 216
A+E +NG +DR+ +VG+ + + ERE E
Sbjct: 67 AIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
>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 = 134 bits (338), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 65/108 (60%), Positives = 86/108 (79%), Gaps = 3/108 (2%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
G+GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+ D +G SKG+GFV FE +E+A+ AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 99 DKLNGMLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTT 144
+K+NGML+ND++VFVG F ++ERE A +F NV++KN +T
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/97 (43%), Positives = 62/97 (63%), Gaps = 1/97 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 295
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 296 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAM 332
NG ++ + ++V + ++ER A L A+ + V +
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYI 102
Score = 75.5 bits (184), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 66/111 (59%), Gaps = 11/111 (9%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +A+E +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 193 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 243
NG +DR+ +VG+ + + ERE EL + ++ N+YIKN G
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFT----------NVYIKNFG 106
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 125 bits (313), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 63/79 (79%), Positives = 70/79 (88%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLESP+
Sbjct: 6 PIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPD 65
Query: 537 ALKAKVAEAMEVLRSVAQQ 555
ALKAKVAEAMEVLRS Q
Sbjct: 66 ALKAKVAEAMEVLRSAQQH 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 119 bits (298), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 75/90 (83%), Gaps = 1/90 (1%)
Query: 229 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 288
+ ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM + G SKG GFV FS+PEEA
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68
Query: 289 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 318
++A+ EMNG+++ +KPLYVA+AQRKEER++
Sbjct: 69 TKAVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 41/82 (50%), Positives = 56/82 (68%), Gaps = 1/82 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
N++VKNLD+ DE L+K F +GTITSA VM +G G+SK FGFV F + ++A KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 193 NGKKFDDREWYVGKAQKKSERE 214
NG+ + YV AQ+K ER+
Sbjct: 76 NGRIVATKPLYVALAQRKEERQ 97
Score = 75.9 bits (185), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
N+++KNLD ID + L FS FG I S K+ +G G+SKGFGFV F + E A A+ ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 102 NGMLINDKQVFVGHFLRKQERET 124
NG ++ K ++V RK+ER++
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 85.9 bits (211), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 24/178 (13%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
LNG K + V A+ S + NLY+ L ++ +++
Sbjct: 66 LNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKEM 107
Query: 252 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 308
++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+ KPL A
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 47/157 (29%), Positives = 88/157 (56%), Gaps = 8/157 (5%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+ + L +++ F S G+I SCK+ D +GQS G+GFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 101 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TIT 159
LNG+ + K + V + R + A + N++V L ++ + ++++++F +YG IT
Sbjct: 66 LNGLKLQTKTIKVSY-----ARPSSA-SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 160 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 196
S +++ G S+ GF+ F+ +A +A++ LNG+K
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 85.5 bits (210), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 53/180 (29%), Positives = 96/180 (53%), Gaps = 17/180 (9%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
++V NLD++ T++ LK+ F G I + +M D + K+ + FV + + DA A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 194 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 253
GK+ ++ + A F+ + D F NL++ +L ++DDE L+
Sbjct: 63 GKQIENNIVKINWA-------------FQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 254 LFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 312
F +F + S VM D +G S+G GFV+F++ ++A A+ M G+ + +PL + A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 85/168 (50%), Gaps = 5/168 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+++ NLDK+I L F G I + KI D + ++ + FV++ A A+ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 162
G I + V + + Q+ + F N+FV +L+ + DE L+ F ++ + S
Sbjct: 63 GKQIENNIVKINWAFQSQQSSS---DDTF-NLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 163 VMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK 209
VM D G S+ +GFV+F + DDA A++++ G+ + R + A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
>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 = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 49/157 (31%), Positives = 90/157 (57%), Gaps = 8/157 (5%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+ + L +++ + F S G I SCK+ D +GQS G+GFV + + + A+ AI+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 101 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TIT 159
LNG+ + K + V + R + A + N++V L ++ T ++L+++F +YG IT
Sbjct: 64 LNGLRLQTKTIKVSY-----ARPSSA-SIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 160 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 196
S +++ G S+ GF+ F+ +A +A++ LNG+K
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 50/169 (29%), Positives = 87/169 (51%), Gaps = 20/169 (11%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 190
N+ V L ++ T E+ + +FG G I S ++RD G+S +GFVN+ + DA KA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 191 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 250
LNG + + V A+ S + NLY+ L ++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 251 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK 298
L++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ E+ + LF G I SCK++RD +G S G GFV + P++A +A+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + +K + V+ A+
Sbjct: 64 LNGLRLQTKTIKVSYAR 80
>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 = 82.4 bits (202), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 92/172 (53%), Gaps = 7/172 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+++ ++ + + F+ FG I S ++ D + + KGF FV++E E+AQ A++++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTK-----FNNVFVKNLDESTTDEDLKKIFGEYG 156
N +++ + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 157 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 207
I SA + RD GK K +GF+ +E A + AV ++N + VGKA
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 62.4 bits (150), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 120 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 178
Q + +AI ++ V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 20 QRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 179 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 237
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 128
Query: 238 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 296
Y+ ++ + D+ +K +F FG I S + RDP +G KG GF+ + + + A++ MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 295
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 296 NGKMI------VSKPLYVAVAQ 311
N M+ V +P + AQ
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQ 112
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 252 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 297
+++FS FG I + +V+ D +G+S+G F+ F EA A+ NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 83/160 (51%), Gaps = 8/160 (5%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 97
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 98 IDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
I+ LNG+ + K + V + + E + K N+++ L + T +D++ +F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY--ARPSSEVI----KDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKK 196
I ++ V+ D G S+ F+ F+ +A +A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 62.0 bits (149), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 56/98 (57%), Gaps = 3/98 (3%)
Query: 7 AARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN 66
A RA++ LN L +K+I++ Y+ PS N++I L +++ K + D FS FG
Sbjct: 57 AERAINTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 67 ILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 103
I++ ++ D +G S+G F++F+ + A+ AI NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 295 MNGKMIVSKPLYVAVAQRKEE 315
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>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 = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 252 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 297
+++FS FG I + +V+ D +G+S+G F+ F EA A+ NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 83/160 (51%), Gaps = 8/160 (5%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 97
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 98 IDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
I+ LNG+ + K + V + + E + K N+++ L + T +D++ +F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY--ARPSSEVI----KDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKK 196
I ++ V+ D G S+ F+ F+ +A +A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 62.4 bits (150), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 56/98 (57%), Gaps = 3/98 (3%)
Query: 7 AARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN 66
A RA++ LN L +K+I++ Y+ PS N++I L +++ K + D FS FG
Sbjct: 57 AERAINTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 67 ILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 103
I++ ++ D +G S+G F++F+ + A+ AI NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 295 MNGKMIVSKPLYVAVAQRKEE 315
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/69 (60%), Positives = 52/69 (75%)
Query: 481 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 540
LST LAN +PEQQ+ +LGE LY + + AAAKVTGMLLEMD E+L+LL++P L A
Sbjct: 11 LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 541 KVAEAMEVL 549
KV EA+EVL
Sbjct: 71 KVQEALEVL 79
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 80.9 bits (198), Expect = 2e-15, Method: Composition-based stats.
Identities = 48/154 (31%), Positives = 83/154 (53%), Gaps = 8/154 (5%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
N+ + L + + + L+ F + G I +C+I D +G S G+ FV F ++ +Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 101 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 160
LNG+ + +K++ V + E K N++V NL + TD+ L IFG+YG+I
Sbjct: 65 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 161 AVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 193
++RD G+ + FV + ++A +A+ ALN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 76.3 bits (186), Expect = 5e-14, Method: Composition-based stats.
Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 65 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 252 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 308
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 309 VA 310
+A
Sbjct: 167 LA 168
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 30/100 (30%), Positives = 53/100 (53%), Gaps = 3/100 (3%)
Query: 7 AARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN 66
+ RA+ VLN + NK +++ Y+ P N+++ NL ++I L F +G+
Sbjct: 58 SQRAIKVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 67 ILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 105
I+ I D +G+ +G FV++ +E AQ AI LN ++
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 52 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 109
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 110 SLRSKVDEAVAVLQA 124
>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 = 80.5 bits (197), Expect = 3e-15, Method: Composition-based stats.
Identities = 53/164 (32%), Positives = 87/164 (53%), Gaps = 11/164 (6%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 90
DP R S T N+ + L + + L+ F + G I +C+I D +G S G+ FV F +
Sbjct: 9 DP--RASNT-NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTS 65
Query: 91 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 150
+ +Q AI LNG+ + +K++ V + E K N++V NL + TD+ L
Sbjct: 66 EXDSQRAIKVLNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDT 119
Query: 151 IFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 193
IFG+YG+I ++RD G+ + FV + ++A +A+ ALN
Sbjct: 120 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 73.9 bits (180), Expect = 2e-13, Method: Composition-based stats.
Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
N+ V L + TD +L +F G I + + RD G S + FV+F + D+ +A++
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 76 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 252 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 308
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 309 VAQ 311
+A+
Sbjct: 178 LAE 180
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 30/100 (30%), Positives = 53/100 (53%), Gaps = 3/100 (3%)
Query: 7 AARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN 66
+ RA+ VLN + NK +++ Y+ P N+++ NL ++I L F +G+
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 126
Query: 67 ILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 105
I+ I D +G+ +G FV++ +E AQ AI LN ++
Sbjct: 127 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip1
Length = 98
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>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 = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 91/172 (52%), Gaps = 7/172 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+++ ++ + + F+ FG I S ++ D + + KGF FV++E E+AQ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 156
N +++ + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 157 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 207
I S + RD GK K +GF+ +E A + AV ++N + VGKA
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 120 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 178
Q + +AI + V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 5 QRQRALAIMCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 61
Query: 179 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 237
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 62 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 113
Query: 238 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 296
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 37.0 bits (84), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 295
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 296 NGKMI------VSKPLYVAVAQ 311
N M+ V +P + AQ
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQ 97
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related Protein
4 (Larp4)
Length = 88
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 4 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 61
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 62 SLRSKVDEAVAVLQA 76
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 477 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 536
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 5 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 62
Query: 537 ALKAKVAEAMEVLRS 551
+L++KV EA+ VL++
Sbjct: 63 SLRSKVDEAVAVLQA 77
>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
Length = 80
Score = 78.6 bits (192), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 477 PITALSTA-LANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESP 535
P+ +L+ + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESP
Sbjct: 2 PLGSLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 61
Query: 536 EALKAKVAEAMEVLRS 551
E+L++KV EA+ VL++
Sbjct: 62 ESLRSKVDEAVAVLQA 77
>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 = 75.1 bits (183), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 87/172 (50%), Gaps = 7/172 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+++ ++ + + F+ FG I S + D + + KGF FV++E E+AQ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 156
N + + + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 157 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 207
I S + RD GK K +GF+ +E A + AV + N + VGKA
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 14/180 (7%)
Query: 120 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 178
Q + +AI + V+V ++ ++ +++ F +G I S D K K F FV
Sbjct: 4 QRQRALAIXCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVE 60
Query: 179 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 237
+E + A A+E N R VG+ GQ + + + ++ + N +
Sbjct: 61 YEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 112
Query: 238 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 296
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 72.4 bits (176), Expect = 7e-13, Method: Composition-based stats.
Identities = 45/162 (27%), Positives = 87/162 (53%), Gaps = 28/162 (17%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE---NADDAAKAV 189
+F+ L+ TT+++L++ FG+YGT+T +M+D G+S+ FGF++FE + D+ K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 190 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 249
L+GK D + +A + E+++ K +++ +G + +
Sbjct: 66 HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 250 KLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 290
+ +E FS++GTI ++M D +G S+G GFV + + + R
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Score = 65.1 bits (157), Expect = 1e-10, Method: Composition-based stats.
Identities = 49/176 (27%), Positives = 88/176 (50%), Gaps = 23/176 (13%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK- 100
+FI L+ L + F +G + KI D +G+S+GFGF+ FE S +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 101 --LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTI 158
L+G +I+ K+ + + E++ K +FV + ++ ++ F ++GTI
Sbjct: 66 HILDGKVIDPKRA-----IPRDEQD------KTGKIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 159 TSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKK---FDDREWYVGKAQKK 210
A +M D D G+S+ FGFV +++AD AV+ + K F DR+ + +A+ +
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSAD----AVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP---EEA 288
+ ++I L ++ L+E F ++GT+T K+M+DP +G S+G GF++F P +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 289 SRALAEMNGKMIVSK 303
+ ++GK+I K
Sbjct: 62 VKTQHILDGKVIDPK 76
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 91
P + TG IF+ + + K + FS +G I+ ++ D +GQS+GFGFV +++
Sbjct: 80 PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139
Query: 92 ES 93
++
Sbjct: 140 DA 141
>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|B Chain B, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|C Chain C, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|D Chain D, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
Length = 98
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 58/83 (69%)
Query: 479 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEAL 538
T ++ LA+A P++Q+ LGE L+PL++ A K+TG LLE+D +E+L+ LESPE+L
Sbjct: 6 TLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESL 65
Query: 539 KAKVAEAMEVLRSVAQQQANNPA 561
++KV EA+ VL++ ++A A
Sbjct: 66 RSKVDEAVAVLQAHQAKEATQKA 88
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 65.5 bits (158), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 190
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 191 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 245
AL+ K L G Q + A E + + L+I +
Sbjct: 78 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 118
Query: 246 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 302
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ S
Sbjct: 119 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Query: 303 KPLYVAVA 310
P+ V A
Sbjct: 179 SPMVVKFA 186
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+FI + K + FSSFG I C+I G S+G FV F + AQ AI ++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPE---E 287
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 288 ASRALAEM 295
A AL M
Sbjct: 75 AQNALHNM 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 65.5 bits (158), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 54/87 (62%), Gaps = 2/87 (2%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIATD-GSGQSKGFGFVQFENKESAQ 95
SG+ IFI NLD ID K L+DTFS+FG IL KI D +G SKG+ F+ F + +++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 96 NAIDKLNGMLINDKQVFVGHFLRKQER 122
AI+ +NG + ++ + V + +K +
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSK 89
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 52/82 (63%), Gaps = 2/82 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
++I NL ID++ L + FS FG I K+MRDP +G SKG F+ F++ + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 295 MNGKMIVSKPLYVAVAQRKEER 316
MNG+ + ++P+ V+ A +K+ +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTIT-SAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 191
+F+ NLD ++ L F +G I + +MRD D G SK + F+NF + D + A+EA
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 192 LNGKKFDDREWYVGKAQKKSER 213
+NG+ +R V A KK +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVE 190
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 191 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 245
AL+ K L G Q + A E + + L+I +
Sbjct: 66 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 106
Query: 246 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 302
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ S
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 303 KPLYVAVA 310
P+ V A
Sbjct: 167 SPMVVKFA 174
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+FI + K + FSSFG I C+I G S+G FV F + AQ AI ++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPE---E 287
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 288 ASRALAEM 295
A AL M
Sbjct: 63 AQNALHNM 70
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
+FV L T ++ L+++F +YG I+ VV++D + +S+ FGFV FEN DDA A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 193 NGKKFDDREWYVGKAQKKSE 212
NGK D R+ V +A K S+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKESAQN 96
S G +F+ L + ++L FS +G I + D Q S+GFGFV FEN + A++
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 97 AIDKLNGMLINDKQVFV 113
A+ +NG ++ +Q+ V
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
L++ L +++ L+++FS++G I+ V++D + S+G GFV F ++A A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 296 NGKMIVSKPLYVAVAQRKEERRA 318
NGK + + + V A + + R+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 63.2 bits (152), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 46/164 (28%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 188
T+ +FV NL T+ED K++F YG + + RD + FGF+ E+ A A
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
L+G R + A G L +KNL + +
Sbjct: 75 KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 249 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
E L++ FS+FG + V+ D G + G GFV F+ A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 39/149 (26%), Positives = 68/149 (45%), Gaps = 17/149 (11%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+F+ NL I + F +G I D +GFGF++ E++ A+ A +L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 161
+G ++ + + + T + VKNL ++E L++ F ++G + A
Sbjct: 79 DGTILKSRPL------------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 162 VVMRDGDGKSKCFGFVNFENADDAAKAVE 190
VV+ D G++ GFV F A KA+E
Sbjct: 127 VVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 8/87 (9%)
Query: 14 LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 73
L+ T L ++ +RI ++ + + +KNL + ++ L FS FG + +
Sbjct: 78 LDGTILKSRPLRIRFA--------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV 129
Query: 74 TDGSGQSKGFGFVQFENKESAQNAIDK 100
D G++ G GFV+F K A+ A+++
Sbjct: 130 VDDRGRATGKGFVEFAAKPPARKALER 156
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
Q L++ NL I +E K LF +G + + RD +G GF+ + A A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 293 AEMNGKMIVSKPLYVAVA 310
AE++G ++ S+PL + A
Sbjct: 76 AELDGTILKSRPLRIRFA 93
>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 = 62.4 bits (150), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 76 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDK 100
IF+ + + + L D F +G I +I TD GSG+ +GF FV F++ +S I K
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 101 LNGMLINDKQVFVGHFLRKQE 121
+ +N V L KQE
Sbjct: 167 YH--TVNGHNCEVRKALSKQE 185
>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 = 62.0 bits (149), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 75 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 129
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 130 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 71 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 117
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDK 100
IF+ + + + L D F +G I +I TD GSG+ +GF FV F++ +S I K
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 165
Query: 101 LNGMLINDKQVFVGHFLRKQE 121
+ +N V L KQE
Sbjct: 166 YH--TVNGHNCEVRKALSKQE 184
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 62.0 bits (149), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 77 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 131
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 132 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 73 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 119
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 120 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDK 100
IF+ + + + L D F +G I +I TD GSG+ +GF FV F++ +S I K
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 167
Query: 101 LNGMLINDKQVFVGHFLRKQE 121
+ +N V L KQE
Sbjct: 168 YH--TVNGHNCEVRKALSKQE 186
>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 = 61.6 bits (148), Expect = 1e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 69 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 65 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 74 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 60.1 bits (144), Expect = 3e-09, Method: Composition-based stats.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 70 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 116
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 61.2 bits (147), Expect = 1e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 99
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 100 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 157
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 76 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 158 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 189
I +M D G GK + F FV F++ D K V
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 60.1 bits (144), Expect = 3e-09, Method: Composition-based stats.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 188
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 249 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 282
L++ F ++G I ++M D SG +G FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>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 = 59.7 bits (143), Expect = 5e-09, Method: Composition-based stats.
Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 135 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVEA 191
FV + + +++DL+++F +YG + V+RD +SK FV F A +A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 192 LNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSI 246
L+ K L G Q + A E + + L+I +
Sbjct: 67 LHNXKV-------------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKC 107
Query: 247 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+ ++ FS FG I C+++R P G+S+G FV F+T A A+
Sbjct: 108 TENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 27/56 (48%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
+FI + K + FSSFG I C+I G S+G FV F + AQ AI
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 47/78 (60%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+F+ L+ T ++ LK +FG++G I+ ++++D KS+ F F+ FEN DA A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 194 GKKFDDREWYVGKAQKKS 211
GK + V +A+K S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 41 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 100
G +FI L++ + K L F G I + D + +S+GF F+ FEN A+NA
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 101 LNGMLINDKQVFV 113
+NG ++ K + V
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+I L +++ LK +F + G I+ +++D + S+G F+ F P +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 297 GKMIVSKPLYVAVAQR 312
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 295
NLYI NL S+D+++L+ + FG + S +++RD SG S+G GF + E+ +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 296 NGKMIVSKP 304
NGK I + P
Sbjct: 87 NGKFIKTPP 95
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 36/65 (55%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
N++I NL S+D + L + FG ++S +I D SG S+G GF + E+ E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 102 NGMLI 106
NG I
Sbjct: 87 NGKFI 91
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N+++ NL S +++L+ + +G + S ++RD G S+ GF E+ + +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 192 LNGK 195
NGK
Sbjct: 86 FNGK 89
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 235 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 293
NL++ +L ++DDE L+ F +F + S VM D +G S+G GFV+F++ ++A A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 294 EMNGKMIVSKPLYVAVAQRKEE 315
M G+ + +PL + A + E
Sbjct: 62 SMQGQDLNGRPLRINWAAKLEH 83
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 40 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 98
T N+F+ +L+ ++D + L + F F + LS + D +G S+G+GFV F +++ AQNA+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 99 DKLNGMLINDK 109
D + G +N +
Sbjct: 61 DSMQGQDLNGR 71
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
N+FV +L+ + DE L+ F ++ + S VM D G S+ +GFV+F + DDA A+++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 192 LNGKKFDDREWYVGKAQK 209
+ G+ + R + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 191
N+F+ +L + TD DL F +G + SA V D SKCFGFV+F+N D A A++A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 192 LNG 194
+NG
Sbjct: 102 MNG 104
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+FI +L + L TF FGN++S K+ D + SK FGFV F+N +SAQ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 101 LNGMLINDKQV 111
+NG + K++
Sbjct: 102 MNGFQVGTKRL 112
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 291
+G NL+I +L D L F FG + S KV D + +SK GFV+F P+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 292 LAEMNGKMIVSKPLYV 307
+ MNG + +K L V
Sbjct: 99 IKAMNGFQVGTKRLKV 114
>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 = 55.8 bits (133), Expect = 6e-08, Method: Composition-based stats.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 232 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 290
FQG NL + L + ++L+ LFS G + S K++RD +G S G GFV + T ++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 291 ALAEMNGKMIVSKPLYVAVAQ 311
A+ +NG + SK + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 192 LNGKKFDDREWYVGKAQ 208
LNG + + V A+
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+ + L ++ L FSS G + S K+ D +G S G+GFV + + A+ AI+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 101 LNGMLINDKQVFVGH 115
LNG+ + K + V +
Sbjct: 81 LNGLRLQSKTIKVSY 95
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 55.5 bits (132), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 4/80 (5%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKV--MRDPSGI--SKGSGFVAFSTPEEASRAL 292
L+IKNL S +E LK +FS+ G I SC + ++ +G+ S G GFV + PE+A +AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 293 AEMNGKMIVSKPLYVAVAQR 312
++ G + L V +++R
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 48/91 (52%), Gaps = 8/91 (8%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFVQFENKES 93
SG+ +FIKNL+ S + L FS G I SC I+ G S GFGFV+++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 94 AQNAIDKLNGMLINDKQVFVGHFLRKQERET 124
AQ A+ +L G ++ ++ V R ER T
Sbjct: 63 AQKALKQLQGHTVDGHKLEV----RISERAT 89
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADDAAK 187
+ +F+KNL+ STT+E LK +F + G I S + + + S FGFV ++ + A K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 188 AVEALNGKKFDDREWYV 204
A++ L G D + V
Sbjct: 66 ALKQLQGHTVDGHKLEV 82
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++ LG DE ++++F FGTI C V+R P G SKG FV F T EA A+ ++
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 297 GKMIV---SKPLYVAVAQRKEE 315
+ S L V A ++E
Sbjct: 75 SSRTLPGASSSLVVKFADTEKE 96
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV L + TDED++K+F +GTI V+R DG SK FV F+ +A A+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 194 GKK 196
+
Sbjct: 75 SSR 77
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ L K + + F FG I C + G SKG FV+F+ AQ AI+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 235 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 293
+ LY+ +L +I ++ L+ +F FG I S ++M D +G SKG GF+ FS E A +AL
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 294 EMNGKMIVSKPLYVA-VAQRKE 314
++NG + +P+ V V +R +
Sbjct: 87 QLNGFELAGRPMKVGHVTERTD 108
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+++ +L +I L F FG I S ++ D +G+SKG+GF+ F + E A+ A+++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 102 NGMLINDKQVFVGHFLRKQE 121
NG + + + VGH + +
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 192
++V +L + T++ L+ IF +G I S +M D + G+SK +GF+ F +++ A KA+E L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 193 NGKKFDDREWYVGKAQKKSE 212
NG + R VG ++++
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+ VFV NLD + LK++F G + A ++ D DGKS+ G V FE + +A +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 192 LNGKKFDDREWYV 204
NG+ DR +V
Sbjct: 76 FNGQLLFDRPMHV 88
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 293
G +++ NL + +KLKE+FS G + ++ D G S+G G V F EA +A++
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 294 EMNGKMIVSKPLYVAVAQR 312
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+F+ NLD + K L + FS G ++ I D G+S+G G V FE A AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 102 NGMLINDKQVFV 113
NG L+ D+ + V
Sbjct: 77 NGQLLFDRPMHV 88
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 126 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADD 184
A+ +VFV N+ T+E LK IF E G + S ++ D + GK K +GF +++ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 185 AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 215
A A+ LNG++F R V A + +E+
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 49/83 (59%), Gaps = 1/83 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
++F+ N+ + L D FS G ++S ++ D +G+ KG+GF +++++E+A +A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 101 LNGMLINDKQVFVGHFLRKQERE 123
LNG + + + V + ++ +E
Sbjct: 70 LNGREFSGRALRVDNAASEKNKE 92
Score = 42.0 bits (97), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 4/84 (4%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
++++ N+ +E+LK++FSE G + S +++ D +G KG GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 295 MNGKMIVSKPLYV---AVAQRKEE 315
+NG+ + L V A + KEE
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEE 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 17/156 (10%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+F+ NL I + + F +G I D KGFGF++ E + A+ A +L
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 78
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 161
+ M + KQ+ V ++ V+NL + ++E L++ F +G + A
Sbjct: 79 DNMPLRGKQL------------RVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 162 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 197
VV+ D G+ G V F A KA++ + F
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSF 162
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 188
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E A A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 74
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 248
L+ R ++L+ +F +L ++NL + +
Sbjct: 75 KVELDNMPL---------------RGKQLRVRF---------ACHSASLTVRNLPQYVSN 110
Query: 249 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
E L+E FS FG + V+ D G G G V FS A +AL
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 8/89 (8%)
Query: 14 LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 73
L+ PL K +R+ ++ + ++ ++NL + + ++ L + FS FG + +
Sbjct: 78 LDNMPLRGKQLRVRFA--------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVI 129
Query: 74 TDGSGQSKGFGFVQFENKESAQNAIDKLN 102
D G+ G G V+F K +A+ A+D+ +
Sbjct: 130 VDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
Q L++ NL I +E++++LF ++G + +D KG GF+ T A A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAK 75
Query: 293 AEMNGKMIVSKPLYVAVA 310
E++ + K L V A
Sbjct: 76 VELDNMPLRGKQLRVRFA 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
NL + + ++D+ +L++LF +G I S K++ D + S+G GFV F + A +A+A
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 295 MNGKMIVSKPLYVAVAQRKEER 316
+NG I++K L VA+A +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 1/86 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+ + + ++D L F +G I S KI D + QS+G+GFV+F++ SAQ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 101 LNGMLINDKQVFVGHFLRKQERETVA 126
LNG I +K++ V +R +A
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIA 129
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 131 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAV 189
N+ V + + + L+++F YG I S ++ D + + S+ +GFV F++ A +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 190 EALNGKKFDDREWYVGKAQKKSER 213
LNG ++ V A +R
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQR 125
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
++F+ +L I + + F+ FG I ++ D +G+SKG+GFV F NK A+NAI +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 101 LNGMLINDKQVFVGHFLRK 119
+ G + +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 192 LNGKKFDDRE 201
+ G+ R+
Sbjct: 77 MGGQWLGGRQ 86
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 4/89 (4%)
Query: 226 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 284
K+T + F ++++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 285 PEEASRALAEMNGKMIVSKPLYVAVAQRK 313
+A A+ +M G+ + + + A RK
Sbjct: 67 KWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 LNGKKFDDREWYVGKAQKKS 211
LNG K + V A+ S
Sbjct: 66 LNGLKLQTKTIKVSYARPSS 85
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+ + L +++ F S G+I SCK+ D +GQS G+GFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 101 LNGMLINDKQVFVGH 115
LNG+ + K + V +
Sbjct: 66 LNGLKLQTKTIKVSY 80
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 192 LNGKKFDDREWYVGKAQKK 210
+ G+ R+ A +K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
++F+ +L I + + F+ FG I ++ D +G+SKG+GFV F NK A+NAI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 101 LNGMLINDKQVFVGHFLRK 119
+ G + +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 48/89 (53%), Gaps = 4/89 (4%)
Query: 226 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 284
K+T + F +++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHFH---VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 285 PEEASRALAEMNGKMIVSKPLYVAVAQRK 313
+A A+ M G+ + + + A RK
Sbjct: 67 KLDAENAIVHMGGQWLGGRQIRTNWATRK 95
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 6e-07, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
LY+ +L +I ++ L+ +F FG I + +M+D +G SKG GF+ FS E A RAL ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 296 NGKMIVSKPLYVA 308
NG + +P+ V
Sbjct: 68 NGFELAGRPMRVG 80
Score = 51.6 bits (122), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 190
+ ++V +L + T++ L+ IF +G I + V+M+D D G+SK +GF+ F +++ A +A+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 191 ALNGKKFDDREWYVGKAQKK 210
LNG + R VG ++
Sbjct: 66 QLNGFELAGRPMRVGHVTER 85
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQN 96
SG+ +++ +L +I L F FG I + + D +G+SKG+GF+ F + E A+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 97 AIDKLNGMLINDKQVFVGH 115
A+++LNG + + + VGH
Sbjct: 63 ALEQLNGFELAGRPMRVGH 81
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + SK + V+ A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 192 LNGKKFDDREWYVGKAQ 208
LNG + + V A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 97
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 98 IDKLNGMLINDKQVFVGH 115
I+ LNG+ + K + V +
Sbjct: 63 INTLNGLRLQSKTIKVSY 80
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 291
+G NL+I +L D+ L ++F FG + S KV D + +SK GFV++ P A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRA 318
+ MNG I K L V + + K + ++
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 191
N+F+ +L + D+DL ++F +G + SA V D SKCFGFV+++N A A+++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 192 LNG 194
+NG
Sbjct: 87 MNG 89
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+FI +L + + L F FGN++S K+ D + SK FGFV ++N SAQ AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 101 LNGMLINDKQVFV 113
+NG I K++ V
Sbjct: 87 MNGFQIGMKRLKV 99
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 51.6 bits (122), Expect = 1e-06, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 97
SG+ IF++NL K L D F+ G++L I + +G+SKG G V+FE+ E A+ A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 61
Query: 98 IDKLNGMLINDKQVFV 113
+NGM ++ +++ V
Sbjct: 62 CRMMNGMKLSGREIDV 77
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+ +FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 64
Query: 192 LNGKKFDDRE 201
+NG K RE
Sbjct: 65 MNGMKLSGRE 74
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 66
Query: 297 GKMIVSKPLYVAV 309
G + + + V +
Sbjct: 67 GMKLSGREIDVRI 79
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 99
+FI L K L D FS FG ++ C + D +G+S+GFGFV F+ ES +D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 100 --KLNGMLINDKQ 110
KLNG +I+ K+
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 294
++I L + LK+ FS+FG + C + DP +G S+G GFV F E + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 295 ---MNGKMIVSK 303
+NGK+I K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 190
+F+ L TT +DLK F ++G + + D G+S+ FGFV F+ ++ K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 191 --ALNGKKFDDR 200
LNGK D +
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 143 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 200
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 82
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 55 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Query: 114 GHFLRKQ 120
+ K+
Sbjct: 87 DFSITKR 93
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 292
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 19 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 293 AEMNG 297
NG
Sbjct: 72 ERANG 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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 188
K N++V NL + TD+ L IFG+YG+I ++RD G+ + FV + ++A +A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 189 VEALN 193
+ ALN
Sbjct: 72 ISALN 76
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 3/79 (3%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
NLY+ NL +I D++L +F ++G+I ++RD +G +G FV ++ EEA A++
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 295 MNGKMIV--SKPLYVAVAQ 311
+N + S+PL V +A+
Sbjct: 75 LNNVIPEGGSQPLSVRLAE 93
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
N+++ NL ++I L F +G+I+ I D +G+ +G FV++ +E AQ AI
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 101 LNGML 105
LN ++
Sbjct: 75 LNNVI 79
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 143 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 200
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 55 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Query: 114 GHFLRKQ 120
+ K+
Sbjct: 90 DFSITKR 96
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 292
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 293 AEMNG 297
NG
Sbjct: 75 ERANG 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
N+++ L K++ K + FS +G I++ +I D +G S+G GF++F+ + A+ AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 101 LNG 103
LNG
Sbjct: 63 LNG 65
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
NLY+ L ++ +++++LFS++G I + +++ D +G+S+G GF+ F EA A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 295 MNGKMIVSKPLYVA 308
+NG+ KPL A
Sbjct: 63 LNGQ----KPLGAA 72
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N++V L ++ + ++++++F +YG ITS +++ G S+ GF+ F+ +A +A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 192 LNGKK 196
LNG+K
Sbjct: 63 LNGQK 67
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 LNGKKFDDREWYVGKAQKKSE 212
LNG ++ V A+ E
Sbjct: 65 LNGITVRNKRLKVSYARPGGE 85
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 18/187 (9%)
Query: 134 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 187
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ------AMKETVDKFQGLNLYIKN 241
A+ A +G F + + ++ Q L G E + TV L+I
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 242 LGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI 300
L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +NG +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 301 VSKPLYV 307
K L V
Sbjct: 182 GDKKLLV 188
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+FI L ++ + + +SFG + + + D +G SKG+ F ++ + AI L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 102 NGMLINDKQVFV 113
NGM + DK++ V
Sbjct: 177 NGMQLGDKKLLV 188
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 194
V L TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 195 KKFDDREWYV 204
+ D R V
Sbjct: 111 MELDGRRIRV 120
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 55 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 292
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 53 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 293 AEMNGKMIVSKPLYV 307
NG + + + V
Sbjct: 106 ERANGMELDGRRIRV 120
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 97
SG IF++NL K L D F+ G++L I + +G+SKG G V+FE+ E A+ A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 64
Query: 98 IDKLNGMLINDKQVFV 113
+NGM ++ +++ V
Sbjct: 65 CRMMNGMKLSGREIDV 80
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 194 GKKFDDRE 201
G K RE
Sbjct: 70 GMKLSGRE 77
Score = 38.9 bits (89), Expect = 0.009, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 297 GKMIVSKPLYVAV 309
G + + + V +
Sbjct: 70 GMKLSGREIDVRI 82
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 143 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 200
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 55 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 292
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 293 AEMNG 297
NG
Sbjct: 75 ERANG 79
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 38/67 (56%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 194 GKKFDDR 200
G D R
Sbjct: 91 GVPLDGR 97
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 297 GKMIVSKPLYV 307
G + +P+ +
Sbjct: 91 GVPLDGRPMNI 101
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NLD + + + F+ FG + + D SG+S G V FE K A A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 103 GMLIN 107
G+ ++
Sbjct: 91 GVPLD 95
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 49.7 bits (117), Expect = 4e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
+++ NL + +E L ELF + G +T + +D G K GFV F PE S A+A +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 297 GKMIVSKPLYVA 308
G + +P+ V+
Sbjct: 79 GIRLYGRPINVS 90
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
VFV NL+ +E L ++F + G +T + +D +GK K FGFV F++ + + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 194 GKKFDDR 200
G + R
Sbjct: 79 GIRLYGR 85
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ NL+ + + L++ F G + I D G+ K FGFV F++ ES AI LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 103 GMLINDKQVFV 113
G+ + + + V
Sbjct: 79 GIRLYGRPINV 89
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++ L +E + LF FG I C V+R P G SKG FV FS+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 297 GKMIV---SKPLYVAVAQRKEE 315
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV L++ ++ED+ ++F +G I V+R DG SK FV F + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 194 GKK 196
G +
Sbjct: 78 GSQ 80
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ L+K + + F FG I C + G SKG FV+F + AQ AI L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 103 G 103
G
Sbjct: 78 G 78
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+++NL +++ +E L++ FS+FG + K ++D + F+ F + A +A+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMN 66
Query: 297 GKMIVSKPLYVAVA----QRKEERRARLQA 322
GK + + + + A Q+++ER+A+ QA
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 50/96 (52%), Gaps = 7/96 (7%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 188
K +FV+NL + T+E L+K F ++G + ++D + F++F+ D A KA
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQA 224
+E +NGK + + A+ ++ +E K Q + A
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97
Score = 36.2 bits (82), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F++NL ++ + L FS FG + K D + F+ F+ ++ A A++++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 103 G 103
G
Sbjct: 67 G 67
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 128 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
K++ + V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 188 AVEALNGKKFDDREWYVGKAQKK 210
A E L+G + R+ V A +
Sbjct: 85 AREKLHGTVVEGRKIEVNNATAR 107
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 228 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE 287
T +K Q L++ N+ D L+++F +FG I +++ + G SKG GFV F +
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 288 ASRALAEMNGKMIVSKPLYV 307
A RA +++G ++ + + V
Sbjct: 82 ADRAREKLHGTVVEGRKIEV 101
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 57 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
L F FG IL +I + G SKGFGFV FEN A A +KL+G ++ +++ V
Sbjct: 46 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 49.3 bits (116), Expect = 6e-06, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 190
+ V+V NL S T+ DL +IF +YG + +M+D D KSK F+ F + D A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 191 ALNGKKFDDR 200
A+N K+ R
Sbjct: 77 AINNKQLFGR 86
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ NL S+ + L+ FS +G ++ I D + +SKG F+ F +K+SAQN
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA- 77
Query: 102 NGMLINDKQVF 112
IN+KQ+F
Sbjct: 78 ----INNKQLF 84
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
+Y+ NL S+ + L +FS++G + +M+D + SKG F+ F + A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 296 NGKMIVSKPLYVAVA 310
N K + + + ++A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 194 GKKFDDR 200
G D R
Sbjct: 92 GVPLDGR 98
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 297 GKMIVSKP 304
G + +P
Sbjct: 92 GVPLDGRP 99
Score = 37.4 bits (85), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NLD + + + F+ FG + + D SG+S G V FE K A A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 103 GMLIN 107
G+ ++
Sbjct: 92 GVPLD 96
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 48.9 bits (115), Expect = 7e-06, Method: Composition-based stats.
Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 236 NLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 294
+L++ +L +DD L E F + + + KV+ D +G+SKG GFV F+ E RAL E
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 295 MNGKM-IVSKPLYVAVAQRKEER 316
G + + SKP+ ++VA K R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
Score = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 100
++F+ +L +D L++ F + + K+ D +G SKG+GFV+F ++ + A+ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 101 LNG 103
G
Sbjct: 71 CQG 73
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 194 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 253
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 254 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 307
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 71/154 (46%), Gaps = 5/154 (3%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+ + NL S+ + + FG++ C + ++ +GQSKG+GF ++ K+SA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITS 160
G + + ++V H+ + + ++ + V L D D L + + T
Sbjct: 158 LGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTF 214
Query: 161 AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 194
+ DG+ K F + +E A+ A +A + +G
Sbjct: 215 CQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 248
Score = 35.4 bits (80), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 6/112 (5%)
Query: 6 SAARALDVLNFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTF 61
SAARA L PL +++ + ++ P++ S + + L D AL
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRAL 206
Query: 62 SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
S+ + C++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 207 SAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 194 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 253
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 254 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 307
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 71/154 (46%), Gaps = 5/154 (3%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+ + NL S+ + + FG++ C + ++ +GQSKG+GF ++ K+SA A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITS 160
G + + ++V H+ + + ++ + V L D D L + + T
Sbjct: 158 LGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTF 214
Query: 161 AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 194
+ DG+ K F + +E A+ A +A + +G
Sbjct: 215 CQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 248
Score = 35.4 bits (80), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 6/112 (5%)
Query: 6 SAARALDVLNFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTF 61
SAARA L PL +++ + ++ P++ S + + L D AL
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRAL 206
Query: 62 SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
S+ + C++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 207 SAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 195
V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +A E L+G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 196 KFDDREWYVGKAQKK 210
+ R+ V A +
Sbjct: 79 VVEGRKIEVNNATAR 93
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 57 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
L F FG IL +I + G SKGFGFV FEN A A +KL+G ++ +++ V
Sbjct: 32 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++ N+ D L+++F +FG I +++ + G SKG GFV F +A RA +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 297 GKMIVSKPLYV 307
G ++ + + V
Sbjct: 77 GTVVEGRKIEV 87
>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 = 48.5 bits (114), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 90
+ S + G F+ L K L D F+ FG ++ C I D +G+S+GFGF+ F++
Sbjct: 3 NASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Query: 91 KESAQNAID----KLNGMLINDKQ 110
S + +D +L+G +I+ K+
Sbjct: 63 AASVEKVLDQKEHRLDGRVIDPKK 86
Score = 37.0 bits (84), Expect = 0.028, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 135 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA-- 191
FV L T+ +DLK F ++G + + D + G+S+ FGF+ F++A K ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 192 --LNGKKFDDRE 201
L+G+ D ++
Sbjct: 75 HRLDGRVIDPKK 86
Score = 35.4 bits (80), Expect = 0.078, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 238 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE-- 294
++ L + LK+ F++FG + C + DP +G S+G GF+ F + L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 295 --MNGKMIVSK 303
++G++I K
Sbjct: 75 HRLDGRVIDPK 85
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 192
+FV+NL ++++EDL+K+F YG ++ D K K F FV F + A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 193 NGKKFDDREWYVGKAQKKSEREQ 215
+G+ F R +V + K E Q
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
L+++NL + +E L++LFS +G ++ D + KG FV F PE A +A AE+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 296 NGKMIVSKPLYVAVAQRKEE 315
+G++ + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+F++NL + + L FS++G + D + + KGF FV F E A A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 102 NGMLINDKQVFVGHFLR 118
+G QVF G L
Sbjct: 71 DG------QVFQGRMLH 81
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTK 130
+ + K++ +G +RKQ T ++ +
Sbjct: 70 QINFHGKKLKLGPAIRKQNLSTYHVQPR 97
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 192 ---LNGKKF 197
+GKK
Sbjct: 70 QINFHGKKL 78
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 282
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 194 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 253
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 77 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 112
Query: 254 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 307
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 113 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 71/154 (46%), Gaps = 5/154 (3%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+ + NL S+ + + FG++ C + ++ +GQSKG+GF ++ K+SA A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITS 160
G + + ++V H+ + + ++ + V L D D L + + T
Sbjct: 156 LGKPLGPRTLYV-HWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTF 212
Query: 161 AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 194
+ DG+ K F + +E A+ A +A + +G
Sbjct: 213 CQLACGQDGQLKGFAVLEYETAEMAEEAQQQADG 246
Score = 35.4 bits (80), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 6/112 (5%)
Query: 6 SAARALDVLNFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTF 61
SAARA L PL +++ + ++ P++ S + + L D AL
Sbjct: 147 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRAL 204
Query: 62 SSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
S+ + C++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 205 SAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 134 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 187
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 247
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 69 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 109
Query: 248 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 306
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 307 V 307
V
Sbjct: 170 V 170
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 53/110 (48%), Gaps = 6/110 (5%)
Query: 5 SSAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSF 64
++ A A D + F +S++I H + G +FI L ++ + + +SF
Sbjct: 66 TTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTSF 120
Query: 65 GNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
G + + + D +G SKG+ F ++ + AI LNGM + DK++ V
Sbjct: 121 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 134 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 187
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 247
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 107
Query: 248 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 306
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 307 V 307
V
Sbjct: 168 V 168
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 53/110 (48%), Gaps = 6/110 (5%)
Query: 5 SSAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSF 64
++ A A D + F +S++I H + G +FI L ++ + + +SF
Sbjct: 64 TTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTSF 118
Query: 65 GNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
G + + + D +G SKG+ F ++ + AI LNGM + DK++ V
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 194
V NL E T + DL+++F +G+I+ + +D G+SK F F++F +DAA+A+ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 195 KKFD 198
+D
Sbjct: 80 FGYD 83
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENK 91
P+ R I + NL + L + F FG+I +A D + GQSKGF F+ F +
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 92 ESAQNAIDKLNG 103
E A AI ++G
Sbjct: 68 EDAARAIAGVSG 79
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 239 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNG 297
+ NL + + L+ELF FG+I+ + +D + G SKG F++F E+A+RA+A ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++ L ++ ++ LF FG I C ++R P G SKG FV +S+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 297 GKMIV---SKPLYVAVAQRKEE 315
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV L++ +++D++++F +G I ++R DG SK FV + + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 194 GKK 196
G +
Sbjct: 78 GSQ 80
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 92
PS RK +F+ L+K + F +FGNI C I G SKG FV++ +
Sbjct: 13 PSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHA 67
Query: 93 SAQNAIDKLNG 103
AQ AI+ L+G
Sbjct: 68 EAQAAINALHG 78
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 117 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 175
L +++RE K +F +F+ L TT+E L+ + ++G +T VVMRD +S+ FG
Sbjct: 17 LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 176 FVNFENADDAAKAVEA 191
FV F + + A+ A
Sbjct: 73 FVTFSSMAEVDAAMAA 88
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 230 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 288
+K Q L+I L +E L+ + ++G +T C VMRDP S S+G GFV FS+ E
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 289 SRALA----EMNGKMIVSK 303
A+A ++G+++ K
Sbjct: 83 DAAMAARPHSIDGRVVEPK 101
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI-- 98
+FI L ++L + + +G + C + D S +S+GFGFV F + A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 99 --DKLNGMLINDKQV 111
++G ++ K+
Sbjct: 89 RPHSIDGRVVEPKRA 103
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 194
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 195 KKFDDREWYVGKAQ 208
D RE V A+
Sbjct: 112 AVLDGRELRVQMAR 125
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 97
G ++ + NL L F +G + I D + +S+GF FV+F +K A++A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 98 IDKLNGMLINDKQVFV 113
+D ++G +++ +++ V
Sbjct: 106 MDAMDGAVLDGRELRV 121
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 295 MNGKMIVSKPLYVAVAQ 311
M+G ++ + L V +A+
Sbjct: 109 MDGAVLDGRELRVQMAR 125
>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
pdb|3NTW|C Chain C, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
Length = 65
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 493 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 549
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 6 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 102 N 102
N
Sbjct: 126 N 126
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 296 NGKMIVSKPLYVAVA 310
N + + + V +A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 193 N 193
N
Sbjct: 126 N 126
>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein:
An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding
Protein
Length = 61
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 493 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 549
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 194 GKKFDDR 200
G D R
Sbjct: 151 GVPLDGR 157
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 293
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 294 EMNGKMIVSKPLYV 307
+ G + +P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161
Score = 36.6 bits (83), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 33/67 (49%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 103 GMLINDK 109
G+ ++ +
Sbjct: 151 GVPLDGR 157
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 70
Query: 103 GMLINDKQVFVGHFLRKQ 120
+ + K++ +G +RKQ
Sbjct: 71 QINFHGKKLKLGPAIRKQ 88
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 192 ---LNGKKF 197
+GKK
Sbjct: 71 QINFHGKKL 79
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 282
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
>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 = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 6/125 (4%)
Query: 115 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC- 173
HF E + +K K ++V NL TT+E + ++F + G I ++ D K+ C
Sbjct: 24 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 174 FGFVNFENADDAAKAVEALNGKKFDDR----EWYVGKAQKKSEREQELKGQFEQAMKETV 229
F FV + + DA A+ +NG + DDR +W G + + GQ ++
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDY 142
Query: 230 DKFQG 234
D +G
Sbjct: 143 DAGRG 147
Score = 35.0 bits (79), Expect = 0.10, Method: Composition-based stats.
Identities = 24/107 (22%), Positives = 54/107 (50%), Gaps = 3/107 (2%)
Query: 4 LSSAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS 63
L A R+ + + ++ R ++ ++KS T +++ NL + +++ FS
Sbjct: 5 LLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCT--LYVGNLSFYTTEEQIYELFSK 62
Query: 64 FGNILSCKIATDGSGQSK-GFGFVQFENKESAQNAIDKLNGMLINDK 109
G+I + D ++ GF FV++ ++ A+NA+ +NG ++D+
Sbjct: 63 SGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDR 109
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 213 REQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-S 271
R+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 21 RDQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK 77
Query: 272 GISKGSGFVAFSTPEEASRALAEMNG 297
+ G FV + + +A A+ +NG
Sbjct: 78 KTACGFCFVEYYSRADAENAMRYING 103
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 103 GMLINDKQVFVGHFLRKQ 120
+ + K++ +G +RKQ
Sbjct: 70 QINFHGKKLKLGPAIRKQ 87
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 192 ---LNGKKF 197
+GKK
Sbjct: 70 QINFHGKKL 78
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 282
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 80/168 (47%), Gaps = 12/168 (7%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
N+FI NL+ + L S + +G ++ FG+V FE+ E + A++ L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 102 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 161
G+ + ++ + + ++ A +T + KNL + T+++LK++F + I
Sbjct: 74 TGLKVFGNEIKLEKPKGRDSKKVRAART----LLAKNLSFNITEDELKEVFEDALEIR-- 127
Query: 162 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE---WYVGK 206
+ DGKSK ++ F++ DA K +E G + D R +Y G+
Sbjct: 128 --LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 193 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 252
G K E + K KG+ + ++ L KNL +I +++LK
Sbjct: 74 TGLKVFGNEIKLEKP----------KGRDSKKVR------AARTLLAKNLSFNITEDELK 117
Query: 253 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 300
E+F + I + G SKG ++ F + +A + L E G I
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 292
G ++I L E L+E F +FG + C VMRDP + S+G GFV F + L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 293 A----EMNGKMIVSKPLYVAVAQRK 313
A E++ K I K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAV-- 189
+F+ L TT E L++ FG++G + +VMRD +S+ FGFV F + K +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 190 --EALNGKKFDDREWYVGKAQKK 210
L+ K D + + +AQ K
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQPK 109
Score = 35.4 bits (80), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
+FI L + L + F FG + C + D + +S+GFGFV F + Q +DK
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD----QAGVDK 82
Query: 101 L 101
+
Sbjct: 83 V 83
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 102 N 102
N
Sbjct: 75 N 75
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 296 NGKMIVSKPLYVAVAQ 311
N + + + V +A+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 35.8 bits (81), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 193 NGKKFDDREWYVGKAQ 208
N + R V A+
Sbjct: 75 NESELFGRTIRVNLAK 90
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
++F+ +L I A+ F+ FG I ++ D +G+SKG+GFV F NK A+NAI +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 101 LNGMLINDKQVFVGHFLRK 119
+ G + +Q+ RK
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 191
+VFV +L T + F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 192 LNGKKFDDRE 201
+ G+ R+
Sbjct: 68 MGGQWLGGRQ 77
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 258 FGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 313
FG I+ +V++D +G SKG GFV+F +A A+ +M G+ + + + A RK
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FVK L E TT+E LK+ F G++ + +V G SK FGFV+F + +DA A EA+
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 194 GKKFD 198
+ D
Sbjct: 76 DGEID 80
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 91
P+ R + +F+K L + + L + SF + +I TD +G SKGFGFV F ++
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 92 ESAQNAIDKLNGMLINDKQV 111
E A+ A + + I+ +V
Sbjct: 65 EDAKAAKEAMEDGEIDGNKV 84
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++K L + +E LKE F G++ + V +G SKG GFV F++ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 297 GKMIVSKPLYVAVAQRK 313
I + + A+ K
Sbjct: 76 DGEIDGNKVTLDWAKPK 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.8 bits (107), Expect = 7e-05, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 194
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 195 KKFDDREWYVGKAQ 208
D RE V A+
Sbjct: 135 AVLDGRELRVQMAR 148
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 39 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 97
G ++ + NL L F +G + I D + +S+GF FV+F +K A++A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 98 IDKLNGMLINDKQVFV 113
+D ++G +++ +++ V
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 32.7 bits (73), Expect = 0.57, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 294
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 295 MNGKMIVSKPLYVAVAQ 311
M+G ++ + L V +A+
Sbjct: 132 MDGAVLDGRELRVQMAR 148
>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 = 45.8 bits (107), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 102 N 102
N
Sbjct: 65 N 65
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 296 NGKMIVSKPLYVAVA 310
N + + + V +A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 36.2 bits (82), Expect = 0.057, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 193 N 193
N
Sbjct: 65 N 65
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.4 bits (106), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 102 N 102
N
Sbjct: 68 N 68
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 296 NGKMIVSKPLYVAVAQ 311
N + + + V +A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 36.2 bits (82), Expect = 0.050, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 193 NGKKFDDREWYVGKAQ 208
N + R V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>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 = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 102 N 102
N
Sbjct: 70 N 70
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 296 NGKMIVSKPLYVAVAQ 311
N + + + V +A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 36.2 bits (82), Expect = 0.053, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 192
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 193 NGKKFDDREWYVGKAQ 208
N + R V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 194 GK 195
G+
Sbjct: 132 GR 133
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 297 GKMI 300
G+ +
Sbjct: 132 GRTL 135
Score = 32.7 bits (73), Expect = 0.53, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+++ NL + + L F +G + S +A + GF FV+FE+ A +A+ +L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD 131
Query: 103 G 103
G
Sbjct: 132 G 132
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 194 GKKFDDR 200
G D R
Sbjct: 98 GVPLDGR 104
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 293
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 294 EMNGKMIVSKPLYV 307
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 33/67 (49%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 103 GMLINDK 109
G+ ++ +
Sbjct: 98 GVPLDGR 104
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 194 GKKFDDR 200
G D R
Sbjct: 98 GVPLDGR 104
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 293
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 294 EMNGKMIVSKPLYV 307
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 33/67 (49%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 103 GMLINDK 109
G+ ++ +
Sbjct: 98 GVPLDGR 104
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 194 GK 195
G+
Sbjct: 132 GR 133
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRDLD 131
Query: 297 GKMI 300
G+ +
Sbjct: 132 GRTL 135
Score = 32.3 bits (72), Expect = 0.81, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+++ NL + + L F +G + S +A + GF FV+FE+ A +A+ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRDLD 131
Query: 103 G 103
G
Sbjct: 132 G 132
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 188
+ +FV LD STT E L+ F +YG + V+M+D +S+ FGFV F++ +
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 189 VEA----LNGKKFDDR 200
+ + L+G+ D +
Sbjct: 75 LASRPHTLDGRNIDPK 90
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 41 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 90
G +F+ LD S + L FS +G ++ C I D + QS+GFGFV+F++
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 294
L++ L S E L+ FS++G + C +M+D + S+G GFV F P LA
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 295 ---MNGKMIVSKP 304
++G+ I KP
Sbjct: 79 PHTLDGRNIDPKP 91
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 70/148 (47%), Gaps = 7/148 (4%)
Query: 68 LSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF--VGHFLRKQERETV 125
LS ++ + S+ F ++ +KE A+ ++KLNG+ I + V + L K +R T
Sbjct: 146 LSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR-TD 204
Query: 126 AIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKS--KCFGFVNFENA 182
+ + + ++NL DE+ L++ F +G+I + S C F FEN
Sbjct: 205 SATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENK 264
Query: 183 DDAAKAVEALNGKKFDDREWYVGKAQKK 210
D A +A++ N +RE V A KK
Sbjct: 265 DSAERALQX-NRSLLGNREISVSLADKK 291
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 236 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 324
L M G KP+ + A+ + A+++ F
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATN 67
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 221
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 64/132 (48%), Gaps = 12/132 (9%)
Query: 78 GQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVK 137
G ++ FG+V FE+ E + A++ L G+ + ++ + K ++ +T + K
Sbjct: 45 GMTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGKDSKKERDART----LLAK 99
Query: 138 NLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 197
NL T ++LK++F + + + + DGKSK ++ F+ DA K E G +
Sbjct: 100 NLPYKVTQDELKEVFED----AAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Query: 198 DDRE---WYVGK 206
D R +Y G+
Sbjct: 156 DGRSISLYYTGE 167
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 46/169 (27%), Positives = 77/169 (45%), Gaps = 23/169 (13%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
N+FV NL+ + + +LK + V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-L 67
Query: 193 NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 251
G K E + K + K S++E++ + L KNL + ++L
Sbjct: 68 TGLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDEL 110
Query: 252 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 300
KE+F + I + G SKG ++ F T +A + E G I
Sbjct: 111 KEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 187
T F +FV L TTD L+K F +G I AVV+ D GKS+ +GFV + A +
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 188 AVE----ALNGKKFDDREWYVG 205
A + ++G+K + Y+G
Sbjct: 75 ACKDPNPIIDGRKANVNLAYLG 96
Score = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
IF+ L +L F FG+I + TD +G+S+G+GFV ++ +A+ A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 102 NGML 105
N ++
Sbjct: 80 NPII 83
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
+++ L D L++ F FG I V+ D +G S+G GFV + A RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 296 N 296
N
Sbjct: 80 N 80
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 295
L+I L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 296 NGKMIVSKPLYV 307
NG + K L V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+FI L ++ + + +SFG + + + D +G SKG+ F ++ + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 102 NGMLINDKQVFV 113
NGM + DK++ V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV+ + +L +IFG +G + ++ F FV FE A+ AAKA+E ++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 86
Query: 194 GKKFDDREWYVGKAQKKSER 213
GK F ++ V ++ ++R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 86
Query: 297 GKMIVSKPLYVAVAQRKEER 316
GK ++PL V ++ +R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
Score = 37.4 bits (85), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F++ + L++ F FG + KI GF FV+FE ESA AI++++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 103 G 103
G
Sbjct: 87 G 87
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 127 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 186
+ K +FV+NL + T+E L+K F E+G + ++D + FV+FE+ A
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 187 KAVEALNGK 195
KA++ +NGK
Sbjct: 64 KAMDEMNGK 72
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 47/82 (57%), Gaps = 7/82 (8%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+++NL ++ +E L++ FSEFG + K ++D FV F A +A+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 297 GKMIVSKPLYVAVAQRKEERRA 318
GK I + + + +A+ +++R+
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F++NL ++ + L +FS FG + K D + FV FE++ +A A+D++N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 103 G 103
G
Sbjct: 71 G 71
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 236 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 324
L M G KP+ + A+ + A+++ F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 221
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 131 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 189
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 190 EALNGKKFDDR 200
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 24 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK-IATDGSGQSKG 82
+++ H DP+ + +F+ ++ L F +G I + + SG+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 83 FGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ F+++E++ +A +G I+ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>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 = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 115 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 174
HF E + +K K ++V NL TT+E + ++F + G I ++ D + F
Sbjct: 3 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 175 GFVNFENADDAAKAVEALNGKKFDDR----EWYVG 205
FV + + DA A+ +NG + DDR +W G
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 35 IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA 94
++KS T +++ NL + +++ FS G+I + D + GF FV++ ++ A
Sbjct: 15 LKKSCT--LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADA 72
Query: 95 QNAIDKLNGMLINDK 109
+NA+ +NG ++D+
Sbjct: 73 ENAMRYINGTRLDDR 87
Score = 32.7 bits (73), Expect = 0.53, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 214 EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI 273
+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 1 DQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT 57
Query: 274 SKGSGFVAFSTPEEASRALAEMNG 297
+ G FV + + +A A+ +NG
Sbjct: 58 ACGFCFVEYYSRADAENAMRYING 81
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+FI L S + L + + G + ++ T+ +G+ KG +V++EN+ A A+ K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 103 GMLINDKQVFVG 114
GM I + + V
Sbjct: 80 GMTIKENIIKVA 91
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 41/74 (55%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+I L S E+L+E+ GT+ +++ + +G KG +V + +AS+A+ +M+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 297 GKMIVSKPLYVAVA 310
G I + VA++
Sbjct: 80 GMTIKENIIKVAIS 93
Score = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+ +F+ L S T E+L++I +GT+ ++ + GK K +V +EN A++AV
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 192 LNG 194
++G
Sbjct: 78 MDG 80
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 236 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 324
L M G KP+ + A+ + A+++ F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF ++G I +V R K + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATN 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 221
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 136 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNG 194
V NL T+ + L+++F +YG + + R+ K+ + F FV F + DA A A++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 195 KKFDDREWYV 204
+ D RE V
Sbjct: 78 AELDGRELRV 87
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ V N+ + T+++L+ F EYG + +++D + FV+ E A+DA +A+ L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 194 GKKFDDREWYV 204
+F + +V
Sbjct: 66 NTEFQGKRMHV 76
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L++ N+ + +++L+ F E+G + C +++D FV E+A A+ ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 297 GKMIVSKPLYVAVAQRK 313
K ++V ++ +
Sbjct: 66 NTEFQGKRMHVQLSTSR 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 190
+FV L +TT ED+K F ++G + A++M D + + FGFV FE+ D K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 36 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI--ATDGSGQSKGFGFVQFENKES 93
+K T I ++N+ + + + + FS+FG + + ++ G+G +GFGFV F K+
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 94 AQNAIDKL 101
A+ A + L
Sbjct: 71 AKKAFNAL 78
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAV 189
+ + V+N+ +++++F +G + + + + G G + FGFV+F DA KA
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 190 EAL 192
AL
Sbjct: 76 NAL 78
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS--KGSGFVAFSTPEEASRAL 292
+ ++N+ + +++ELFS FG + + ++ + +G +G GFV F T ++A +A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 293
++I L E L+E F +FG + C VMRDP + S+G GFV F + LA
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 294 --EMNGKMIVSK 303
E++ K I K
Sbjct: 63 RHELDSKTIDPK 74
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNF 179
+F+ L TT E L++ FG++G + +VMRD +S+ FGFV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+FI L + L + F FG + C + D + +S+GFGFV F + Q +DK+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD----QAGVDKV 58
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
N+Y+ NL S E++KELFS+FG + + K++ D + KG GFV E S A+A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 295 MNGKMIVSKPLYVAVAQRKE 314
++ + + + V A K+
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 100
NI++ NL S + + + FS FG + + K+ D + + KGFGFV+ + +ES AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 101 LNGMLINDKQVFVGHFLRKQE 121
L D F+G +R E
Sbjct: 62 L------DNTDFMGRTIRVTE 76
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEA 191
N++V NL S T E +K++F ++G + + ++ D + K K FGFV + + ++A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 192 LNGKKFDDREWYVGKAQKKSERE 214
L+ F R V +A K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 190
+ ++++ L TTD+DL K+ YG I S + D K K +GFV+F++ A KAV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 191 AL 192
AL
Sbjct: 66 AL 67
Score = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENKESAQN 96
SG+ ++I+ L + L +G I+S K D + + KG+GFV F++ +AQ
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 97 AIDKL 101
A+ L
Sbjct: 63 AVTAL 67
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV+ + +L +IFG +G + ++ F FV FE A+ AAKA+E ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 59
Query: 194 GKKFDDR 200
GK F ++
Sbjct: 60 GKSFANQ 66
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 297 GKMIVSKPLYVAVAQ 311
GK ++PL V ++
Sbjct: 60 GKSFANQPLEVVYSK 74
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+F++ + L++ F FG + KI GF FV+FE ESA AI++++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 103 G 103
G
Sbjct: 60 G 60
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 58/117 (49%), Gaps = 16/117 (13%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA+D L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 159
G ++++ + V ++ N F K +D +E LK + +YG T
Sbjct: 69 GFNVSNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 111
Score = 34.3 bits (77), Expect = 0.18, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A+ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 297 GKMIVSKPLYV 307
G + ++ L V
Sbjct: 69 GFNVSNRYLVV 79
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 131 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 189
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 190 EALNGKKFDDR 200
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 24 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK-IATDGSGQSKG 82
+++ H DP+ + +F+ ++ L F +G I + + SG+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 83 FGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+ F+++E++ +A +G I+ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 97
SG +FI NL + + + F +G +L C I K +GFV E+K +A++A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 98 ID-----KLNGMLIN 107
I KL+G+ IN
Sbjct: 59 IRNLHHYKLHGVNIN 73
>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A) Binding
Protein From Saccharomyces Cerevisiae
Length = 92
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 491 EQQRTLLGESLYPLV--EQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 548
++QR LGE LY V + +AA K+TGM+L++ EV LLES E + EA
Sbjct: 18 QKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAA 77
Query: 549 LRSVAQQQ 556
S ++Q
Sbjct: 78 YESFKKEQ 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 220 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 279
+FE + ++ K +Y + + D+ +++ FS FG I +V + KG F
Sbjct: 13 RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSF 65
Query: 280 VAFSTPEEASRALAEMNGKMI 300
V FST E A+ A+ +NG I
Sbjct: 66 VRFSTHESAAHAIVSVNGTTI 86
Score = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
++ + + + + TFS FG I+ ++ + KG+ FV+F ESA +AI +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 103 GMLI 106
G I
Sbjct: 83 GTTI 86
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 66
Query: 293 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 321
M G KP+ + A+ + A+++
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 1 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 56
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 57 KEVSSATNALRSMQGFPFYDK 77
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 64
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSD 89
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 236 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 292 LAEMNGKMIVSKPLYVAVAQ 311
L M G KP+ + A+
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 36.6 bits (83), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 235 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 293
+ L+I + ++D++ LK LF EFG I V++D +G+ KG F+ + E A +A +
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 294 EMN 296
++
Sbjct: 74 ALH 76
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+FI + +++D K L F FG I + D +G KG F+ + +ESA A L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 102 N 102
+
Sbjct: 76 H 76
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 192
+F+ + + ++DLK +F E+G I V++D G K F+ + + A KA AL
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 193 NGKK 196
+ +K
Sbjct: 76 HEQK 79
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 293 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 321
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 59
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 60 KEVSSATNALRSMQGFPFYDK 80
Score = 35.8 bits (81), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 293 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 321
M G KP+ + A+ + A+++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
Score = 35.8 bits (81), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 6/90 (6%)
Query: 236 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRARLQ 321
L M G KP+ + A+ + A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 59
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 60 KEVSSATNALRSMQGFPFYDK 80
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 188 AVEALNGKKFDDREWYVGKAQKKSEREQELKG 219
A+ ++ G F D+ + A+ S+ ++KG
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG 99
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 13/100 (13%)
Query: 235 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 294
+ +Y+ NLG +L+ FS +G + + + R+P G + FV F P +A A+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRG 56
Query: 295 MNGKMIVSKPLYVAVA---------QRKEERRARLQAQFS 325
++GK+I + V ++ R RR L+ F+
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFN 96
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
V+V NL +L++ F YG + + + R+ G F FV FE+ DA AV L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 194 GK 195
GK
Sbjct: 59 GK 60
Score = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+++ NL L FS +G + + IA + GF FV+FE+ A++A+ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 103 GMLINDKQVFV 113
G +I +V V
Sbjct: 59 GKVICGSRVRV 69
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 65
Query: 293 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 321
M G KP+ + A+ + A+++
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 43 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 99 DKLNGMLINDK 109
+ G DK
Sbjct: 66 RSMQGFPFYDK 76
Score = 35.4 bits (80), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 63
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSD 88
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 293 AEMNGKMIVSKPLYVAVAQRKEERRARL 320
M G KP+ + A+ + A++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
Score = 35.8 bits (81), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 63
Query: 293 AEMNGKMIVSKPLYVAVAQ 311
M G KP+ + A+
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 43 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 99 DKLNGMLINDK 109
+ G DK
Sbjct: 64 RSMQGFPFYDK 74
Score = 35.4 bits (80), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSD 86
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 237 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 64
Query: 293 AEMNGKMIVSKPLYVAVAQ 311
M G KP+ + A+
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 43 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 99 DKLNGMLINDK 109
+ G DK
Sbjct: 65 RSMQGFPFYDK 75
Score = 35.4 bits (80), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 62
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ ++ G F D+ + A+ S+
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSD 87
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
++V+NL ST++E ++K E+ I V R K + + FV+F N +DA +A++ALN
Sbjct: 18 LYVRNLMLSTSEEMIEK---EFNNIKPGAVERVK--KIRDYAFVHFSNREDAVEAMKALN 72
Query: 194 GKKFD 198
GK D
Sbjct: 73 GKVLD 77
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 237 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 294
LY++NL S +E +++ F+ G + K +RD FV FS E+A A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 295 MNGKMIVSKPLYVAVAQ 311
+NGK++ P+ V +A+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 1 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 56
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ G DK
Sbjct: 57 KEVSSATNALRSXQGFPFYDK 77
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 64
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ + G F D+ + A+ S+
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSD 89
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+FV N+ + T ++L+ +F G + V++D + FV+ E DA A+ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 194 GKKFDDREWYV---GKAQKKS 211
GK+ + V K QKKS
Sbjct: 65 GKEVKGKRINVELSTKGQKKS 85
Score = 35.8 bits (81), Expect = 0.062, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 40 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 99
T IF+ N+ + + L F G ++ C + D + FV E + A+ AI
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIA 61
Query: 100 KLNGMLINDKQVFVGHFLRKQER 122
+LNG + K++ V + Q++
Sbjct: 62 QLNGKEVKGKRINVELSTKGQKK 84
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRDGDGKSKCFGFVNFENADDAAK 187
K V + L + T + + +IF YG I V R SK + +V FEN D+A K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 188 AVEALNGKKFDDRE 201
A++ ++G + D +E
Sbjct: 63 ALKHMDGGQIDGQE 76
Score = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRDPSGISKGSGFVAFSTPEEASRALAE 294
++I L ++ + + E+FS +G I V R +SKG +V F P+EA +AL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 295 MNGKMI 300
M+G I
Sbjct: 67 MDGGQI 72
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNI--LSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 100
+ I L +++ + + FS++G I + + SKG+ +V+FEN + A+ A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 101 LNGMLINDKQV 111
++G I+ +++
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 235 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 293
+ L++ + +D++ LK LF EFG I V++D +G+ KG F+ + + A +A +
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 294 EMN 296
++
Sbjct: 76 ALH 78
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
+FV + ++DLK +F E+G I V++D G K F+ + D A KA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 192 LNGKK 196
L+ +K
Sbjct: 77 LHEQK 81
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
+F+ + + +D + L F FG I + D +G KG F+ + ++SA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 101 LN 102
L+
Sbjct: 77 LH 78
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 7/93 (7%)
Query: 230 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 288
D +G ++I+NL ++E L E+ +FG + +V+ P + SKG F F T E A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 289 SRAL------AEMNGKMIVSKPLYVAVAQRKEE 315
+ L AE G + + L V +A ++E
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 98
+FI+NL + +AL + FG++ ++ + SKG F QF +E+AQ +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 7/91 (7%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAK 187
T+ VF++NL + +E L ++ ++G + VV+ SK F F + A K
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 188 AVEALN------GKKFDDREWYVGKAQKKSE 212
+ A + G K D R+ V A + E
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 193 NGK 195
NG+
Sbjct: 70 NGQ 72
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NG 103
NG
Sbjct: 70 NG 71
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 32 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 89
+P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 90 NKESAQNAIDKLNG 103
+ AQ A++ LNG
Sbjct: 73 TYKEAQAAMEGLNG 86
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 193 NGK 195
NG+
Sbjct: 85 NGQ 87
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 43 IFIKNLDKSIDHKA-LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+FI NL+ + K+ + FS +G I+ C + KGF FVQ+ N+ +A+ A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 70
Query: 102 NGMLI 106
+G +I
Sbjct: 71 DGRMI 75
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKV-MRDPSGISKGSGFVAFSTPEEASRALAEM 295
LY+KNL + + L LF+ F + R +G +G F+ F E A +AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 296 NGKMIVSKPLYVAVAQRKEER 316
NG + K L + + K++R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
Score = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 43 IFIKNLDKSIDHKALHDTFSSF----GNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 98
+++KNL + + L F+ F G + ++ T G+ +G F+ F NKE A A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 99 DKLNGMLINDKQVFVGHFLRKQERET 124
+NG + K + + K++R +
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVV-MRDGDGKSKCFGFVNFENADDAAKAVEAL 192
+++KNL T+ DL +F + + R G+ + F+ F N + A +A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 193 NGKKFDDREWYVGKAQKKSER 213
NG K + + + K +R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 33 PSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 90
P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 91 KESAQNAIDKLNG 103
+ AQ A++ LNG
Sbjct: 61 YKEAQAAMEGLNG 73
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 193 NGK 195
NG+
Sbjct: 72 NGQ 74
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 32 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 89
+P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 90 NKESAQNAIDKLNG 103
+ AQ A++ LNG
Sbjct: 74 TYKEAQAAMEGLNG 87
Score = 37.7 bits (86), Expect = 0.017, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 193 NGK 195
NG+
Sbjct: 86 NGQ 88
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 193 NGK 195
NG+
Sbjct: 70 NGQ 72
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NG 103
NG
Sbjct: 70 NG 71
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 192
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 193 NGK 195
NG+
Sbjct: 70 NGQ 72
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 101
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 102 NG 103
NG
Sbjct: 70 NG 71
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 56/117 (47%), Gaps = 16/117 (13%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 159
G + ++ + V ++ N F K +D +E LK + +YG T
Sbjct: 79 GFNVCNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 121
Score = 33.9 bits (76), Expect = 0.24, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 297 GKMIVSKPLYV 307
G + ++ L V
Sbjct: 79 GFNVCNRYLVV 89
Score = 32.7 bits (73), Expect = 0.57, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 117 LRKQERETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 174
++ +R + + + N + +++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 175 GFVNFENADDAAKAVEALNG 194
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 58
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ G DK
Sbjct: 59 KEVSSATNALRSXQGFPFYDK 79
Score = 32.7 bits (73), Expect = 0.57, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 66
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ + G F D+ + A+ S+
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSD 91
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 88
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 59
Query: 89 ENKESAQNAIDKLNGMLINDK 109
+ SA NA+ G DK
Sbjct: 60 KEVSSATNALRSXQGFPFYDK 80
Score = 32.7 bits (73), Expect = 0.57, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 132 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 67
Query: 188 AVEALNGKKFDDREWYVGKAQKKSE 212
A+ + G F D+ + A+ S+
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 287
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 288 ASRALAEMNGKMIVSKPLYVAVAQRKEE 315
A A+ +GK P+ V+ A R+ +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 103 GMLINDKQVFVGHF 116
G + ++ + V ++
Sbjct: 73 GFNVCNRYLVVLYY 86
Score = 35.0 bits (79), Expect = 0.10, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 297 GKMIVSKPLYV 307
G + ++ L V
Sbjct: 73 GFNVCNRYLVV 83
Score = 33.1 bits (74), Expect = 0.41, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 122 RETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNF 179
R + + + N + +++NL T E++ IFG+YG I +R G+ +++ +V +
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVY 58
Query: 180 ENADDAAKAVEALNG 194
E+ DA A + L+G
Sbjct: 59 EDIFDAKNACDHLSG 73
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 11/76 (14%)
Query: 32 DPSIRKSGTGNIFIKNLDKSIDHKALHDT-FSSFGNILSCKIATDGSGQSKGFGFVQFEN 90
DP KS +FI NL+ ++ K+ +T FS +G + C + KG+ FVQ+ N
Sbjct: 22 DP---KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSN 71
Query: 91 KESAQNAIDKLNGMLI 106
+ A+ A+ NG ++
Sbjct: 72 ERHARAAVLGENGRVL 87
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%), Gaps = 7/68 (10%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDGDGKSKCFGFVNFENADDAAK 187
+ N +++ NL + T +DL+++FG+ + V+++ G + FV++ + + A +
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG------YAFVDYPDQNWAIR 59
Query: 188 AVEALNGK 195
A+E L+GK
Sbjct: 60 AIETLSGK 67
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 193
+ + NL S T+E L+++F + I V ++ +GKSK + F+ F + +DA +A+ + N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 194 GKKFDDR 200
++ + R
Sbjct: 75 KREIEGR 81
Score = 36.2 bits (82), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L + NL S +E L+E+F + T KV ++ +G SKG F+ F++ E+A AL N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 297 GKMI 300
+ I
Sbjct: 75 KREI 78
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ + NL S + L + F I K+ + +G+SKG+ F++F + E A+ A++ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 103 GMLINDKQV 111
I + +
Sbjct: 75 KREIEGRAI 83
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 31/157 (19%), Positives = 67/157 (42%), Gaps = 16/157 (10%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ +KNL KS + ++ F G I+ +A D ++ F ++F + A AI K +
Sbjct: 7 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 162
++ ++ V H +++ N S T +++ + + + ++
Sbjct: 66 -KVVGQNEIIVSHLTE-------------CTLWMTNFPPSYTQRNIRDLLQDINVVALSI 111
Query: 163 VMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFD 198
+ S+ F +++ + +DA VE LNG K +
Sbjct: 112 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 148
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 37.4 bits (85), Expect = 0.021, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 40 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKES 93
T ++ + L + L + FS+FG +L ++ D +G SKGFGFV+F E+
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Score = 35.4 bits (80), Expect = 0.078, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 130 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKA 188
K +++ V L TT++DLK+ F +G + V +D G SK FGFV F + K
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 189 V 189
+
Sbjct: 74 M 74
Score = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 248 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 294
++ LKE FS FG + +V +D +G SKG GFV F+ E + +++
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 230 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA 288
++ Q +Y+ L + + + L ELF + G + + + +D +G +G GFV F + E+A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 289 SRALAEMNGKMIVSKPLYV 307
A+ M+ + KP+ V
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 89
Score = 37.0 bits (84), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 33 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENK 91
P ++ +++ LD+ + L + F G +++ + D +GQ +G+GFV+F ++
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 92 ESAQNAIDKLNGMLINDKQVFV 113
E A AI ++ + + K + V
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRV 89
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 192
V+V LDE ++ L ++F + G + + + +D G+ + +GFV F + +DA A++ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 193 NGKKFDDREWYVGKA 207
+ K + V KA
Sbjct: 78 DMIKLYGKPIRVNKA 92
>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 = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 101
+++ ++ + + D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 102 NGMLINDKQVFVGH 115
NG + + + G+
Sbjct: 67 NGYQLGSRFLKCGY 80
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 296 NGKMIVSKPL 305
NG + S+ L
Sbjct: 67 NGYQLGSRFL 76
Score = 33.9 bits (76), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 192
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 193 NGKKFDDR 200
NG + R
Sbjct: 67 NGYQLGSR 74
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 55/117 (47%), Gaps = 16/117 (13%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+ I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 159
G + ++ + V ++ N F K +D +E LK + +YG T
Sbjct: 79 GFNVCNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 121
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 117 LRKQERETVAIKTKFNNVF-VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 174
++ +R + + + N + ++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 175 GFVNFENADDAAKAVEALNG 194
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>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 = 36.6 bits (83), Expect = 0.040, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 59 DTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH 115
D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ LNG + + + G+
Sbjct: 22 DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 79
Score = 36.6 bits (83), Expect = 0.042, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 296 NGKMIVSKPL 305
NG + S+ L
Sbjct: 66 NGYQLGSRFL 75
Score = 33.1 bits (74), Expect = 0.42, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 192
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 193 NGKKFDDR 200
NG + R
Sbjct: 66 NGYQLGSR 73
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.041, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 59 DTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH 115
D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ LNG + + + G+
Sbjct: 21 DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 78
Score = 36.6 bits (83), Expect = 0.044, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 295
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 296 NGKMIVSKPL 305
NG + S+ L
Sbjct: 65 NGYQLGSRFL 74
Score = 33.1 bits (74), Expect = 0.43, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 192
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 193 NGKKFDDR 200
NG + R
Sbjct: 65 NGYQLGSR 72
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 36.6 bits (83), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 38 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 90
Query: 293 AEMNGKMIVSKPLYVAVAQRK 313
AE+NG + S L V +A+++
Sbjct: 91 AELNGTQVESVQLKVNIARKQ 111
Score = 35.8 bits (81), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 36 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 95
RK T ++ +++ ++ L FS FGNI+ + + FV +E ESA
Sbjct: 37 RKGNTLYVYGEDMTPTL----LRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESAD 87
Query: 96 NAIDKLNGMLINDKQVFVGHFLRKQ 120
A+ +LNG + Q+ V + RKQ
Sbjct: 88 QAVAELNGTQVESVQLKV-NIARKQ 111
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 234 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPE---E 287
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 288 ASRALAEM 295
A AL M
Sbjct: 63 AQNALHNM 70
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 190
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 191 ALNGKK 196
AL+ K
Sbjct: 66 ALHNMK 71
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 36.2 bits (82), Expect = 0.057, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78
Query: 193 NGKKF 197
K F
Sbjct: 79 GLKVF 83
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.8 bits (81), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 292
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 14 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 66
Query: 293 AEMNGKMIVSKPLYVAVAQRK 313
AE+NG + S L V +A+++
Sbjct: 67 AELNGTQVESVQLKVNIARKQ 87
Score = 35.4 bits (80), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 36 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 95
RK T ++ +++ ++ L FS FGNI+ + + FV +E ESA
Sbjct: 13 RKGNTLYVYGEDMTPTL----LRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESAD 63
Query: 96 NAIDKLNGMLINDKQVFVGHFLRKQ 120
A+ +LNG + Q+ V + RKQ
Sbjct: 64 QAVAELNGTQVESVQLKV-NIARKQ 87
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 35.8 bits (81), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 49/98 (50%), Gaps = 15/98 (15%)
Query: 114 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK- 172
G LRKQE + ++ N V K++D+ E + + G++G + ++ ++ G+ +
Sbjct: 7 GKLLRKQESTVMVLR---NMVDPKDIDDDLEGE-VTEECGKFGAVNRVIIYQEKQGEEED 62
Query: 173 ----CFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 206
FV F A + KA++ALNG+ W+ G+
Sbjct: 63 AEIIVKIFVEFSIASETHKAIQALNGR------WFAGR 94
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 35.8 bits (81), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 236 NLYIKNLGDSIDDE----KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 291
+YI NL + I E L +FS+FG I ++ +G FV F AS A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEIGSASNA 65
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 329
L M G KP+ +A ++ + A+++ F + RP
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE-RP 102
Score = 32.0 bits (71), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 21/95 (22%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 133 NVFVKNLDEST----TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 188
+++ NL+E + L IF ++G I V ++ + + FV F+ A+ A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQA--FVIFKEIGSASNA 65
Query: 189 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 223
+ + G F D+ + ++ S+ ++KG F++
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE 100
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 43 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 99
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 134 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 190
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.079, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKAV 189
++V NL +D++ +F +YG I RD D K++ F FV FE+ DA AV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 190 EALNGKKFD 198
+G +D
Sbjct: 79 YGRDGYDYD 87
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
I++ NL I K + D F +G I + G F FV+FE+ A++A+ +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGRD 82
Query: 103 G 103
G
Sbjct: 83 G 83
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 35.4 bits (80), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 11/70 (15%)
Query: 30 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFE 89
H P + GN+ +KN+ K + L FS +G+I+ I FGF+QF+
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN-------AFGFIQFD 53
Query: 90 NKESAQNAID 99
N +S ++AI+
Sbjct: 54 NPQSVRDAIE 63
Score = 32.3 bits (72), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 134 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 43 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 99
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 32.3 bits (72), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 134 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 76
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRD-GDGKSKCFGFVNFENADDAAKAV 189
N V ++ L ++ T++D++ +G V +MR+ G+S+ F FV F + DA + +
Sbjct: 2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM 61
Query: 190 EA 191
EA
Sbjct: 62 EA 63
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 192
+ KNL + T+++LK++F + + + DGKSK ++ F++ DA K +E
Sbjct: 18 TLLAKNLSFNITEDELKEVFED----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 193 NGKKFDDRE---WYVGK 206
G + D R +Y G+
Sbjct: 74 QGAEIDGRSVSLYYTGE 90
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 295
L KNL +I +++LKE+F + I + G SKG ++ F + +A + L E
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 296 NGKMI 300
G I
Sbjct: 74 QGAEI 78
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
+I++ N+D + L F G++ I D SG KGF +++F +KES + ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 101 LNGMLINDKQVFV 113
L+ L +Q+ V
Sbjct: 67 LDESLFRGRQIKV 79
Score = 28.9 bits (63), Expect = 9.3, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
+++V N+D T E+L+ F G++ ++ D G K F ++ F + + ++ A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 192 LNGKKFDDRE 201
L+ F R+
Sbjct: 67 LDESLFRGRQ 76
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
+I++ N+D + L F G++ I D SG KGF +++F +KES + ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 101 LNGMLINDKQVFV 113
L+ L +Q+ V
Sbjct: 66 LDESLFRGRQIKV 78
Score = 28.5 bits (62), Expect = 9.4, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 191
+++V N+D T E+L+ F G++ ++ D G K F ++ F + + ++ A
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 192 LNGKKFDDRE 201
L+ F R+
Sbjct: 66 LDESLFRGRQ 75
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 291
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 292 LAEMNGKMIVSKPLYV 307
+NG I+ + + V
Sbjct: 85 KEALNGAEIMGQTIQV 100
Score = 33.9 bits (76), Expect = 0.24, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 192
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 193 NGKK 196
NG +
Sbjct: 89 NGAE 92
Score = 32.7 bits (73), Expect = 0.51, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 32 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 89
+P ++S G I F+ ++ + + + F +G I + + D +G SKG+ V++E
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 90 NKESAQNAIDKLNGMLINDKQVFV 113
+ A A + LNG I + + V
Sbjct: 77 THKQALAAKEALNGAEIMGQTIQV 100
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 43 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 99
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 55
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 134 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 56
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 9/91 (9%)
Query: 116 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK--- 172
LRKQE ++ N V K++D+ E ++ G++G + ++ ++ G+ +
Sbjct: 14 LLRKQESTVXVLR---NXVDPKDIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAE 69
Query: 173 --CFGFVNFENADDAAKAVEALNGKKFDDRE 201
FV F A + KA++ALNG+ F R+
Sbjct: 70 IIVKIFVEFSIASETHKAIQALNGRWFAGRK 100
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 14/114 (12%)
Query: 211 SEREQELKGQFEQAMKETVDKFQG-------LNLYIKNLGDSIDDEKLKELFSEFGTITS 263
S RE E KG+ + ET+ F+ +Y+KNL + ++ LK +F + +S
Sbjct: 16 SRRELE-KGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74
Query: 264 --CKVMRD----PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 311
++M D G KG F+ + A++AL E NG ++ KP+ V A+
Sbjct: 75 ETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 54/108 (50%), Gaps = 13/108 (12%)
Query: 99 DKLNGMLINDKQVFVGHFLRKQERETVAIKTKFN------NVFVKNLDESTTDEDLKKIF 152
D++ I+ +++ G R +E ET+++ + ++VKNL + ++DLK IF
Sbjct: 8 DEMPSECISRRELEKGRISR-EEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIF 66
Query: 153 GEYGTITSAV--VMRD----GDGKSKCFGFVNFENADDAAKAVEALNG 194
G Y +S +M D +G+ K F+ N AAKA++ NG
Sbjct: 67 GRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 1/89 (1%)
Query: 230 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 289
D Q LY+ NL + + + +LFS+ G SCK++ + + + FV F +A+
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69
Query: 290 RALAEMNGKMIVSKPLYVAVAQRKEERRA 318
ALA MNG+ I+ K + V A +++
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKS 98
Score = 28.5 bits (62), Expect = 10.0, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
+++ NL + + + FS G SCK+ T+ + + FV+F A A+ +N
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMN 76
Query: 103 GMLINDKQVFV 113
G I K+V V
Sbjct: 77 GRKILGKEVKV 87
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 129 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN 181
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLET 60
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+F+ NL I + + F +G I D KGFGF++ E + A+ A +L
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71
Query: 102 NGMLINDKQVFV 113
+ M + KQ+ V
Sbjct: 72 DNMPLRGKQLRV 83
Score = 32.0 bits (71), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 295
L++ NL I +E++++LF ++G + +D KG GF+ T A A E+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71
Query: 296 NGKMIVSKPLYVAVA 310
+ + K L V A
Sbjct: 72 DNMPLRGKQLRVRFA 86
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 287
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 288 ASRALAEMNGKMIVSKPLYVAVA 310
A A+ +GK P+ V+ A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
LY+ LGD+I + L+ F +FG I + V++ + F+ F+T + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSF 69
Query: 297 GKMIVS 302
K+IV+
Sbjct: 70 NKLIVN 75
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 34.3 bits (77), Expect = 0.18, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 192 LNGKKFDDRE 201
L+ KF E
Sbjct: 70 LDNTKFRSHE 79
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 34.3 bits (77), Expect = 0.18, Method: Composition-based stats.
Identities = 21/88 (23%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 233 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 291
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 292 LAEMNGKMIVSKPLYVAVAQRKEERRAR 319
+NG I+ + + V K +R +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVK 158
Score = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 192
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 193 NGKKFDDR----EWYVGKAQKKSEREQE 216
NG + + +W K K+ ++ ++
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEK 162
Score = 32.3 bits (72), Expect = 0.84, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 32 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 89
+P ++S G I F+ ++ + + + F +G I + + D +G SKG+ V++E
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 90 NKESAQNAIDKLNGMLINDKQVFV 113
+ A A + LNG I + + V
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQV 146
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 287
+Y++ L DS+ + L + F + G + K P +G KG V++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 288 ASRALAEMNGKMIVSKPLYVAVAQRK 313
A A+ +GK L V++A++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITS---------AVVMRDGDGKSKCFGFVNFENADD 184
++V+ L++S T +DL F + G + + + GK K V++E+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 185 AAKAVEALNGKKFDDREWYVGKAQKK 210
A AVE +GK F + V A+KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|4FYQ|A Chain A, Human Aminopeptidase N (Cd13)
pdb|4FYR|A Chain A, Human Aminopeptidase N (Cd13) In Complex With Bestatin
pdb|4FYS|A Chain A, Human Aminopeptidase N (Cd13) In Complex With Angiotensin
Iv
pdb|4FYT|A Chain A, Human Aminopeptidase N (Cd13) In Complex With Amastatin
Length = 903
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 12/97 (12%)
Query: 70 CKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH----------FLRK 119
C G + F + QF N + N DKL L K++++ + +RK
Sbjct: 734 CNAIAQGGEEEWDFAWEQFRNA-TLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRK 792
Query: 120 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 156
Q+ + I NNV + L + KK+F +YG
Sbjct: 793 QDATSTIISIT-NNVIGQGLVWDFVQSNWKKLFNDYG 828
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 33.9 bits (76), Expect = 0.23, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 192 LNGKKFDDRE 201
L+ KF E
Sbjct: 70 LDNTKFRSHE 79
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 33.9 bits (76), Expect = 0.26, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 70
Query: 192 LNGKKFDDRE 201
L+ KF E
Sbjct: 71 LDNTKFRSHE 80
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQS-KGFGFVQFENKESAQNAID 99
IF+ + + L + F FG + + D Q +GFGF+ FE+++S A++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.49, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 236 NLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 293
+L++ +L +D+ + F+ G T+ S K++R+ +GI G FV F+ A + L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 294 EMNGK 298
++NGK
Sbjct: 71 KINGK 75
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 41 GNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDG-SGQSKGFGFVQFENKESAQNAI 98
++++ +L+ +D + F++ G ++S KI + +G G+ FV+F + +A+ +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 99 DKLNG 103
K+NG
Sbjct: 70 HKING 74
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 48/97 (49%), Gaps = 6/97 (6%)
Query: 20 NNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG--NILSCKIATD-G 76
NNK+ I+Y++ R++ +++ + + L S G +++ K A +
Sbjct: 38 NNKTPAILYTYSGLRNRRAA---VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 77 SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
+GQSKG+ V ++ S ++ L G ++N ++V V
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDV 131
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 32.0 bits (71), Expect = 0.84, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 42 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
++++ N+D + L FSS G+I I D SG KG+ +++F + +N++D
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF----AERNSVDA 93
Query: 101 LNGMLINDKQVFVGHFLRKQERET 124
M D+ VF G ++ + T
Sbjct: 94 AVAM---DETVFRGRTIKVLPKRT 114
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 133 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNF--ENADDAAKAV 189
+V+V N+D +T +DL+ F G+I ++ D G K + ++ F N+ DAA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 190 E 190
+
Sbjct: 98 D 98
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 32.0 bits (71), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 10/108 (9%)
Query: 29 SHRDPSIRKSGTG---NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGF 85
SH D + +G I ++NL + LH FS FG +L KI T + ++
Sbjct: 19 SHMDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIIT-FTKNNQFQAL 75
Query: 86 VQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 133
+Q+ + SAQ+A L+G I + LR + ++ K+NN
Sbjct: 76 LQYADPVSAQHAKLSLDGQNIYNACC----TLRIDFSKLTSLNVKYNN 119
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 148 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 203
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 24 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 55 KALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 113
KAL FS G +++ + D +G++KGF FV+ + A+ I +G ++ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86
Query: 114 GHFLRKQER 122
+ ++ ER
Sbjct: 87 LYTMKDVER 95
Score = 28.9 bits (63), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 148 LKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 206
L +F + G + + + + GK+K F FV + +DA K +++ +GK+ D +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLY 88
Query: 207 AQKKSER 213
K ER
Sbjct: 89 TMKDVER 95
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 148 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 203
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 38 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 248 DEKLKELFSE----FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 303
DE +E+F+E +G + V + G+ +V F E+A +A+ ++N + +
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 304 PLYVAVA 310
P++ ++
Sbjct: 97 PIHAELS 103
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 190
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
IF+ L + + + F FG + S ++ D + + +GF F+ F+ +E + ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 163 VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE 216
V+ D +G+ V F+N DDA K+ E L+ KK + RE +V + RE E
Sbjct: 48 VLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIE 100
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 134 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 190
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 100
IF+ L + + + F FG + S ++ D + + +GF F+ F+ +E + ++K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 97
SG+ I +KNL + + + +HD + ++ C + ++K FV N E AQNA
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYV-----DRNKRTAFVTLLNGEQAQNA 56
Query: 98 IDKLNGMLINDKQVFV 113
I + K + V
Sbjct: 57 IQMFHQYSFRGKDLIV 72
>pdb|3UX8|A Chain A, Crystal Structure Of Uvra
Length = 670
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 270 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 324
P G +G VA TPEE + G+ + KP+ E RAR+QA++
Sbjct: 620 PEGGDRGGQIVAVGTPEEVAEVKESHTGRYL--KPIL-------ERDRARMQARY 665
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 270 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 324
P G +G VA TPEE + G+ + KP+ E RAR+QA++
Sbjct: 922 PEGGDRGGQIVAVGTPEEVAEVKESHTGRYL--KPIL-------ERDRARMQARY 967
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 102
I ++NL + LH FS FG +L KI T + ++ +Q+ + SAQ+A L+
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVL--KIIT-FTKNNQFQALLQYADPVSAQHAKLSLD 105
Query: 103 GMLINDKQVFVGHFLRKQERETVAIKTKFNN 133
G I + LR + ++ K+NN
Sbjct: 106 GQNIYNACC----TLRIDFSKLTSLNVKYNN 132
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 29.6 bits (65), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 132 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 191
+ VFV E T E+L++ F +YG + + + + F FV F ADD K ++
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTF--ADD--KVAQS 63
Query: 192 LNGK 195
L G+
Sbjct: 64 LCGE 67
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 237 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 296
L I+N+ + E L L ++G + SC+ + S + + V +S+ ++A +AL ++N
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN--VTYSSKDQARQALDKLN 75
Query: 297 GKMIVSKPLYVA 308
G + + L VA
Sbjct: 76 GFQLENFTLKVA 87
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 29.3 bits (64), Expect = 5.7, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 38 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 97
SG+ I I+ L + ++ +HD S + + C + + KG FV N E A+ A
Sbjct: 3 SGSSGILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAA 56
Query: 98 IDKLNGMLINDKQVFV 113
I+ + + ++++ V
Sbjct: 57 INTFHQSRLRERELSV 72
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 55 KALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQ 110
KAL FS G +++ + D +G++KGF FV+ + A+ I +G ++ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH 83
>pdb|4EGB|A Chain A, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|B Chain B, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|C Chain C, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|D Chain D, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|E Chain E, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|F Chain F, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|G Chain G, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|H Chain H, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
Length = 346
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 187 KAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ 233
K +E + + DR + + + K+E + E K FEQ ++ETV ++
Sbjct: 289 KDIEYVTDRLGHDRRYAINAEKXKNEFDWEPKYTFEQGLQETVQWYE 335
>pdb|1B8D|A Chain A, Crystal Structure Of A Phycourobilin-Containing
Phycoerythrin
pdb|1B8D|K Chain K, Crystal Structure Of A Phycourobilin-Containing
Phycoerythrin
Length = 164
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 204 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD-EKLKELFSEF 258
+ +A + E Q+L G E +KE D Y+KN G++ D EK+ + + +
Sbjct: 31 IQRAAARLEAAQKLSGNHEAVVKEAGDACFAKYSYLKNAGEAGDSPEKINKCYRDI 86
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 139 LDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSK-----CFGFVNFENADDAAKAV 189
+D D+DL+ + G++G + ++ ++ G+ + FV F A + KA+
Sbjct: 133 VDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAI 192
Query: 190 EALNGKKFDDREWYVGKAQKKSEREQE 216
+ALNG+ W+ G+ +QE
Sbjct: 193 QALNGR------WFAGRKVVAEVYDQE 213
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 28.5 bits (62), Expect = 10.0, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 43 IFIKNLDKSIDHKALHDTFSSFGNI-LSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 101
+++ N S + + D + LS ++ + S+ F ++ +KE A+ ++KL
Sbjct: 6 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 65
Query: 102 NGMLI 106
NG+ I
Sbjct: 66 NGLKI 70
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
0.317 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,682,555
Number of Sequences: 62578
Number of extensions: 581775
Number of successful extensions: 2642
Number of sequences better than 100.0: 257
Number of HSP's better than 100.0 without gapping: 137
Number of HSP's successfully gapped in prelim test: 120
Number of HSP's that attempted gapping in prelim test: 1917
Number of HSP's gapped (non-prelim): 617
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)